From f207c571d82665fa826cae811aa3463a7df24663 Mon Sep 17 00:00:00 2001
From: Jiri Novak <jirinovak@atlas.cz>
Date: Wed, 21 Feb 2018 15:10:29 +0100
Subject: [PATCH] release 1.0.1106

---
 CycloBranch/CycloBranch.desktop               |   9 +
 CycloBranch/CycloBranch.pro                   |  87 ++
 CycloBranch/CycloBranch.vcxproj               | 334 +++++--
 CycloBranch/CycloBranch.vcxproj.filters       |  79 +-
 CycloBranch/CycloBranch.vcxproj.user          |   4 +-
 CycloBranch/core/cAllocator.h                 | 111 +++
 CycloBranch/core/cBrick.cpp                   |  23 +-
 CycloBranch/core/cBrick.h                     |  15 +-
 CycloBranch/core/cBricksDatabase.cpp          |  25 +-
 CycloBranch/core/cBricksDatabase.h            |  11 +-
 CycloBranch/core/cCandidate.cpp               | 252 +++++-
 CycloBranch/core/cCandidate.h                 | 112 ++-
 CycloBranch/core/cDeNovoGraph.cpp             | 102 ++-
 CycloBranch/core/cDeNovoGraph.h               |   2 +-
 CycloBranch/core/cDeNovoGraphNode.cpp         |   4 +-
 CycloBranch/core/cDeNovoGraphNode.h           |   8 +-
 CycloBranch/core/cFragmentIons.cpp            | 539 +++++++----
 CycloBranch/core/cFragmentIons.h              | 203 +++--
 CycloBranch/core/cParameters.cpp              | 277 ++++--
 CycloBranch/core/cParameters.h                |  16 +-
 CycloBranch/core/cPeak.h                      |   4 +-
 CycloBranch/core/cPeaksList.cpp               | 119 ++-
 CycloBranch/core/cPeaksList.h                 |  47 +-
 CycloBranch/core/cSequence.cpp                |  17 +-
 CycloBranch/core/cSequence.h                  |  17 +-
 CycloBranch/core/cSequenceDatabase.cpp        |   7 +-
 CycloBranch/core/cSequenceDatabase.h          |   1 +
 CycloBranch/core/cSummaryFormula.cpp          |   4 +-
 CycloBranch/core/cSummaryFormula.h            |   5 +-
 CycloBranch/core/cTheoreticalSpectrum.cpp     | 846 ++++++------------
 CycloBranch/core/cTheoreticalSpectrum.h       | 135 +--
 CycloBranch/core/cTheoreticalSpectrumList.cpp |  50 +-
 CycloBranch/core/cTheoreticalSpectrumList.h   |   6 +
 CycloBranch/core/utilities.cpp                | 177 ++++
 CycloBranch/core/utilities.h                  | 101 +++
 CycloBranch/cyclobranch.rc                    |   1 +
 CycloBranch/gui/cAboutWidget.cpp              |  27 +-
 CycloBranch/gui/cAboutWidget.h                |  10 +
 CycloBranch/gui/cBranchedWidget.cpp           | 465 ++++++----
 CycloBranch/gui/cBranchedWidget.h             |  24 +
 CycloBranch/gui/cBricksDatabaseWidget.cpp     | 212 +++--
 CycloBranch/gui/cBricksDatabaseWidget.h       |  27 +-
 CycloBranch/gui/cCyclicWidget.cpp             | 346 +++++--
 CycloBranch/gui/cCyclicWidget.h               |  32 +-
 CycloBranch/gui/cDrawPeptideWidget.cpp        | 665 ++++++++++++++
 CycloBranch/gui/cDrawPeptideWidget.h          | 176 ++++
 CycloBranch/gui/cEventFilter.cpp              |  14 +
 CycloBranch/gui/cEventFilter.h                |  35 +
 CycloBranch/gui/cGraphWidget.cpp              |  12 +-
 CycloBranch/gui/cGraphWidget.h                |  11 +
 CycloBranch/gui/cLassoWidget.cpp              | 332 ++++---
 CycloBranch/gui/cLassoWidget.h                |  32 +-
 CycloBranch/gui/cLinearWidget.cpp             | 155 +++-
 CycloBranch/gui/cLinearWidget.h               |  26 +-
 CycloBranch/gui/cMainThread.cpp               | 312 ++-----
 CycloBranch/gui/cMainThread.h                 |  57 +-
 CycloBranch/gui/cMainWindow.cpp               | 660 +++++++++-----
 CycloBranch/gui/cMainWindow.h                 |  51 +-
 CycloBranch/gui/cModificationsWidget.cpp      | 434 +++++++++
 CycloBranch/gui/cModificationsWidget.h        | 119 +++
 CycloBranch/gui/cParametersWidget.cpp         | 685 +++++++-------
 CycloBranch/gui/cParametersWidget.h           |  91 +-
 CycloBranch/gui/cSequenceDatabaseWidget.cpp   | 223 +++--
 CycloBranch/gui/cSequenceDatabaseWidget.h     |  35 +-
 CycloBranch/gui/cSpectrumDetailWidget.cpp     | 598 +++++++++----
 CycloBranch/gui/cSpectrumDetailWidget.h       |  83 +-
 CycloBranch/gui/cSpectrumSceneWidget.cpp      | 646 +++++++++++++
 CycloBranch/gui/cSpectrumSceneWidget.h        | 210 +++++
 CycloBranch/images.qrc                        |  32 +
 CycloBranch/images/cb.cdr                     | Bin 0 -> 15312 bytes
 CycloBranch/images/cb.ico                     | Bin 0 -> 101098 bytes
 CycloBranch/images/cb.png                     | Bin 0 -> 2191 bytes
 CycloBranch/images/icons/2.png                | Bin 0 -> 673 bytes
 CycloBranch/images/icons/20.png               | Bin 0 -> 705 bytes
 CycloBranch/images/icons/22.png               | Bin 0 -> 789 bytes
 CycloBranch/images/icons/26.png               | Bin 0 -> 709 bytes
 CycloBranch/images/icons/3.png                | Bin 0 -> 887 bytes
 CycloBranch/images/icons/32.png               | Bin 0 -> 640 bytes
 CycloBranch/images/icons/33.png               | Bin 0 -> 1269 bytes
 CycloBranch/images/icons/4.png                | Bin 0 -> 911 bytes
 CycloBranch/images/icons/48.png               | Bin 0 -> 937 bytes
 CycloBranch/images/icons/52.png               | Bin 0 -> 738 bytes
 CycloBranch/images/icons/54.png               | Bin 0 -> 718 bytes
 CycloBranch/images/icons/57.png               | Bin 0 -> 657 bytes
 CycloBranch/images/icons/61.png               | Bin 0 -> 973 bytes
 CycloBranch/images/icons/62.png               | Bin 0 -> 922 bytes
 CycloBranch/images/icons/64.png               | Bin 0 -> 722 bytes
 CycloBranch/images/icons/68.png               | Bin 0 -> 810 bytes
 CycloBranch/images/icons/73.png               | Bin 0 -> 859 bytes
 CycloBranch/images/icons/77.png               | Bin 0 -> 1269 bytes
 CycloBranch/images/icons/80.png               | Bin 0 -> 614 bytes
 CycloBranch/images/icons/81.png               | Bin 0 -> 788 bytes
 CycloBranch/images/icons/82.png               | Bin 0 -> 883 bytes
 CycloBranch/images/icons/83.png               | Bin 0 -> 917 bytes
 CycloBranch/images/icons/84.png               | Bin 0 -> 984 bytes
 CycloBranch/images/icons/89.png               | Bin 0 -> 814 bytes
 CycloBranch/images/icons/93.png               | Bin 0 -> 980 bytes
 CycloBranch/images/icons/96.png               | Bin 0 -> 1041 bytes
 CycloBranch/images/splash.cdr                 | Bin 0 -> 99027 bytes
 CycloBranch/images/splash.png                 | Bin 0 -> 52065 bytes
 CycloBranch/licence.txt                       | 674 ++++++++++++++
 CycloBranch/main.cpp                          |  29 +-
 CycloBranch/parallel/cGraphReaderThread.cpp   |  45 +-
 CycloBranch/parallel/cGraphReaderThread.h     |   4 +-
 .../parallel/cSpectrumComparatorThread.cpp    |  32 +-
 .../parallel/cSpectrumComparatorThread.h      |  16 +-
 CycloBranch/readme-linux-compile.txt          |  12 +
 readme.txt                                    |   2 +-
 108 files changed, 8313 insertions(+), 3088 deletions(-)
 create mode 100644 CycloBranch/CycloBranch.desktop
 create mode 100644 CycloBranch/CycloBranch.pro
 create mode 100644 CycloBranch/core/cAllocator.h
 create mode 100644 CycloBranch/cyclobranch.rc
 create mode 100644 CycloBranch/gui/cDrawPeptideWidget.cpp
 create mode 100644 CycloBranch/gui/cDrawPeptideWidget.h
 create mode 100644 CycloBranch/gui/cEventFilter.cpp
 create mode 100644 CycloBranch/gui/cEventFilter.h
 create mode 100644 CycloBranch/gui/cModificationsWidget.cpp
 create mode 100644 CycloBranch/gui/cModificationsWidget.h
 create mode 100644 CycloBranch/gui/cSpectrumSceneWidget.cpp
 create mode 100644 CycloBranch/gui/cSpectrumSceneWidget.h
 create mode 100644 CycloBranch/images.qrc
 create mode 100644 CycloBranch/images/cb.cdr
 create mode 100644 CycloBranch/images/cb.ico
 create mode 100644 CycloBranch/images/cb.png
 create mode 100644 CycloBranch/images/icons/2.png
 create mode 100644 CycloBranch/images/icons/20.png
 create mode 100644 CycloBranch/images/icons/22.png
 create mode 100644 CycloBranch/images/icons/26.png
 create mode 100644 CycloBranch/images/icons/3.png
 create mode 100644 CycloBranch/images/icons/32.png
 create mode 100644 CycloBranch/images/icons/33.png
 create mode 100644 CycloBranch/images/icons/4.png
 create mode 100644 CycloBranch/images/icons/48.png
 create mode 100644 CycloBranch/images/icons/52.png
 create mode 100644 CycloBranch/images/icons/54.png
 create mode 100644 CycloBranch/images/icons/57.png
 create mode 100644 CycloBranch/images/icons/61.png
 create mode 100644 CycloBranch/images/icons/62.png
 create mode 100644 CycloBranch/images/icons/64.png
 create mode 100644 CycloBranch/images/icons/68.png
 create mode 100644 CycloBranch/images/icons/73.png
 create mode 100644 CycloBranch/images/icons/77.png
 create mode 100644 CycloBranch/images/icons/80.png
 create mode 100644 CycloBranch/images/icons/81.png
 create mode 100644 CycloBranch/images/icons/82.png
 create mode 100644 CycloBranch/images/icons/83.png
 create mode 100644 CycloBranch/images/icons/84.png
 create mode 100644 CycloBranch/images/icons/89.png
 create mode 100644 CycloBranch/images/icons/93.png
 create mode 100644 CycloBranch/images/icons/96.png
 create mode 100644 CycloBranch/images/splash.cdr
 create mode 100644 CycloBranch/images/splash.png
 create mode 100644 CycloBranch/licence.txt
 create mode 100644 CycloBranch/readme-linux-compile.txt

diff --git a/CycloBranch/CycloBranch.desktop b/CycloBranch/CycloBranch.desktop
new file mode 100644
index 0000000..c2b747b
--- /dev/null
+++ b/CycloBranch/CycloBranch.desktop
@@ -0,0 +1,9 @@
+[Desktop Entry]
+Comment=A tool for de novo sequencing of nonribosomal peptides from accurate product ion mass spectra. 
+Exec=CycloBranch
+Icon=/usr/share/cyclobranch/images/cb.png
+Name=CycloBranch
+NoDisplay=false
+StartupNotify=false
+Terminal=false
+Type=Application
diff --git a/CycloBranch/CycloBranch.pro b/CycloBranch/CycloBranch.pro
new file mode 100644
index 0000000..6791882
--- /dev/null
+++ b/CycloBranch/CycloBranch.pro
@@ -0,0 +1,87 @@
+######################################################################
+# Automatically generated by qmake (3.0) Fri Dec 5 03:02:26 2014
+######################################################################
+
+TEMPLATE = app
+TARGET = CycloBranch
+QT += core gui widgets printsupport svg
+INCLUDEPATH += . core gui parallel
+QMAKE_CXXFLAGS += -std=c++0x -DUNIX -m64
+QMAKE_LIBS += -lboost_regex
+OBJECTS_DIR = build/
+MOC_DIR = moc/
+
+# Input
+RESOURCES = images.qrc
+HEADERS += core/cAllocator.h \
+           core/cBrick.h \
+           core/cBricksDatabase.h \
+           core/cCandidate.h \
+           core/cCandidateSet.h \
+           core/cDeNovoGraph.h \
+           core/cDeNovoGraphNode.h \
+           core/cFragmentIons.h \
+           core/cParameters.h \
+           core/cPeak.h \
+           core/cPeaksList.h \
+           core/cSequence.h \
+           core/cSequenceDatabase.h \
+           core/cSummaryFormula.h \
+           core/cTheoreticalSpectrum.h \
+           core/cTheoreticalSpectrumList.h \
+           core/utilities.h \
+           gui/cAboutWidget.h \
+           gui/cBranchedWidget.h \
+           gui/cBricksDatabaseWidget.h \
+           gui/cCyclicWidget.h \
+           gui/cDrawPeptideWidget.h \
+           gui/cEventFilter.h \
+           gui/cFragmentIonsListWidget.h \
+           gui/cGraphWidget.h \
+           gui/cLassoWidget.h \
+           gui/cLinearWidget.h \
+           gui/cMainThread.h \
+           gui/cMainWindow.h \
+           gui/cModificationsWidget.h \
+           gui/cParametersWidget.h \
+           gui/cSequenceDatabaseWidget.h \
+           gui/cSpectrumDetailWidget.h \
+           gui/cSpectrumSceneWidget.h \
+           parallel/cGraphReaderThread.h \
+           parallel/cSpectrumComparatorThread.h
+SOURCES += core/cBrick.cpp \
+           core/cBricksDatabase.cpp \
+           core/cCandidate.cpp \
+           core/cCandidateSet.cpp \
+           core/cDeNovoGraph.cpp \
+           core/cDeNovoGraphNode.cpp \
+           core/cFragmentIons.cpp \
+           core/cParameters.cpp \
+           core/cPeak.cpp \
+           core/cPeaksList.cpp \
+           core/cSequence.cpp \
+           core/cSequenceDatabase.cpp \
+           core/cSummaryFormula.cpp \
+           core/cTheoreticalSpectrum.cpp \
+           core/cTheoreticalSpectrumList.cpp \
+           core/utilities.cpp \
+           gui/cAboutWidget.cpp \
+           gui/cBranchedWidget.cpp \
+           gui/cBricksDatabaseWidget.cpp \
+           gui/cCyclicWidget.cpp \
+           gui/cDrawPeptideWidget.cpp \
+           gui/cEventFilter.cpp \
+           gui/cFragmentIonsListWidget.cpp \
+           gui/cGraphWidget.cpp \
+           gui/cLassoWidget.cpp \
+           gui/cLinearWidget.cpp \
+           gui/cMainThread.cpp \
+           gui/cMainWindow.cpp \
+           gui/cModificationsWidget.cpp \
+           gui/cParametersWidget.cpp \
+           gui/cSequenceDatabaseWidget.cpp \
+           gui/cSpectrumDetailWidget.cpp \
+           gui/cSpectrumSceneWidget.cpp \
+           parallel/cGraphReaderThread.cpp \
+           parallel/cSpectrumComparatorThread.cpp \
+           main.cpp
diff --git a/CycloBranch/CycloBranch.vcxproj b/CycloBranch/CycloBranch.vcxproj
index 23c88a4..12d8bf3 100644
--- a/CycloBranch/CycloBranch.vcxproj
+++ b/CycloBranch/CycloBranch.vcxproj
@@ -74,8 +74,8 @@
   </PropertyGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
     <ClCompile>
-      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;QT_PRINTSUPPORT_LIB;QT_SVG_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;$(QTDIR)\include\QtPrintSupport;$(QTDIR)\include\QtSvg;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
       <Optimization>Disabled</Optimization>
       <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
       <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
@@ -86,13 +86,13 @@
       <OutputFile>$(OutDir)\$(ProjectName).exe</OutputFile>
       <AdditionalLibraryDirectories>$(QTDIR)\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <GenerateDebugInformation>true</GenerateDebugInformation>
-      <AdditionalDependencies>qtmaind.lib;Qt5Cored.lib;Qt5Guid.lib;Qt5Widgetsd.lib;%(AdditionalDependencies)</AdditionalDependencies>
+      <AdditionalDependencies>qtmaind.lib;Qt5Cored.lib;Qt5Guid.lib;Qt5Widgetsd.lib;Qt5PrintSupportd.lib;Qt5Svgd.lib;%(AdditionalDependencies)</AdditionalDependencies>
     </Link>
   </ItemDefinitionGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
     <ClCompile>
-      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;QT_PRINTSUPPORT_LIB;QT_SVG_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;$(QTDIR)\include\QtPrintSupport;$(QTDIR)\include\QtSvg;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
       <Optimization>Disabled</Optimization>
       <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
       <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
@@ -103,13 +103,13 @@
       <OutputFile>$(OutDir)\$(ProjectName).exe</OutputFile>
       <AdditionalLibraryDirectories>$(QTDIR)\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <GenerateDebugInformation>true</GenerateDebugInformation>
-      <AdditionalDependencies>qtmaind.lib;Qt5Cored.lib;Qt5Guid.lib;Qt5Widgetsd.lib;%(AdditionalDependencies)</AdditionalDependencies>
+      <AdditionalDependencies>qtmaind.lib;Qt5Cored.lib;Qt5Guid.lib;Qt5Widgetsd.lib;Qt5PrintSupportd.lib;Qt5Svgd.lib;%(AdditionalDependencies)</AdditionalDependencies>
     </Link>
   </ItemDefinitionGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
     <ClCompile>
-      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_NO_DEBUG;NDEBUG;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_NO_DEBUG;NDEBUG;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;QT_PRINTSUPPORT_LIB;QT_SVG_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;$(QTDIR)\include\QtPrintSupport;$(QTDIR)\include\QtSvg;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
       <DebugInformationFormat />
       <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
       <TreatWChar_tAsBuiltInType>false</TreatWChar_tAsBuiltInType>
@@ -119,13 +119,13 @@
       <OutputFile>$(OutDir)\$(ProjectName).exe</OutputFile>
       <AdditionalLibraryDirectories>$(QTDIR)\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <GenerateDebugInformation>false</GenerateDebugInformation>
-      <AdditionalDependencies>qtmain.lib;Qt5Core.lib;Qt5Gui.lib;Qt5Widgets.lib;%(AdditionalDependencies)</AdditionalDependencies>
+      <AdditionalDependencies>qtmain.lib;Qt5Core.lib;Qt5Gui.lib;Qt5Widgets.lib;Qt5PrintSupport.lib;Qt5Svg.lib;%(AdditionalDependencies)</AdditionalDependencies>
     </Link>
   </ItemDefinitionGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
     <ClCompile>
-      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_NO_DEBUG;NDEBUG;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <AdditionalIncludeDirectories>.\GeneratedFiles;.;$(QTDIR)\include;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <PreprocessorDefinitions>UNICODE;WIN32;WIN64;QT_DLL;QT_NO_DEBUG;NDEBUG;QT_CORE_LIB;QT_GUI_LIB;QT_WIDGETS_LIB;QT_PRINTSUPPORT_LIB;QT_SVG_LIB;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <AdditionalIncludeDirectories>.;.\GeneratedFiles;.\GeneratedFiles\$(ConfigurationName);$(QTDIR)\include;$(QTDIR)\include\QtCore;$(QTDIR)\include\QtGui;$(QTDIR)\include\QtWidgets;$(QTDIR)\include\QtSvg;$(QTDIR)\include\QtPrintSupport;C:\boost_1_57_0\;C:\boost_1_57_0\boost;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
       <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
       <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
       <TreatWChar_tAsBuiltInType>true</TreatWChar_tAsBuiltInType>
@@ -138,9 +138,9 @@
     <Link>
       <SubSystem>Windows</SubSystem>
       <OutputFile>$(OutDir)\$(ProjectName).exe</OutputFile>
-      <AdditionalLibraryDirectories>$(QTDIR)\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
+      <AdditionalLibraryDirectories>$(QTDIR)\lib;C:\boost_1_57_0\lib64-msvc-11.0;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <GenerateDebugInformation>true</GenerateDebugInformation>
-      <AdditionalDependencies>qtmain.lib;Qt5Core.lib;Qt5Gui.lib;Qt5Widgets.lib;%(AdditionalDependencies)</AdditionalDependencies>
+      <AdditionalDependencies>qtmain.lib;Qt5Core.lib;Qt5Gui.lib;Qt5Widgets.lib;Qt5Svgd.lib;Qt5PrintSupport.lib;libboost_regex-vc110-mt-1_57.lib;%(AdditionalDependencies)</AdditionalDependencies>
       <OptimizeReferences>true</OptimizeReferences>
       <EnableCOMDATFolding>true</EnableCOMDATFolding>
       <LinkTimeCodeGeneration>UseLinkTimeCodeGeneration</LinkTimeCodeGeneration>
@@ -179,11 +179,15 @@
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
     </ClCompile>
-    <ClCompile Include="GeneratedFiles\Debug\moc_cFragmentIonsListWidget.cpp">
+    <ClCompile Include="GeneratedFiles\Debug\moc_cDrawPeptideWidget.cpp">
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
     </ClCompile>
-    <ClCompile Include="GeneratedFiles\Debug\moc_cGraphicalSpectrumWidget.cpp">
+    <ClCompile Include="GeneratedFiles\Debug\moc_cEventFilter.cpp">
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cFragmentIonsListWidget.cpp">
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
     </ClCompile>
@@ -211,6 +215,10 @@
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cModificationsWidget.cpp">
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
+    </ClCompile>
     <ClCompile Include="GeneratedFiles\Debug\moc_cParametersWidget.cpp">
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
@@ -227,6 +235,20 @@
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cSpectrumSceneWidget.cpp">
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\qrc_images.cpp">
+      <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+      </PrecompiledHeader>
+      <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+      </PrecompiledHeader>
+      <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+      </PrecompiledHeader>
+      <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+      </PrecompiledHeader>
+    </ClCompile>
     <ClCompile Include="GeneratedFiles\Release\moc_cAboutWidget.cpp">
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
@@ -243,11 +265,15 @@
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
     </ClCompile>
-    <ClCompile Include="GeneratedFiles\Release\moc_cFragmentIonsListWidget.cpp">
+    <ClCompile Include="GeneratedFiles\Release\moc_cDrawPeptideWidget.cpp">
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cEventFilter.cpp">
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-    <ClCompile Include="GeneratedFiles\Release\moc_cGraphicalSpectrumWidget.cpp">
+    <ClCompile Include="GeneratedFiles\Release\moc_cFragmentIonsListWidget.cpp">
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     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cSpectrumSceneWidget.cpp">
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     <ClCompile Include="gui\cBranchedWidget.cpp" />
     <ClCompile Include="gui\cBricksDatabaseWidget.cpp" />
     <ClCompile Include="gui\cCyclicWidget.cpp" />
+    <ClCompile Include="gui\cDrawPeptideWidget.cpp" />
+    <ClCompile Include="gui\cEventFilter.cpp" />
     <ClCompile Include="gui\cFragmentIonsListWidget.cpp" />
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     <ClCompile Include="gui\cLinearWidget.cpp" />
     <ClCompile Include="gui\cMainThread.cpp" />
     <ClCompile Include="gui\cMainWindow.cpp" />
+    <ClCompile Include="gui\cModificationsWidget.cpp" />
     <ClCompile Include="gui\cParametersWidget.cpp" />
     <ClCompile Include="gui\cSequenceDatabaseWidget.cpp" />
     <ClCompile Include="gui\cSpectrumDetailWidget.cpp" />
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     <ClCompile Include="main.cpp" />
     <ClCompile Include="parallel\cGraphReaderThread.cpp" />
     <ClCompile Include="parallel\cSpectrumComparatorThread.cpp" />
   </ItemGroup>
   <ItemGroup>
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     <ClInclude Include="core\cCandidate.h" />
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+  <ItemGroup>
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diff --git a/CycloBranch/CycloBranch.vcxproj.filters b/CycloBranch/CycloBranch.vcxproj.filters
index a06dc21..f42329c 100644
--- a/CycloBranch/CycloBranch.vcxproj.filters
+++ b/CycloBranch/CycloBranch.vcxproj.filters
@@ -42,6 +42,9 @@
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-      <Filter>Generated Files\Debug</Filter>
-    </ClCompile>
-    <ClCompile Include="GeneratedFiles\Release\moc_cGraphicalSpectrumWidget.cpp">
-      <Filter>Generated Files\Release</Filter>
-    </ClCompile>
-    <ClCompile Include="gui\cGraphicalSpectrumWidget.cpp">
-      <Filter>Source Files\gui</Filter>
-    </ClCompile>
     <ClCompile Include="core\cCandidateSet.cpp">
       <Filter>Source Files\core</Filter>
     </ClCompile>
@@ -239,6 +233,45 @@
     <ClCompile Include="GeneratedFiles\Release\moc_cSequenceDatabaseWidget.cpp">
       <Filter>Generated Files\Release</Filter>
     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cModificationsWidget.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cModificationsWidget.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cModificationsWidget.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cDrawPeptideWidget.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cDrawPeptideWidget.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cDrawPeptideWidget.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\qrc_images.cpp">
+      <Filter>Generated Files</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cEventFilter.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cEventFilter.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cEventFilter.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cSpectrumSceneWidget.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cSpectrumSceneWidget.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cSpectrumSceneWidget.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <CustomBuild Include="gui\cAboutWidget.h">
@@ -262,9 +295,6 @@
     <CustomBuild Include="gui\cSpectrumDetailWidget.h">
       <Filter>Header Files\gui</Filter>
     </CustomBuild>
-    <CustomBuild Include="gui\cGraphicalSpectrumWidget.h">
-      <Filter>Header Files\gui</Filter>
-    </CustomBuild>
     <CustomBuild Include="parallel\cSpectrumComparatorThread.h">
       <Filter>Header Files\parallel</Filter>
     </CustomBuild>
@@ -292,6 +322,24 @@
     <CustomBuild Include="gui\cSequenceDatabaseWidget.h">
       <Filter>Header Files\gui</Filter>
     </CustomBuild>
+    <CustomBuild Include="gui\cModificationsWidget.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
+    <CustomBuild Include="gui\cDrawPeptideWidget.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
+    <CustomBuild Include="images.qrc">
+      <Filter>Resources</Filter>
+    </CustomBuild>
+    <CustomBuild Include="core\utilities.h">
+      <Filter>Header Files\core</Filter>
+    </CustomBuild>
+    <CustomBuild Include="gui\cEventFilter.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
+    <CustomBuild Include="gui\cSpectrumSceneWidget.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="core\cBrick.h">
@@ -336,8 +384,13 @@
     <ClInclude Include="core\cSequence.h">
       <Filter>Header Files\core</Filter>
     </ClInclude>
-    <ClInclude Include="core\utilities.h">
+    <ClInclude Include="core\cAllocator.h">
       <Filter>Header Files\core</Filter>
     </ClInclude>
   </ItemGroup>
+  <ItemGroup>
+    <ResourceCompile Include="cyclobranch.rc">
+      <Filter>Resources</Filter>
+    </ResourceCompile>
+  </ItemGroup>
 </Project>
\ No newline at end of file
diff --git a/CycloBranch/CycloBranch.vcxproj.user b/CycloBranch/CycloBranch.vcxproj.user
index dfe0f79..b65447a 100644
--- a/CycloBranch/CycloBranch.vcxproj.user
+++ b/CycloBranch/CycloBranch.vcxproj.user
@@ -9,14 +9,14 @@
     <QTDIR>C:\Qt\5.1.1\msvc2012_64\</QTDIR>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
-    <QTDIR>C:\Qt\5.1.1\msvc2012_64</QTDIR>
+    <QTDIR>C:\Qt\Qt5.2.1\5.2.1\msvc2012_64</QTDIR>
     <LocalDebuggerEnvironment>PATH=$(QTDIR)\bin%3b"$(QTDIR)\bin%3b$(PATH)</LocalDebuggerEnvironment>
     <LocalDebuggerCommandArguments>
     </LocalDebuggerCommandArguments>
     <DebuggerFlavor>WindowsLocalDebugger</DebuggerFlavor>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
-    <QTDIR>C:\Qt\5.1.1\msvc2012_64</QTDIR>
+    <QTDIR>C:\Qt\Qt5.2.1\5.2.1\msvc2012_64</QTDIR>
     <LocalDebuggerEnvironment>PATH=$(QTDIR)\bin%3b%PATH%%3b"$(PATH)</LocalDebuggerEnvironment>
     <DebuggerFlavor>WindowsLocalDebugger</DebuggerFlavor>
     <LocalDebuggerCommandArguments>
diff --git a/CycloBranch/core/cAllocator.h b/CycloBranch/core/cAllocator.h
new file mode 100644
index 0000000..5fee5b3
--- /dev/null
+++ b/CycloBranch/core/cAllocator.h
@@ -0,0 +1,111 @@
+/**
+	\file cAllocator.h
+	\brief An allocator of objects.
+*/
+
+
+#ifndef _CALLOCATOR_H
+#define _CALLOCATOR_H
+
+#include <vector>
+
+using namespace std;
+
+
+/**
+	\brief An allocator of objects.
+*/
+template <class T>
+class cAllocator
+{
+
+	vector<T*> strips;
+	int itemsperstrip;
+
+	int currentfreestrip;
+	int currentfreeitem;
+
+public:
+
+
+	/**
+		\brief The constructor.
+	*/ 
+	cAllocator();
+
+
+	/**
+		\brief The destructor.
+	*/ 
+	~cAllocator();
+
+
+	/**
+		\brief Remove all allocated items.
+	*/ 
+	void reset();
+
+
+	/**
+		\brief Get a reference to a new item.
+		\retval reference to a new item
+	*/ 
+	T* getNewItem();
+
+};
+
+
+template <class T>
+cAllocator<T>::cAllocator() {
+	strips.clear();
+	itemsperstrip = 500;
+	currentfreestrip = 0;
+	currentfreeitem = 0;
+
+	T* newstrip = new T[itemsperstrip];
+	strips.push_back(newstrip);
+}
+
+
+template <class T>
+cAllocator<T>::~cAllocator() {
+	for (int i = 0; i < (int)strips.size(); i++) {
+		delete [] strips[i];
+	}
+}
+
+
+template <class T>
+void cAllocator<T>::reset() {
+	for (int i = 0; i < (int)strips.size(); i++) {
+		delete [] strips[i];
+	}
+
+	strips.clear();
+	itemsperstrip = 500;
+	currentfreestrip = 0;
+	currentfreeitem = 0;
+
+	T* newstrip = new T[itemsperstrip];
+	strips.push_back(newstrip);
+}
+
+
+template <class T>
+T* cAllocator<T>::getNewItem() {
+	T* freeitem = &strips[currentfreestrip][currentfreeitem];
+
+	currentfreeitem++;
+	if (currentfreeitem == itemsperstrip) {
+		currentfreestrip++;
+		currentfreeitem = 0;
+		T* newstrip = new T[itemsperstrip];
+		strips.push_back(newstrip);
+	}
+
+	return freeitem;
+}
+
+
+#endif
+
diff --git a/CycloBranch/core/cBrick.cpp b/CycloBranch/core/cBrick.cpp
index 4b6c764..3737504 100644
--- a/CycloBranch/core/cBrick.cpp
+++ b/CycloBranch/core/cBrick.cpp
@@ -1,7 +1,7 @@
 #include "core/cBrick.h"
 
 
-int getNumberOfBricks(string& composition) {
+int getNumberOfBricks(const string& composition) {
 	if (composition.size() == 0) {
 		return 0;
 	}
@@ -64,7 +64,7 @@ string& cBrick::getName() {
 }
 
 
-void cBrick::setName(string& name) {
+void cBrick::setName(const string& name) {
 	this->name = name;
 }
 
@@ -103,7 +103,7 @@ string cBrick::getReverseComposition() {
 }
 
 
-double cBrick::getMass() {
+double cBrick::getMass() const {
 	return mass;
 }
 
@@ -113,7 +113,7 @@ void cBrick::setMass(double mass) {
 }
 
 
-void cBrick::setComposition(string& composition, bool normalize) {
+void cBrick::setComposition(const string& composition, bool normalize) {
 	this->composition = composition;
 	if (normalize) {
 		normalizeComposition();
@@ -121,12 +121,12 @@ void cBrick::setComposition(string& composition, bool normalize) {
 }
 
 
-void cBrick::setSummary(string& summary) {
+void cBrick::setSummary(const string& summary) {
 	this->summary = summary;
 }
 
 
-void cBrick::setAcronyms(string& acronyms) {
+void cBrick::setAcronyms(const string& acronyms) {
 	this->acronyms.clear();
 	string s = "";
 	int i = 0;
@@ -148,7 +148,7 @@ void cBrick::setAcronyms(string& acronyms) {
 }
 
 
-void cBrick::setReferences(string& references) {
+void cBrick::setReferences(const string& references) {
 	this->references.clear();
 	string s = "";
 	int i = 0;
@@ -194,7 +194,7 @@ void cBrick::explodeToIntComposition(vector<int>& bricks) {
 	int item;
 	int first = 0;
 	int last = (int)composition.find('-');
-	while (last != string::npos) {
+	while (last != (int)string::npos) {
 		item = atoi(composition.substr(first, last - first).c_str());
 		bricks.push_back(item);
 		first = last+1;
@@ -214,7 +214,7 @@ void cBrick::explodeToStringComposition(vector<string>& bricks) {
 	string item;
 	int first = 0;
 	int last = (int)composition.find('-');
-	while (last != string::npos) {
+	while (last != (int)string::npos) {
 		item = composition.substr(first, last - first);
 		bricks.push_back(item);
 		first = last+1;
@@ -259,7 +259,7 @@ string cBrick::getFirstAcronymAsString() {
 
 string cBrick::getAcronymsWithReferencesAsHTMLString() {
 	if (acronyms.size() != references.size()) {
-		return "";
+		return getAcronymsAsString();
 	}
 
 	string s = "";
@@ -339,8 +339,7 @@ string cBrick::getAcronymsWithReferencesAsHTMLString() {
 			}
 
 		}
-		catch (std::regex_error& e) {
-			e;
+		catch (regex_error& /*e*/) {
 			// nothing to do
 		}
 
diff --git a/CycloBranch/core/cBrick.h b/CycloBranch/core/cBrick.h
index fcbfd9d..5a717be 100644
--- a/CycloBranch/core/cBrick.h
+++ b/CycloBranch/core/cBrick.h
@@ -12,7 +12,6 @@
 #include <string>
 #include <vector>
 #include <algorithm>
-#include <regex>
 #include "core/utilities.h"
 
 using namespace std;
@@ -23,7 +22,7 @@ using namespace std;
 	\param composition string containing ids of bricks separated by '-'
 	\retval number number of bricks
 */ 
-int getNumberOfBricks(string& composition);
+int getNumberOfBricks(const string& composition);
 
 
 /**
@@ -78,7 +77,7 @@ class cBrick {
 		\brief Set a full name of the brick.
 		\param name reference to a string
 	*/ 
-	void setName(string& name);
+	void setName(const string& name);
 
 	
 	/**
@@ -120,7 +119,7 @@ class cBrick {
 		\brief Get the mass of the brick.
 		\retval double mass
 	*/ 
-	double getMass();
+	double getMass() const;
 
 
 	/**
@@ -135,28 +134,28 @@ class cBrick {
 		\param composition reference to a string with composition (ids of bricks separated by '-')
 		\param normalize if true then ids of bricks are sorted in ascending order
 	*/ 
-	void setComposition(string& composition, bool normalize);
+	void setComposition(const string& composition, bool normalize);
 
 
 	/**
 		\brief Set the summary molecular formula of the brick.
 		\param summary reference to a string
 	*/ 
-	void setSummary(string& summary);
+	void setSummary(const string& summary);
 
 
 	/**
 		\brief Set acronyms of all izomers corresponding to the brick.
 		\param acronyms reference to a string where the acronyms are separated by '/'
 	*/ 
-	void setAcronyms(string& acronyms);
+	void setAcronyms(const string& acronyms);
 
 
 	/**
 		\brief Set references (e.g., to ChemSpider) of all izomers corresponding to the brick.
 		\param references reference to a string where references to izomers are separated by '/'
 	*/ 
-	void setReferences(string& references);
+	void setReferences(const string& references);
 
 
 	/**
diff --git a/CycloBranch/core/cBricksDatabase.cpp b/CycloBranch/core/cBricksDatabase.cpp
index 6702b0d..810fde9 100644
--- a/CycloBranch/core/cBricksDatabase.cpp
+++ b/CycloBranch/core/cBricksDatabase.cpp
@@ -4,7 +4,7 @@
 #include "gui/cMainThread.h"
 
 
-bool compareBrickMasses(cBrick& a, cBrick& b) {
+bool compareBrickMasses(const cBrick& a, const cBrick& b) {
 	return (a.getMass() < b.getMass());
 }
 
@@ -109,7 +109,7 @@ cBricksDatabase::cBricksDatabase() {
 }
 
 
-int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormessage) {
+int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormessage, bool ignoreerrors) {
 	string s;
 	cBrick b;
 	size_t pos;
@@ -178,10 +178,15 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 		}
 
 		// load references
+		#if OS_TYPE == UNX
+			if ((s.size() > 0) && (s.back() == '\r')) {
+				s = s.substr(0, s.size() - 1);
+			}
+		#endif
 		b.setReferences(s);
 
 		// store brick
-		if (!b.empty()) {
+		if (ignoreerrors || (!ignoreerrors && !b.empty())) {
 
 			// calculate mass from the summary
 			formula.clear();
@@ -190,11 +195,13 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 				b.setMass(formula.getMass());
 			}
 			else {
-				error = true;
-				break;
+				if (!ignoreerrors) {
+					error = true;
+					break;
+				}
 			}
 
-			if (b.getMass() == 0) {
+			if (!ignoreerrors && (b.getMass() == 0)) {
 				error = true;
 				errormessage = "Invalid brick no. " + to_string(size() + 1) + ".\n\n";
 				break;
@@ -204,7 +211,7 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 		}
 	}
 
-	if (error) {
+	if (!ignoreerrors && error) {
 		return -1;
 	}
 
@@ -213,7 +220,7 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 
 
 void cBricksDatabase::storeToPlainTextStream(ofstream &stream) {
-	for (int i = 0; i < bricks.size(); i++) {
+	for (int i = 0; i < (int)bricks.size(); i++) {
 		stream << bricks[i].getName() << "\t";
 		stream << bricks[i].getAcronymsAsString() << "\t";
 		stream << bricks[i].getSummary() << "\t";
@@ -322,7 +329,7 @@ string cBricksDatabase::getTagName(string& composition) {
 }
 
 
-string cBricksDatabase::getAcronymNameOfTPeptide(string& tcomposition, bool useHTMLReferences) {
+string cBricksDatabase::getAcronymNameOfTPeptide(const string& tcomposition, bool useHTMLReferences) {
 	string comp = tcomposition;
 
 	int leftbracket = getNumberOfBricks(comp.substr(0, comp.find('(')));
diff --git a/CycloBranch/core/cBricksDatabase.h b/CycloBranch/core/cBricksDatabase.h
index a9fd148..c2a50de 100644
--- a/CycloBranch/core/cBricksDatabase.h
+++ b/CycloBranch/core/cBricksDatabase.h
@@ -14,7 +14,7 @@
 #include <algorithm>
 #include <iomanip>
 
-
+#include "core/utilities.h"
 #include "core/cBrick.h"
 #include "core/cSummaryFormula.h"
 
@@ -31,7 +31,7 @@ class cMainThread;
 	\param b second brick
 	\retval bool true if the mass of \a a is less than the mass of \a b
 */ 
-bool compareBrickMasses(cBrick& a, cBrick& b);
+bool compareBrickMasses(const cBrick& a, const cBrick& b);
 
 
 /**
@@ -90,9 +90,10 @@ class cBricksDatabase {
 		\brief Load the database of bricks from a plain text stream.
 		\param stream reference to an input file stream
 		\param errormessage reference to a string where an error message might be stored
+		\param ignoreerrors if true errors are ignored
 		\retval int 0 when the database was successfully loaded, -1 when an error occurred (\a errormessage is filled up)
 	*/ 
-	int loadFromPlainTextStream(ifstream &stream, string& errormessage);
+	int loadFromPlainTextStream(ifstream &stream, string& errormessage, bool ignoreerrors);
 
 
 	/**
@@ -169,7 +170,7 @@ class cBricksDatabase {
 		\param useHTMLReferences if true then each acronym is converted to a link to its reference (e.g., in ChemSpider)
 		\retval string name of the peptide
 	*/ 
-	string getAcronymNameOfTPeptide(string& tcomposition, bool useHTMLReferences);
+	string getAcronymNameOfTPeptide(const string& tcomposition, bool useHTMLReferences);
 
 
 	/**
@@ -224,4 +225,4 @@ class cBricksDatabase {
 };
 
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/core/cCandidate.cpp b/CycloBranch/core/cCandidate.cpp
index 80b391f..b7cdb27 100644
--- a/CycloBranch/core/cCandidate.cpp
+++ b/CycloBranch/core/cCandidate.cpp
@@ -1,6 +1,7 @@
 #include "core/cCandidate.h"
 
 #include "core/cCandidateSet.h"
+#include "core/cDeNovoGraph.h"
 
 
 void cCandidate::updateInternalComposition() {
@@ -96,7 +97,7 @@ void cCandidate::attachAllBranches(cCandidate& candidate, cCandidateSet& result,
 }
 
 
-void cCandidate::getPartialRotations(string& composition, vector<string>& rotations) {
+void cCandidate::getPartialRotations(const string& composition, vector<string>& rotations) {
 	cBrick b;
 	string s;
 	vector<string> bricks;
@@ -134,7 +135,7 @@ void cCandidate::getPartialRotations(string& composition, vector<string>& rotati
 }
 
 
-void cCandidate::getPartialLassoRotations(string& composition, vector<cCandidate>& lassorotations, int branchstart, int branchend) {
+void cCandidate::getPartialLassoRotations(const string& composition, vector<cCandidate>& lassorotations, int branchstart, int branchend) {
 	cBrick b;
 	string s;
 	bool leftbracketput;
@@ -188,16 +189,20 @@ cCandidate::cCandidate() {
 
 
 cCandidate::cCandidate(vector<string>& composition, vector<nodeEdge>& path, int startmodifID, int endmodifID, int middlemodifID, int middlepos) {
+	clear();
 	setCandidate(composition, path, startmodifID, endmodifID, middlemodifID, middlepos);
 }
 
 
 cCandidate::cCandidate(vector<string>& composition, vector<nodeEdge>& path, int startmodifID, int endmodifID, int middlemodifID, int branchstart, int branchend) {
+	clear();
 	setCandidate(composition, path, startmodifID, endmodifID, middlemodifID, branchstart, branchend);
 }
 
 
 void cCandidate::setCandidate(vector<string>& composition, vector<nodeEdge>& path, int startmodifID, int endmodifID, int middlemodifID, int middlepos) {
+	clear();
+
 	this->composition = composition;
 	updateInternalComposition();
 
@@ -222,6 +227,8 @@ void cCandidate::setCandidate(vector<string>& composition, vector<nodeEdge>& pat
 
 
 void cCandidate::setCandidate(vector<string>& composition, vector<nodeEdge>& path, int startmodifID, int endmodifID, int middlemodifID, int branchstart, int branchend) {
+	clear();
+
 	this->composition = composition;
 	updateInternalComposition();
 
@@ -245,6 +252,13 @@ void cCandidate::clear() {
 	branchend = -1;
 	path.clear();
 	name = "";
+
+	realpeptidename = "";
+	acronympeptidename = "";
+	acronyms.clear();
+	backboneacronyms.clear();
+	branchacronyms.clear();
+	stringpath = "";
 }
 
 
@@ -284,22 +298,53 @@ void cCandidate::revertComposition() {
 }
 
 
-void cCandidate::prepareBranchedCandidate(cCandidateSet& result, peptideType peptidetype, bool* terminatecomputation) {
+void cCandidate::prepareBranchedCandidates(cCandidateSet& result, peptideType peptidetype, bool* terminatecomputation) {
 	cCandidate c;
 	result.getSet().clear();
 
-	// branching is unknown
-	if ((branchstart == -1) && (branchend == -1)) {
-		attachAllBranches(*this, result, peptidetype, terminatecomputation);
-	}
-	// branching is determined by a modification of the T-branch
-	else {
-		attachSubBranchCandidates(*this, result, peptidetype, terminatecomputation);
+	if (peptidetype == lasso) {
+
+		// just one from startmodifid and middlemodifid may be > 0 (checked in getCandidatesIter)
+		// endmodifid is always 0 because precursor_ion is not used in initializeFragmentIonsForDeNovoGraphOfLassoPeptides
+		// startmodifid is always N-terminal because only b-ions are used in the de novo graph
+
+		if ((startmodifID > 0) && (composition.size() > 0)) {
+			middlemodifID = startmodifID;
+			startmodifID = 0;
+			branchstart = 0;
+			
+			cBrick b;
+			vector<int> intvector;
+			b.setComposition(composition[0], false);
+			b.explodeToIntComposition(intvector);
+			branchend = (int)intvector.size() - 1;
+		}
+
+		// branch-cyclic series types D,H
+		if ((branchstart == -1) || (branchstart == 0)) {
+			for (int i = 1; i < numberofinternalbricks - 1; i++) {
+				c = *this;
+				c.branchstart = 0;
+				c.branchend = i;
+				result.getSet().insert(c);
+			}
+		}
+
+		// branch-cyclic series types B,C,F,G
+		if ((branchend == -1) || (branchend == numberofinternalbricks - 1)) {
+			for (int i = 1; i < numberofinternalbricks - 1; i++) {
+				c = *this;
+				c.branchstart = i;
+				c.branchend = numberofinternalbricks - 1;
+				result.getSet().insert(c);
+			}
+		}
+
 	}
 
 	if (peptidetype == branched) {
 
-		// below, middlemodifID is always > 0 because branchstart == 0 (or branchend == 0)
+		// below, middlemodifID is always > 0 because branchstart == 0 (or branchend == numberofinternalbricks - 1)
 
 		// startmodifID and middlemodifID collide on the first detected combination of bricks
 		if (branchstart == 0) {
@@ -339,6 +384,15 @@ void cCandidate::prepareBranchedCandidate(cCandidateSet& result, peptideType pep
 
 	}
 
+	// branching is unknown
+	if ((branchstart == -1) && (branchend == -1)) {
+		attachAllBranches(*this, result, peptidetype, terminatecomputation);
+	}
+	// branching is determined by a modification of the T-branch
+	else {
+		attachSubBranchCandidates(*this, result, peptidetype, terminatecomputation);
+	}
+
 }
 
 
@@ -710,7 +764,7 @@ double cCandidate::getPrecursorMass(cBricksDatabase& brickdatabasewithcombinatio
 		mass += brickdatabasewithcombinations[bricks[i] - 1].getMass();
 	}
 	
-	return mass;
+	return (parameters->precursorcharge > 0)?mass:mass-2*Hplus;
 }
 
 
@@ -948,6 +1002,13 @@ void cCandidate::store(ofstream& os) {
 	storeString(internalcomposition, os);
 
 	os.write((char *)&numberofinternalbricks, sizeof(int));
+
+	storeString(realpeptidename, os);
+	storeString(acronympeptidename, os);
+	storeStringVector(acronyms, os);
+	storeStringVector(backboneacronyms, os);
+	storeStringVector(branchacronyms, os);
+	storeString(stringpath, os);
 }
 
 
@@ -971,6 +1032,13 @@ void cCandidate::load(ifstream& is) {
 	loadString(internalcomposition, is);
 
 	is.read((char *)&numberofinternalbricks, sizeof(int));
+
+	loadString(realpeptidename, is);
+	loadString(acronympeptidename, is);
+	loadStringVector(acronyms, is);
+	loadStringVector(backboneacronyms, is);
+	loadStringVector(branchacronyms, is);
+	loadString(stringpath, is);
 }
 
 
@@ -984,6 +1052,166 @@ string& cCandidate::getName() {
 }
 
 
+void cCandidate::setAcronyms(cBricksDatabase& bricksdatabase) {
+	vector<int> bricks;
+	cBrick b;
+	b.clear();
+	b.setComposition(internalcomposition, false);
+	b.explodeToIntComposition(bricks);
+
+	acronyms.clear();
+	for (int i = 0; i < (int)bricks.size(); i++) {
+		acronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
+	}
+}
+
+
+void cCandidate::setBackboneAcronyms(cBricksDatabase& bricksdatabase) {
+	vector<int> bricks;
+	cBrick b;
+	b.clear();
+	b.setComposition(internalcomposition, false);
+	b.explodeToIntComposition(bricks);
+
+	backboneacronyms.clear();
+	for (int i = 0; i < (int)bricks.size(); i++) {
+		if ((branchstart >= 0) && (branchend >= 0) && ((i <= branchstart) || (i > branchend))) {
+			backboneacronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
+		}
+	}
+}
+
+
+void cCandidate::setBranchAcronyms(cBricksDatabase& bricksdatabase) {
+	vector<int> bricks;
+	cBrick b;
+	b.clear();
+	b.setComposition(internalcomposition, false);
+	b.explodeToIntComposition(bricks);
+
+	branchacronyms.clear();
+	for (int i = 0; i < (int)bricks.size(); i++) {
+		if ((branchstart >= 0) && (branchend >= 0) && (i > branchstart) && (i <= branchend)) {
+			branchacronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
+		}
+	}
+}
+
+
+vector<string>& cCandidate::getAcronyms() {
+	return acronyms;
+}
+
+
+vector<string>& cCandidate::getBackboneAcronyms() {
+	return backboneacronyms;
+}
+
+
+vector<string>& cCandidate::getBranchAcronyms() {
+	return branchacronyms;
+}
+
+
+void cCandidate::setPath(cDeNovoGraph& graph, cParameters* parameters) {
+	cDeNovoGraphNode* currentnode;
+	cDeNovoGraphNode* targetnode;
+	cEdge* currentedge;
+	stringpath = "";
+	for (int i = 0; i < (int)path.size(); i++) {
+		currentnode = &graph[path[i].nodeid];
+		currentedge = &((*currentnode)[path[i].edgeid]);
+		targetnode = &graph[currentedge->targetnode];
+
+		stringpath += to_string(currentnode->getMZRatio());
+		stringpath += " -> ";
+		stringpath += to_string(targetnode->getMZRatio());
+		stringpath += " using brick(s): ";
+		if (currentedge->composition.compare("0") == 0) {
+			stringpath += "none";
+		}
+		else {
+			stringpath += graph.getBrickDatabaseWithCombinations()->getAcronymName(currentedge->composition, true);
+		}
+
+		stringpath += " (mass difference: " + to_string(currentedge->massdifference) + ", ";
+		stringpath += "source intensity: " + to_string(currentnode->getIntensity()) + ", ";
+		stringpath += "target intensity: " + to_string(targetnode->getIntensity()) + ", ";
+		stringpath += "ppm error: " + to_string(currentedge->ppmerror) + ", ";
+		stringpath += "source charge: " + to_string(currentedge->sourcecharge) + ", ";
+		stringpath += "target charge: " + to_string(currentedge->targetcharge);
+		if ((parameters->peptidetype == branched) || (parameters->peptidetype == lasso)) {
+			if (currentedge->middlemodifID > 0) {
+				stringpath += ", branch modification: " + parameters->searchedmodifications[currentedge->middlemodifID].name;
+			}
+		}
+		if (currentedge->endmodifID > 0) {
+			stringpath += ", terminal modification: " + parameters->searchedmodifications[currentedge->endmodifID].name;
+		}
+		//path += currentedge->printSourceAnnotation(fragmentdefinitions);
+		//path += "->";
+		//path += currentedge->printTargetAnnotation(fragmentdefinitions);
+		stringpath += ")<br/>";
+	}	
+}
+
+
+string& cCandidate::getPathAsString() {
+	return stringpath;
+}
+
+
+void cCandidate::setRealPeptideName(cBricksDatabase& bricksdatabase, peptideType peptidetype) {
+	switch (peptidetype)
+	{
+	case linear:
+	case cyclic:
+	case linearpolysaccharide:
+		realpeptidename = bricksdatabase.getRealName(internalcomposition);
+		break;
+	case branched:
+	case lasso:
+		realpeptidename = getRealNameTComposition(bricksdatabase);
+		break;
+	case other:
+	default:
+		realpeptidename = "";
+		break;
+	}
+}
+
+
+void cCandidate::setAcronymPeptideNameWithHTMLReferences(cBricksDatabase& bricksdatabase, peptideType peptidetype) {
+	switch (peptidetype)
+	{
+	case linear:
+	case cyclic:
+	case linearpolysaccharide:
+		acronympeptidename = bricksdatabase.getAcronymName(internalcomposition, true);
+		break;
+	case branched:
+	case lasso:
+		acronympeptidename = getAcronymsTComposition(bricksdatabase);
+		break;
+	case other:
+	default:
+		acronympeptidename = "";
+		break;
+	}
+}
+
+
+string& cCandidate::getRealPeptideName() {
+	return realpeptidename;
+}
+
+
+string& cCandidate::getAcronymPeptideNameWithHTMLReferences() {
+	return acronympeptidename;
+}
+
+
 bool operator == (cCandidate const& a, cCandidate const& b) {
 	return ((cCandidate &)a).isEqualTo((cCandidate &)b); 
 }
+
diff --git a/CycloBranch/core/cCandidate.h b/CycloBranch/core/cCandidate.h
index 110a3f8..145b90b 100644
--- a/CycloBranch/core/cCandidate.h
+++ b/CycloBranch/core/cCandidate.h
@@ -17,9 +17,11 @@
 #include "core/cSummaryFormula.h"
 
 class cCandidateSet;
+class cDeNovoGraph;
 
 
 using namespace std;
+using namespace boost;
 
 
 /**
@@ -140,6 +142,13 @@ class cCandidate {
 	string internalcomposition;
 	int numberofinternalbricks;
 
+	string realpeptidename;
+	string acronympeptidename;
+	vector<string> acronyms;
+	vector<string> backboneacronyms;
+	vector<string> branchacronyms;
+	string stringpath;
+
 	void updateInternalComposition();
 
 	void getPermutationsIter(cCandidateSet& permutations, vector<string>& currentcandidate, int position, bool* terminatecomputation);
@@ -148,9 +157,9 @@ class cCandidate {
 
 	void attachAllBranches(cCandidate& candidate, cCandidateSet& result, peptideType peptidetype, bool* terminatecomputation);
 
-	void getPartialRotations(string& composition, vector<string>& rotations);
+	void getPartialRotations(const string& composition, vector<string>& rotations);
 
-	void getPartialLassoRotations(string& composition, vector<cCandidate>& lassorotations, int branchstart, int branchend);
+	void getPartialLassoRotations(const string& composition, vector<cCandidate>& lassorotations, int branchstart, int branchend);
 
 public:
 
@@ -230,12 +239,12 @@ class cCandidate {
 
 
 	/**
-		\brief Prepare candidates of a branched or a lasso peptide.
+		\brief Prepare candidates of a branched or a branch-cyclic peptide.
 		\param result reference to an output set of possible peptide sequence candidates
 		\param peptidetype a type of an analyzed peptide
 		\param terminatecomputation pointer to a variable determining that the computation must be stopped
 	*/ 
-	void prepareBranchedCandidate(cCandidateSet& result, peptideType peptidetype, bool* terminatecomputation);
+	void prepareBranchedCandidates(cCandidateSet& result, peptideType peptidetype, bool* terminatecomputation);
 
 
 	/**
@@ -404,9 +413,9 @@ class cCandidate {
 
 
 	/**
-		\brief Get lasso rotations of a lasso peptide sequence.
-		\param lassorotations reference to an output vector containing lasso rotations of a sequence
-		\param includerevertedrotations if true then reverted lasso rotations are also included
+		\brief Get branch-cyclic rotations of a branch-cyclic peptide sequence.
+		\param lassorotations reference to an output vector containing branch-cyclic rotations of a sequence
+		\param includerevertedrotations if true then reverted branch-cyclic rotations are also included
 	*/ 
 	void getLassoRotations(vector<cCandidate>& lassorotations, bool includerevertedrotations);
 
@@ -447,6 +456,93 @@ class cCandidate {
 	*/ 
 	string& getName();
 
+
+	/**
+		\brief Set a vector of acronyms corresponding to a peptide sequence candidate.
+		\param bricksdatabase a database of building blocks
+	*/ 
+	void setAcronyms(cBricksDatabase& bricksdatabase);
+
+
+	/**
+		\brief Set a vector of acronyms corresponding to a backbone of a peptide sequence candidate.
+		\param bricksdatabase a database of building blocks
+	*/ 
+	void setBackboneAcronyms(cBricksDatabase& bricksdatabase);
+
+
+	/**
+		\brief Set a vector of acronyms corresponding to a branch of a peptide sequence candidate.
+		\param bricksdatabase a database of building blocks
+	*/ 
+	void setBranchAcronyms(cBricksDatabase& bricksdatabase);
+
+
+	/**
+		\brief Get a vector of acronyms corresponding to a peptide sequence candidate.
+		\retval vector<string> a vector of acronyms
+	*/ 
+	vector<string>& getAcronyms();
+
+
+	/**
+		\brief Get a vector of acronyms corresponding to a backbone of a peptide sequence candidate.
+		\retval vector<string> a vector of acronyms
+	*/ 
+	vector<string>& getBackboneAcronyms();
+
+
+	/**
+		\brief Get a vector of acronyms corresponding to a branch of a peptide sequence candidate.
+		\retval vector<string> a vector of acronyms
+	*/ 
+	vector<string>& getBranchAcronyms();
+
+
+	/**
+		\brief Set a path in the de novo graph corresponding to the candidate.
+		\param graph reference to the de novo graph
+		\param parameters parameters of the application
+	*/ 
+	void setPath(cDeNovoGraph& graph, cParameters* parameters);
+
+
+	/**
+		\brief Get a path in the de novo graph corresponding to the candidate as a string.
+		\retval string reference to a path corresponding to the spectrum
+	*/ 
+	string& getPathAsString();
+
+
+	/**
+		\brief Set a real peptide name.
+		\param bricksdatabase the database of building blocks
+		\param peptidetype the type of peptide
+	*/ 
+	void setRealPeptideName(cBricksDatabase& bricksdatabase, peptideType peptidetype);
+
+
+	/**
+		\brief Set an acronym peptide name.
+		\param bricksdatabase the database of building blocks
+		\param peptidetype the type of peptide
+	*/ 
+	void setAcronymPeptideNameWithHTMLReferences(cBricksDatabase& bricksdatabase, peptideType peptidetype);
+
+
+	/**
+		\brief Get a real peptide name.
+		\retval string reference to the real peptide name
+	*/ 
+	string& getRealPeptideName();
+
+
+	/**
+		\brief Get an acronym peptide name.
+		\retval string reference to the acronym peptide name
+	*/ 
+	string& getAcronymPeptideNameWithHTMLReferences();
+
 };
 
 
@@ -461,7 +557,7 @@ struct hash_cCandidate {
 		\retval size_t hashed candidate
 	*/
 	size_t operator()(const cCandidate& candidate) const {
-		return hash<string>()(((cCandidate&)candidate).getComposition());
+		return std::hash<string>()(((cCandidate&)candidate).getComposition());
 	}
 
 };
diff --git a/CycloBranch/core/cDeNovoGraph.cpp b/CycloBranch/core/cDeNovoGraph.cpp
index c9c1039..9c9c1e8 100644
--- a/CycloBranch/core/cDeNovoGraph.cpp
+++ b/CycloBranch/core/cDeNovoGraph.cpp
@@ -22,11 +22,12 @@ cDeNovoGraph::cDeNovoGraph() {
 }
 
 
-bool cDeNovoGraph::findPath(int sourcenodeid, int edgeid, int targetnodeid, string& composition, string brickspath, int maximumbricksincombination, vector<int>& path) {
+bool cDeNovoGraph::findPath(int sourcenodeid, int edgeid, int targetnodeid, string& composition, string brickspath, int maximumbricksincombination, vector<nodeEdge>& path) {
 	string localbrickpath;
 	bool found;
 	bool badpath;
 	int count = getNumberOfBricks(brickspath);
+	nodeEdge ne;
 
 	if ((path.size() > 1) && (sourcenodeid == targetnodeid)) {
 		cBrick b;
@@ -42,9 +43,15 @@ bool cDeNovoGraph::findPath(int sourcenodeid, int edgeid, int targetnodeid, stri
 			if ((i == edgeid) && (path.size() == 0)) {
 				continue;
 			}
+
+			// target charge of an edge must be equal to the source charge of a following edge
+			if ((path.size() > 0) && (graph[sourcenodeid][i].sourcecharge != graph[path.back().nodeid][path.back().edgeid].targetcharge)) {
+				continue;
+			}
+
 			badpath = false;
 			for (int j = 0; j < (int)path.size(); j++) {
-				if (path[j] == sourcenodeid) {
+				if (path[j].nodeid == sourcenodeid) {
 					badpath = true;
 					break;
 				}
@@ -52,14 +59,21 @@ bool cDeNovoGraph::findPath(int sourcenodeid, int edgeid, int targetnodeid, stri
 			if (badpath) {
 				continue;
 			}
+
 			localbrickpath = brickspath;
 			if (localbrickpath.size() > 0) {
 				localbrickpath += '-';
 			}
 			localbrickpath += graph[sourcenodeid][i].composition;
-			path.push_back(sourcenodeid);
+
+			ne.nodeid = sourcenodeid;
+			ne.edgeid = i;
+			path.push_back(ne);
+
 			found = findPath(graph[sourcenodeid][i].targetnode, i, targetnodeid, composition, localbrickpath, maximumbricksincombination, path);
+			
 			path.pop_back();
+			
 			if (found) {
 				//*os << graph[sourcenodeid].getMZRatio() << " ";
 				return true;
@@ -118,14 +132,14 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 	double termmass;
 	int left, right, middle;
 	cEdge e, e1, e2;
-	double unchargedprecursormass = uncharge(parameters->precursormass, parameters->precursorcharge);
+	double unchargedprecursormass = charge(uncharge(parameters->precursormass, parameters->precursorcharge), (parameters->precursorcharge > 0)?1:-1);
 	double unchargedmz;
 	int i;
 	
 	sortedpeaklist = parameters->peaklist;
 	// insert the single charged precursor, if neccessary
 	sortedpeaklist.sortbyMass();
-	sortedpeaklist.cropMaximumMZRatio(unchargedprecursormass);
+	sortedpeaklist.cropMaximumMZRatio(unchargedprecursormass, parameters->precursormasserrortolerance);
 	if ((sortedpeaklist.size() > 0) && (!isInPpmMassErrorTolerance(sortedpeaklist[sortedpeaklist.size() - 1].mzratio, unchargedprecursormass, parameters->precursormasserrortolerance))) { 
 		cPeak p;
 		p.mzratio = unchargedprecursormass;
@@ -146,12 +160,14 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 	sortedpeaklist.removeNeutralLoss(- NH3, parameters->precursorcharge, parameters->fragmentmasserrortolerance);
 	*os << "Number of nodes when deamidated ions are removed: " << sortedpeaklist.size() << endl;	
 
+	double negativeshift = (parameters->precursorcharge > 0)?0:-2*Hplus;
+
 	// insert system nodes
 	switch (parameters->peptidetype)
 	{
 	case cyclic:
 		node.clear();
-		node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference);
+		node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + negativeshift);
 		node.setIntensity(0);
 		node.addIonAnnotation(b_ion);
 		graph.push_back(node);
@@ -166,13 +182,13 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 		graph.push_back(node);
 
 		node.clear();
-		node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference);
+		node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + negativeshift);
 		node.setIntensity(0);
 		node.addIonAnnotation(b_ion);
 		graph.push_back(node);
 
 		node.clear();
-		node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference);
+		node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference + negativeshift);
 		node.setIntensity(0);
 		node.addIonAnnotation(y_ion);
 		graph.push_back(node);
@@ -195,13 +211,13 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 			e.targetnode = i + 2;
 
 			if (parameters->searchedmodifications[i].nterminal) {
-				node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + parameters->searchedmodifications[i].massdifference);
+				node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + parameters->searchedmodifications[i].massdifference + negativeshift);
 				node.setIntensity(0);
 				node.addIonAnnotation(b_ion);
 			}
 
 			if (parameters->searchedmodifications[i].cterminal) {
-				node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference + parameters->searchedmodifications[i].massdifference);
+				node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference + parameters->searchedmodifications[i].massdifference + negativeshift);
 				node.setIntensity(0);
 				node.addIonAnnotation(y_ion);
 			}
@@ -226,13 +242,13 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 		graph.push_back(node);
 
 		node.clear();
-		node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference);
+		node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + negativeshift);
 		node.setIntensity(0);
 		node.addIonAnnotation(b_ion);
 		graph.push_back(node);
 
 		//node.clear();
-		//node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference);
+		//node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference + negativeshift);
 		//node.setIntensity(0);
 		//node.addIonAnnotation(y_ion);
 		//graph.push_back(node);
@@ -256,13 +272,13 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 			e.targetnode = i + 2;
 
 			if (parameters->searchedmodifications[i].nterminal) {
-				node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + parameters->searchedmodifications[i].massdifference);
+				node.setMZRatio(parameters->fragmentdefinitions[b_ion].massdifference + parameters->searchedmodifications[i].massdifference + negativeshift);
 				node.setIntensity(0);
 				node.addIonAnnotation(b_ion);
 			}
 
 			if (parameters->searchedmodifications[i].cterminal) {
-				node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference + parameters->searchedmodifications[i].massdifference);
+				node.setMZRatio(parameters->fragmentdefinitions[y_ion].massdifference + parameters->searchedmodifications[i].massdifference + negativeshift);
 				node.setIntensity(0);
 				node.addIonAnnotation(y_ion);
 			}
@@ -284,13 +300,13 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 		graph.push_back(node);
 
 		node.clear();
-		node.setMZRatio(H2O + Hplus);
+		node.setMZRatio(H2O + Hplus + negativeshift);
 		node.setIntensity(0);
 		node.addIonAnnotation(ms_nterminal_ion_hplus);
 		graph.push_back(node);
 
 		//node.clear();
-		//node.setMZRatio(H2O + Hplus);
+		//node.setMZRatio(H2O + Hplus + negativeshift);
 		//node.setIntensity(0);
 		//node.addIonAnnotation(ms_cterminal_ion_hplus);
 		//graph.push_back(node);
@@ -313,13 +329,13 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 			e.targetnode = i + 1;//2;
 
 			//if (parameters->searchedmodifications[i].nterminal) {
-				node.setMZRatio(H2O + Hplus + parameters->searchedmodifications[i].massdifference);
+				node.setMZRatio(H2O + Hplus + parameters->searchedmodifications[i].massdifference + negativeshift);
 				node.setIntensity(0);
 				node.addIonAnnotation(ms_nterminal_ion_hplus);
 			//}
 
 			//if (parameters->searchedmodifications[i].cterminal) {
-			//	node.setMZRatio(H2O + Hplus +parameters->searchedmodifications[i].massdifference);
+			//	node.setMZRatio(H2O + Hplus + parameters->searchedmodifications[i].massdifference + negativeshift);
 			//	node.setIntensity(0);
 			//	node.addIonAnnotation(ms_cterminal_ion_hplus);
 			//}
@@ -461,7 +477,7 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 							continue;
 						}
 
-						// middle modifications for branched and lasso peptides
+						// middle modifications for branched and branch-cyclic peptides
 						for (int p = 0; p < (int)parameters->searchedmodifications.size(); p++) {
 
 							if ((p > 0) && ((parameters->peptidetype == linear) || (parameters->peptidetype == cyclic) || (parameters->peptidetype == linearpolysaccharide))) {
@@ -488,11 +504,11 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 
 							}
 
-							for (int z1 = 1; z1 <= parameters->precursorcharge; z1++) {
+							for (int z1 = 1; z1 <= abs(parameters->precursorcharge); z1++) {
 
-								for (int z2 = 1; z2 <= parameters->precursorcharge; z2++) {
+								for (int z2 = 1; z2 <= abs(parameters->precursorcharge); z2++) {
 
-									unchargedmz = uncharge(graph[i].getMZRatio(), z1);
+									unchargedmz = charge(uncharge(graph[i].getMZRatio(), (parameters->precursorcharge > 0)?z1:-z1), (parameters->precursorcharge > 0)?1:-1);
 									if ((!isInPpmMassErrorTolerance(unchargedmz, unchargedprecursormass, parameters->fragmentmasserrortolerance)) && (unchargedmz > unchargedprecursormass)) {
 										continue;
 									}
@@ -521,12 +537,12 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 									while (left <= right) {
 
 										middle = (left + right) / 2;
-										if (isInPpmMassErrorTolerance(uncharge(graph[middle].getMZRatio(), z2), mass, parameters->fragmentmasserrortolerance)) {
+										if (isInPpmMassErrorTolerance(charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1), mass, parameters->fragmentmasserrortolerance)) {
 											// found
-											while ((middle > lastsystemnode + 1) && isInPpmMassErrorTolerance(uncharge(graph[middle - 1].getMZRatio(), z2), mass, parameters->fragmentmasserrortolerance)) {
+											while ((middle > lastsystemnode + 1) && isInPpmMassErrorTolerance(charge(uncharge(graph[middle - 1].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1), mass, parameters->fragmentmasserrortolerance)) {
 												middle--;
 											}
-											while ((middle < (int)graph.size()) && (isInPpmMassErrorTolerance(uncharge(graph[middle].getMZRatio(), z2), mass, parameters->fragmentmasserrortolerance))) {
+											while ((middle < (int)graph.size()) && (isInPpmMassErrorTolerance(charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1), mass, parameters->fragmentmasserrortolerance))) {
 
 												// target node cannot be a system node
 												if (middle <= lastsystemnode) {
@@ -541,7 +557,7 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 												}
 
 												// mass corresponding to the target node must be <= uncharged precursor mass
-												if (uncharge(graph[middle].getMZRatio(), z2) > unchargedprecursormass) {
+												if (charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1) > unchargedprecursormass) {
 													middle++;
 													continue;
 												}
@@ -558,10 +574,10 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 												if (i == (int)graph.size() - 1) {
 													e.targetnode = i;
 													e.brickid = j;
-													e.ppmerror = ppmError(uncharge(graph[middle].getMZRatio(), z2), mass);
-													e.massdifference = abs(unchargedmz - uncharge(graph[middle].getMZRatio(), z2));
-													e.sourcecharge = z2;
-													e.targetcharge = z1;
+													e.ppmerror = ppmError(charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1), mass);
+													e.massdifference = abs(unchargedmz - charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1));
+													e.sourcecharge = (parameters->precursorcharge > 0)?z2:-z2;
+													e.targetcharge = (parameters->precursorcharge > 0)?z1:-z1;
 													e.targetintensity = graph[i].getIntensity();
 													e.composition = bricksdatabasewithcombinations[j].getComposition();
 													e.endmodifID = n;
@@ -573,10 +589,10 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 												else {
 													e.targetnode = middle;
 													e.brickid = j;
-													e.ppmerror = ppmError(uncharge(graph[middle].getMZRatio(), z2), mass);
-													e.massdifference = abs(uncharge(graph[middle].getMZRatio(), z2) - unchargedmz);
-													e.sourcecharge = z1;
-													e.targetcharge = z2;
+													e.ppmerror = ppmError(charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1), mass);
+													e.massdifference = abs(charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1) - unchargedmz);
+													e.sourcecharge = (parameters->precursorcharge > 0)?z1:-z1;
+													e.targetcharge = (parameters->precursorcharge > 0)?z2:-z2;
 													e.targetintensity = graph[middle].getIntensity();
 													e.composition = bricksdatabasewithcombinations[j].getComposition();
 													e.endmodifID = n;
@@ -593,7 +609,7 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 											}
 											break;
 										}
-										if (mass < uncharge(graph[middle].getMZRatio(), z2)) {
+										if (mass < charge(uncharge(graph[middle].getMZRatio(), (parameters->precursorcharge > 0)?z2:-z2), (parameters->precursorcharge > 0)?1:-1)) {
 											right = middle - 1;
 										}
 										else {
@@ -640,7 +656,7 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 
 int cDeNovoGraph::removeEdgesFormingPathsNotFinishingInPrecursor(bool& terminatecomputation) {
 	*os << "Removing edges forming blind paths (not finishing in the precursor)... ";
-	double unchargedprecursormass = uncharge(parameters->precursormass, parameters->precursorcharge);
+	double neutralprecursormass = uncharge(parameters->precursormass, parameters->precursorcharge);
 	bool removed = true;
 	bool isprecursor;
 	int edgesremoved = 0;
@@ -658,8 +674,8 @@ int cDeNovoGraph::removeEdgesFormingPathsNotFinishingInPrecursor(bool& terminate
 
 				// Is the target precursor ?
 				isprecursor = false;
-				for (int k = 1; k <= parameters->precursorcharge; k++) {
-					if (isInPpmMassErrorTolerance(graph[graph[i][j].targetnode].getMZRatio(), charge(unchargedprecursormass, k), parameters->precursormasserrortolerance)) {
+				for (int k = 1; k <= abs(parameters->precursorcharge); k++) {
+					if (isInPpmMassErrorTolerance(graph[graph[i][j].targetnode].getMZRatio(), charge(neutralprecursormass, (parameters->precursorcharge > 0)?k:-k), parameters->precursormasserrortolerance)) {
 						isprecursor = true;
 						break;
 					}
@@ -748,8 +764,8 @@ int cDeNovoGraph::connectEdgesFormingPathsNotFinishingInPrecursor(bool& terminat
 			e.brickid = (int)bricksdatabasewithcombinations.size() + 1;
 			e.ppmerror = 0;
 			e.massdifference = abs(graph[precursorposition].getMZRatio() - graph[i].getMZRatio());
-			e.sourcecharge = 1;
-			e.targetcharge = 1;
+			e.sourcecharge = (parameters->precursorcharge > 0)?1:-1;
+			e.targetcharge = (parameters->precursorcharge > 0)?1:-1;
 			e.targetintensity = graph[e.targetnode].getIntensity();
 			e.composition = to_string(e.brickid);
 			e.endmodifID = 0;
@@ -813,8 +829,8 @@ int cDeNovoGraph::connectEdgesFormingPathsNotStartingFromFirstNode(bool& termina
 				e.brickid = (int)bricksdatabasewithcombinations.size() + 1;
 				e.ppmerror = 0;
 				e.massdifference = abs(graph[i].getMZRatio() - graph[j].getMZRatio());
-				e.sourcecharge = 1;
-				e.targetcharge = 1;
+				e.sourcecharge = (parameters->precursorcharge > 0)?1:-1;
+				e.targetcharge = (parameters->precursorcharge > 0)?1:-1;
 				e.targetintensity = graph[i].getIntensity();
 				e.composition = to_string(e.brickid);
 				e.endmodifID = 0;
@@ -849,7 +865,7 @@ int cDeNovoGraph::removePathsWhichCanBeSubstitutedByLongerPath(bool& terminateco
 	*os << "Removing edges forming paths which can be substituted by longer paths... ";
 	int edgesremoved = 0;
 	int j;
-	vector<int> path;
+	vector<nodeEdge> path;
 	
 	for (int i = startnode; i < (int)graph.size(); i++) {
 
diff --git a/CycloBranch/core/cDeNovoGraph.h b/CycloBranch/core/cDeNovoGraph.h
index 422bf77..c5b49ed 100644
--- a/CycloBranch/core/cDeNovoGraph.h
+++ b/CycloBranch/core/cDeNovoGraph.h
@@ -55,7 +55,7 @@ class cDeNovoGraph {
 
 	cGraphReaderThread* graphreaderthread;
 
-	bool findPath(int sourcenodeid, int edgeid, int targetnodeid, string& composition, string brickspath, int maximumbricksincombination, vector<int>& path);
+	bool findPath(int sourcenodeid, int edgeid, int targetnodeid, string& composition, string brickspath, int maximumbricksincombination, vector<nodeEdge>& path);
 
 	// create vectors of edges from temporary unordered_sets
 	void createVectorsOfEdges();
diff --git a/CycloBranch/core/cDeNovoGraphNode.cpp b/CycloBranch/core/cDeNovoGraphNode.cpp
index 4c3b4d1..453b7e5 100644
--- a/CycloBranch/core/cDeNovoGraphNode.cpp
+++ b/CycloBranch/core/cDeNovoGraphNode.cpp
@@ -18,12 +18,12 @@ bool operator == (cEdge const& a, cEdge const& b) {
 }
 
 
-bool compareEdgesByPPMError(cEdge& a, cEdge& b) {
+bool compareEdgesByPPMError(const cEdge& a, const cEdge& b) {
 	return (a.ppmerror < b.ppmerror);
 }
 
 
-bool compareEdgesByTargetNodeIntensityDesc(cEdge& a, cEdge& b) {
+bool compareEdgesByTargetNodeIntensityDesc(const cEdge& a, const cEdge& b) {
 	return (a.targetintensity > b.targetintensity);
 }
 
diff --git a/CycloBranch/core/cDeNovoGraphNode.h b/CycloBranch/core/cDeNovoGraphNode.h
index 8ee33bd..4dda405 100644
--- a/CycloBranch/core/cDeNovoGraphNode.h
+++ b/CycloBranch/core/cDeNovoGraphNode.h
@@ -153,7 +153,7 @@ struct hash_cEdge {
 		\retval size_t hashed edge
 	*/
 	size_t operator()(const cEdge& e) const {
-		return hash<int>()(e.targetnode) ^ hash<int>()(e.brickid);
+		return std::hash<int>()(e.targetnode) ^ std::hash<int>()(e.brickid);
 	}
 
 };
@@ -174,7 +174,7 @@ bool operator == (cEdge const& a, cEdge const& b);
 	\param b second edge
 	\retval bool true when \a a has smaller ppm error than \a b
 */
-bool compareEdgesByPPMError(cEdge& a, cEdge& b);
+bool compareEdgesByPPMError(const cEdge& a, const cEdge& b);
 
 
 /**
@@ -183,7 +183,7 @@ bool compareEdgesByPPMError(cEdge& a, cEdge& b);
 	\param b second edge
 	\retval bool true when the target node of \a a has bigger intensity than the target node of \a b
 */
-bool compareEdgesByTargetNodeIntensityDesc(cEdge& a, cEdge& b);
+bool compareEdgesByTargetNodeIntensityDesc(const cEdge& a, const cEdge& b);
 
 
 /**
@@ -318,4 +318,4 @@ class cDeNovoGraphNode {
 };
 
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/core/cFragmentIons.cpp b/CycloBranch/core/cFragmentIons.cpp
index 9531dbc..c10b320 100644
--- a/CycloBranch/core/cFragmentIons.cpp
+++ b/CycloBranch/core/cFragmentIons.cpp
@@ -1,4 +1,5 @@
 #include "core/cFragmentIons.h"
+#include "core/cSummaryFormula.h"
 
 
 cPeriodicTableMap::cPeriodicTableMap() {
@@ -47,66 +48,13 @@ int cPeriodicTableMap::count(string& element) {
 }
 
 
-peptideType getPeptideTypeFromString(string s) {
-	if (s.compare("linear") == 0) {
-		return linear;
-	}
-	if (s.compare("cyclic") == 0) {
-		return cyclic;
-	}
-	if (s.compare("branched") == 0) {
-		return branched;
-	}
-	if (s.compare("lasso") == 0) {
-		return lasso;
-	}
-	if (s.compare("linearpolysaccharide") == 0) {
-		return linearpolysaccharide;
-	}
-	if (s.compare("other") == 0) {
-		return other;
-	}
-
-	return other;
+double charge(double neutralmass, int charge) {
+	return (neutralmass + (double)charge*Hplus)/(double)abs(charge);
 }
 
 
-string getStringFromPeptideType(peptideType peptidetype) {
-	switch (peptidetype)
-	{
-	case linear:
-		return "linear";
-		break;
-	case cyclic:
-		return "cyclic";
-		break;
-	case branched:
-		return "branched";
-		break;
-	case lasso:
-		return "lasso";
-		break;
-	case linearpolysaccharide:
-		return "linearpolysaccharide";
-		break;
-	case other:
-		return "other";
-		break;
-	default:
-		break;
-	}
-
-	return "other";
-}
-
-
-double charge(double mass, int charge) {
-	return (mass + ((double)(charge - 1))*Hplus)/(double)charge;
-}
-
-
-double uncharge(double mass, int charge) {
-	return mass*(double)charge - ((double)(charge - 1))*Hplus;
+double uncharge(double mzratio, int charge) {
+	return mzratio*(double)abs(charge) - (double)charge*Hplus;
 }
 
 
@@ -135,12 +83,13 @@ void fragmentDescription::load(ifstream& is) {
 
 
 cFragmentIons::cFragmentIons() {
-	recalculateFragments(false, false);
+	string s = "";
+	recalculateFragments(false, false, s);
 }
 
 
-cFragmentIons::cFragmentIons(bool cyclicnterminus, bool cycliccterminus) {
-	recalculateFragments(cyclicnterminus, cycliccterminus);
+cFragmentIons::cFragmentIons(bool cyclicnterminus, bool cycliccterminus, string& precursoradduct) {
+	recalculateFragments(cyclicnterminus, cycliccterminus, precursoradduct);
 }
 
 
@@ -149,208 +98,299 @@ fragmentDescription &cFragmentIons::operator[](fragmentIonType iontype) {
 }
 
 
-void cFragmentIons::recalculateFragments(bool cyclicnterminus, bool cycliccterminus) {
+void cFragmentIons::recalculateFragments(bool cyclicnterminus, bool cycliccterminus, string& precursoradduct) {
 
 	fragmentions.clear();
 
 	double nterminusshift = cyclicnterminus?-H2O:0;
 	double cterminusshift = cycliccterminus?-H2O:0;
-	
-	// initialize B-ion
-	fragmentions[b_ion].nterminal = true;
-	fragmentions[b_ion].cterminal = false;
-	fragmentions[b_ion].name = "B";
-	fragmentions[b_ion].massdifference = B_ION + nterminusshift;
-	fragmentions[b_ion].parent = b_ion;
+	double adductshift = 0;
 
-	// initialize B-H2O ion
-	fragmentions[b_ion_water_loss].nterminal = true;
-	fragmentions[b_ion_water_loss].cterminal = false;
-	fragmentions[b_ion_water_loss].name = "B*";
-	fragmentions[b_ion_water_loss].massdifference = B_ION - H2O + nterminusshift;
-	fragmentions[b_ion_water_loss].parent = b_ion;
-
-	// initialize B-NH3 ion
-	fragmentions[b_ion_ammonia_loss].nterminal = true;
-	fragmentions[b_ion_ammonia_loss].cterminal = false;
-	fragmentions[b_ion_ammonia_loss].name = "Bx";
-	fragmentions[b_ion_ammonia_loss].massdifference = B_ION - NH3 + nterminusshift;
-	fragmentions[b_ion_ammonia_loss].parent = b_ion;
-
-	// initialize B-H2O-NH3 ion
-	fragmentions[b_ion_water_and_ammonia_loss].nterminal = true;
-	fragmentions[b_ion_water_and_ammonia_loss].cterminal = false;
-	fragmentions[b_ion_water_and_ammonia_loss].name = "B*x";
-	fragmentions[b_ion_water_and_ammonia_loss].massdifference = B_ION - H2O - NH3 + nterminusshift;
-	fragmentions[b_ion_water_and_ammonia_loss].parent = b_ion;
+	if (precursoradduct.compare("") != 0) {
+		cSummaryFormula formula;
+		formula.setFormula(precursoradduct);
+		adductshift = formula.getMass() - H;
+	}
 	
 	// initialize A-ion
 	fragmentions[a_ion].nterminal = true;
 	fragmentions[a_ion].cterminal = false;
 	fragmentions[a_ion].name = "A";
-	fragmentions[a_ion].massdifference = A_ION + nterminusshift;
+	fragmentions[a_ion].massdifference = A_ION + nterminusshift + adductshift;
 	fragmentions[a_ion].parent = b_ion; // ok
 	
 	// initialize A-H2O ion
-	fragmentions[a_ion_water_loss].nterminal = true;
-	fragmentions[a_ion_water_loss].cterminal = false;
-	fragmentions[a_ion_water_loss].name = "A*";
-	fragmentions[a_ion_water_loss].massdifference = A_ION - H2O + nterminusshift;
-	fragmentions[a_ion_water_loss].parent = a_ion;
+	fragmentions[a_ion_dehydrated].nterminal = true;
+	fragmentions[a_ion_dehydrated].cterminal = false;
+	fragmentions[a_ion_dehydrated].name = "A*";
+	fragmentions[a_ion_dehydrated].massdifference = A_ION - H2O + nterminusshift + adductshift;
+	fragmentions[a_ion_dehydrated].parent = a_ion;
 
 	// initialize A-NH3 ion
-	fragmentions[a_ion_ammonia_loss].nterminal = true;
-	fragmentions[a_ion_ammonia_loss].cterminal = false;
-	fragmentions[a_ion_ammonia_loss].name = "Ax";
-	fragmentions[a_ion_ammonia_loss].massdifference = A_ION - NH3 + nterminusshift;
-	fragmentions[a_ion_ammonia_loss].parent = a_ion;
+	fragmentions[a_ion_deamidated].nterminal = true;
+	fragmentions[a_ion_deamidated].cterminal = false;
+	fragmentions[a_ion_deamidated].name = "Ax";
+	fragmentions[a_ion_deamidated].massdifference = A_ION - NH3 + nterminusshift + adductshift;
+	fragmentions[a_ion_deamidated].parent = a_ion;
 
 	// initialize A-H2O-NH3 ion
-	fragmentions[a_ion_water_and_ammonia_loss].nterminal = true;
-	fragmentions[a_ion_water_and_ammonia_loss].cterminal = false;
-	fragmentions[a_ion_water_and_ammonia_loss].name = "A*x";
-	fragmentions[a_ion_water_and_ammonia_loss].massdifference = A_ION - H2O - NH3 + nterminusshift;
-	fragmentions[a_ion_water_and_ammonia_loss].parent = a_ion;
+	fragmentions[a_ion_dehydrated_and_deamidated].nterminal = true;
+	fragmentions[a_ion_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[a_ion_dehydrated_and_deamidated].name = "A*x";
+	fragmentions[a_ion_dehydrated_and_deamidated].massdifference = A_ION - H2O - NH3 + nterminusshift + adductshift;
+	fragmentions[a_ion_dehydrated_and_deamidated].parent = a_ion;
+
+	// initialize B-ion
+	fragmentions[b_ion].nterminal = true;
+	fragmentions[b_ion].cterminal = false;
+	fragmentions[b_ion].name = "B";
+	fragmentions[b_ion].massdifference = B_ION + nterminusshift + adductshift;
+	fragmentions[b_ion].parent = b_ion;
+
+	// initialize B-H2O ion
+	fragmentions[b_ion_dehydrated].nterminal = true;
+	fragmentions[b_ion_dehydrated].cterminal = false;
+	fragmentions[b_ion_dehydrated].name = "B*";
+	fragmentions[b_ion_dehydrated].massdifference = B_ION - H2O + nterminusshift + adductshift;
+	fragmentions[b_ion_dehydrated].parent = b_ion;
+
+	// initialize B-NH3 ion
+	fragmentions[b_ion_deamidated].nterminal = true;
+	fragmentions[b_ion_deamidated].cterminal = false;
+	fragmentions[b_ion_deamidated].name = "Bx";
+	fragmentions[b_ion_deamidated].massdifference = B_ION - NH3 + nterminusshift + adductshift;
+	fragmentions[b_ion_deamidated].parent = b_ion;
+
+	// initialize B-H2O-NH3 ion
+	fragmentions[b_ion_dehydrated_and_deamidated].nterminal = true;
+	fragmentions[b_ion_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[b_ion_dehydrated_and_deamidated].name = "B*x";
+	fragmentions[b_ion_dehydrated_and_deamidated].massdifference = B_ION - H2O - NH3 + nterminusshift + adductshift;
+	fragmentions[b_ion_dehydrated_and_deamidated].parent = b_ion;
+
+	// initialize C-ion
+	fragmentions[c_ion].nterminal = true;
+	fragmentions[c_ion].cterminal = false;
+	fragmentions[c_ion].name = "C";
+	fragmentions[c_ion].massdifference = C_ION + nterminusshift + adductshift;
+	fragmentions[c_ion].parent = c_ion;
+	
+	// initialize C-H2O ion
+	fragmentions[c_ion_dehydrated].nterminal = true;
+	fragmentions[c_ion_dehydrated].cterminal = false;
+	fragmentions[c_ion_dehydrated].name = "C*";
+	fragmentions[c_ion_dehydrated].massdifference = C_ION - H2O + nterminusshift + adductshift;
+	fragmentions[c_ion_dehydrated].parent = c_ion;
+
+	// initialize C-NH3 ion
+	fragmentions[c_ion_deamidated].nterminal = true;
+	fragmentions[c_ion_deamidated].cterminal = false;
+	fragmentions[c_ion_deamidated].name = "Cx";
+	fragmentions[c_ion_deamidated].massdifference = C_ION - NH3 + nterminusshift + adductshift;
+	fragmentions[c_ion_deamidated].parent = c_ion;
+
+	// initialize C-H2O-NH3 ion
+	fragmentions[c_ion_dehydrated_and_deamidated].nterminal = true;
+	fragmentions[c_ion_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[c_ion_dehydrated_and_deamidated].name = "C*x";
+	fragmentions[c_ion_dehydrated_and_deamidated].massdifference = C_ION - H2O - NH3 + nterminusshift + adductshift;
+	fragmentions[c_ion_dehydrated_and_deamidated].parent = c_ion;
+
+	// initialize X ion
+	fragmentions[x_ion].nterminal = false;
+	fragmentions[x_ion].cterminal = true;
+	fragmentions[x_ion].name = "X";
+	fragmentions[x_ion].massdifference = X_ION + cterminusshift + adductshift;
+	fragmentions[x_ion].parent = x_ion;
+
+	// initialize X-H2O ion
+	fragmentions[x_ion_dehydrated].nterminal = false;
+	fragmentions[x_ion_dehydrated].cterminal = true;
+	fragmentions[x_ion_dehydrated].name = "X*";
+	fragmentions[x_ion_dehydrated].massdifference = X_ION - H2O + cterminusshift + adductshift;
+	fragmentions[x_ion_dehydrated].parent = x_ion;
+
+	// initialize X-NH3 ion
+	fragmentions[x_ion_deamidated].nterminal = false;
+	fragmentions[x_ion_deamidated].cterminal = true;
+	fragmentions[x_ion_deamidated].name = "Xx";
+	fragmentions[x_ion_deamidated].massdifference = X_ION - NH3 + cterminusshift + adductshift;
+	fragmentions[x_ion_deamidated].parent = x_ion;
+
+	// initialize X-H2O-NH3 ion
+	fragmentions[x_ion_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[x_ion_dehydrated_and_deamidated].cterminal = true;
+	fragmentions[x_ion_dehydrated_and_deamidated].name = "X*x";
+	fragmentions[x_ion_dehydrated_and_deamidated].massdifference = X_ION - H2O - NH3 + cterminusshift + adductshift;
+	fragmentions[x_ion_dehydrated_and_deamidated].parent = x_ion;
 
 	// initialize Y ion
 	fragmentions[y_ion].nterminal = false;
 	fragmentions[y_ion].cterminal = true;
 	fragmentions[y_ion].name = "Y";
-	fragmentions[y_ion].massdifference = Y_ION + cterminusshift;
+	fragmentions[y_ion].massdifference = Y_ION + cterminusshift + adductshift;
 	fragmentions[y_ion].parent = y_ion;
 
 	// initialize Y-H2O ion
-	fragmentions[y_ion_water_loss].nterminal = false;
-	fragmentions[y_ion_water_loss].cterminal = true;
-	fragmentions[y_ion_water_loss].name = "Y*";
-	fragmentions[y_ion_water_loss].massdifference = Y_ION - H2O + cterminusshift;
-	fragmentions[y_ion_water_loss].parent = y_ion;
+	fragmentions[y_ion_dehydrated].nterminal = false;
+	fragmentions[y_ion_dehydrated].cterminal = true;
+	fragmentions[y_ion_dehydrated].name = "Y*";
+	fragmentions[y_ion_dehydrated].massdifference = Y_ION - H2O + cterminusshift + adductshift;
+	fragmentions[y_ion_dehydrated].parent = y_ion;
 
 	// initialize Y-NH3 ion
-	fragmentions[y_ion_ammonia_loss].nterminal = false;
-	fragmentions[y_ion_ammonia_loss].cterminal = true;
-	fragmentions[y_ion_ammonia_loss].name = "Yx";
-	fragmentions[y_ion_ammonia_loss].massdifference = Y_ION - NH3 + cterminusshift;
-	fragmentions[y_ion_ammonia_loss].parent = y_ion;
+	fragmentions[y_ion_deamidated].nterminal = false;
+	fragmentions[y_ion_deamidated].cterminal = true;
+	fragmentions[y_ion_deamidated].name = "Yx";
+	fragmentions[y_ion_deamidated].massdifference = Y_ION - NH3 + cterminusshift + adductshift;
+	fragmentions[y_ion_deamidated].parent = y_ion;
 
 	// initialize Y-H2O-NH3 ion
-	fragmentions[y_ion_water_and_ammonia_loss].nterminal = false;
-	fragmentions[y_ion_water_and_ammonia_loss].cterminal = true;
-	fragmentions[y_ion_water_and_ammonia_loss].name = "Y*x";
-	fragmentions[y_ion_water_and_ammonia_loss].massdifference = Y_ION - H2O - NH3 + cterminusshift;
-	fragmentions[y_ion_water_and_ammonia_loss].parent = y_ion;
+	fragmentions[y_ion_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[y_ion_dehydrated_and_deamidated].cterminal = true;
+	fragmentions[y_ion_dehydrated_and_deamidated].name = "Y*x";
+	fragmentions[y_ion_dehydrated_and_deamidated].massdifference = Y_ION - H2O - NH3 + cterminusshift + adductshift;
+	fragmentions[y_ion_dehydrated_and_deamidated].parent = y_ion;
+
+	// initialize Z ion
+	fragmentions[z_ion].nterminal = false;
+	fragmentions[z_ion].cterminal = true;
+	fragmentions[z_ion].name = "Z";
+	fragmentions[z_ion].massdifference = Z_ION + cterminusshift + adductshift;
+	fragmentions[z_ion].parent = z_ion;
+
+	// initialize Z-H2O ion
+	fragmentions[z_ion_dehydrated].nterminal = false;
+	fragmentions[z_ion_dehydrated].cterminal = true;
+	fragmentions[z_ion_dehydrated].name = "Z*";
+	fragmentions[z_ion_dehydrated].massdifference = Z_ION - H2O + cterminusshift + adductshift;
+	fragmentions[z_ion_dehydrated].parent = z_ion;
+
+	// initialize Z-NH3 ion
+	fragmentions[z_ion_deamidated].nterminal = false;
+	fragmentions[z_ion_deamidated].cterminal = true;
+	fragmentions[z_ion_deamidated].name = "Zx";
+	fragmentions[z_ion_deamidated].massdifference = Z_ION - NH3 + cterminusshift + adductshift;
+	fragmentions[z_ion_deamidated].parent = z_ion;
+
+	// initialize Z-H2O-NH3 ion
+	fragmentions[z_ion_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[z_ion_dehydrated_and_deamidated].cterminal = true;
+	fragmentions[z_ion_dehydrated_and_deamidated].name = "Z*x";
+	fragmentions[z_ion_dehydrated_and_deamidated].massdifference = Z_ION - H2O - NH3 + cterminusshift + adductshift;
+	fragmentions[z_ion_dehydrated_and_deamidated].parent = z_ion;
 
 	// initialize precursor ion
 	fragmentions[precursor_ion].nterminal = false;
 	fragmentions[precursor_ion].cterminal = false;
 	fragmentions[precursor_ion].name = "[M+zH]+";
-	fragmentions[precursor_ion].massdifference = PRECURSOR_ION + nterminusshift  + cterminusshift;
+	fragmentions[precursor_ion].massdifference = PRECURSOR_ION + nterminusshift + cterminusshift + adductshift;
 	fragmentions[precursor_ion].parent = precursor_ion;
 
 	// initialize precursor ion - H2O
-	fragmentions[precursor_ion_water_loss].nterminal = false;
-	fragmentions[precursor_ion_water_loss].cterminal = false;
-	fragmentions[precursor_ion_water_loss].name = "[M+zH]+ *";
-	fragmentions[precursor_ion_water_loss].massdifference = PRECURSOR_ION - H2O + nterminusshift  + cterminusshift;
-	fragmentions[precursor_ion_water_loss].parent = precursor_ion;
+	fragmentions[precursor_ion_dehydrated].nterminal = false;
+	fragmentions[precursor_ion_dehydrated].cterminal = false;
+	fragmentions[precursor_ion_dehydrated].name = "[M+zH]+ *";
+	fragmentions[precursor_ion_dehydrated].massdifference = PRECURSOR_ION - H2O + nterminusshift + cterminusshift + adductshift;
+	fragmentions[precursor_ion_dehydrated].parent = precursor_ion;
 
 	// initialize precursor ion - NH3
-	fragmentions[precursor_ion_ammonia_loss].nterminal = false;
-	fragmentions[precursor_ion_ammonia_loss].cterminal = false;
-	fragmentions[precursor_ion_ammonia_loss].name = "[M+zH]+ x";
-	fragmentions[precursor_ion_ammonia_loss].massdifference = PRECURSOR_ION - NH3 + nterminusshift  + cterminusshift;
-	fragmentions[precursor_ion_ammonia_loss].parent = precursor_ion;
+	fragmentions[precursor_ion_deamidated].nterminal = false;
+	fragmentions[precursor_ion_deamidated].cterminal = false;
+	fragmentions[precursor_ion_deamidated].name = "[M+zH]+ x";
+	fragmentions[precursor_ion_deamidated].massdifference = PRECURSOR_ION - NH3 + nterminusshift + cterminusshift + adductshift;
+	fragmentions[precursor_ion_deamidated].parent = precursor_ion;
 
 	// initialize precursor ion - H2O - NH3
-	fragmentions[precursor_ion_water_and_ammonia_loss].nterminal = false;
-	fragmentions[precursor_ion_water_and_ammonia_loss].cterminal = false;
-	fragmentions[precursor_ion_water_and_ammonia_loss].name = "[M+zH]+ *x";
-	fragmentions[precursor_ion_water_and_ammonia_loss].massdifference = PRECURSOR_ION - H2O - NH3 + nterminusshift  + cterminusshift;
-	fragmentions[precursor_ion_water_and_ammonia_loss].parent = precursor_ion;
+	fragmentions[precursor_ion_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[precursor_ion_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[precursor_ion_dehydrated_and_deamidated].name = "[M+zH]+ *x";
+	fragmentions[precursor_ion_dehydrated_and_deamidated].massdifference = PRECURSOR_ION - H2O - NH3 + nterminusshift + cterminusshift + adductshift;
+	fragmentions[precursor_ion_dehydrated_and_deamidated].parent = precursor_ion;
 
 	// initialize precursor ion - CO
 	fragmentions[precursor_ion_co_loss].nterminal = false;
 	fragmentions[precursor_ion_co_loss].cterminal = false;
 	fragmentions[precursor_ion_co_loss].name = "[M+zH]+ -CO";
-	fragmentions[precursor_ion_co_loss].massdifference = PRECURSOR_ION - CO + nterminusshift  + cterminusshift;
+	fragmentions[precursor_ion_co_loss].massdifference = PRECURSOR_ION - CO + nterminusshift + cterminusshift + adductshift;
 	fragmentions[precursor_ion_co_loss].parent = precursor_ion;
 
 	// initialize precursor ion - CO - H2O
-	fragmentions[precursor_ion_co_loss_water_loss].nterminal = false;
-	fragmentions[precursor_ion_co_loss_water_loss].cterminal = false;
-	fragmentions[precursor_ion_co_loss_water_loss].name = "[M+zH]+ *-CO";
-	fragmentions[precursor_ion_co_loss_water_loss].massdifference = PRECURSOR_ION - CO - H2O + nterminusshift  + cterminusshift;
-	fragmentions[precursor_ion_co_loss_water_loss].parent = precursor_ion_co_loss;
+	fragmentions[precursor_ion_co_loss_and_dehydrated].nterminal = false;
+	fragmentions[precursor_ion_co_loss_and_dehydrated].cterminal = false;
+	fragmentions[precursor_ion_co_loss_and_dehydrated].name = "[M+zH]+ *-CO";
+	fragmentions[precursor_ion_co_loss_and_dehydrated].massdifference = PRECURSOR_ION - CO - H2O + nterminusshift + cterminusshift + adductshift;
+	fragmentions[precursor_ion_co_loss_and_dehydrated].parent = precursor_ion_co_loss;
 
 	// initialize precursor ion - CO - NH3
-	fragmentions[precursor_ion_co_loss_ammonia_loss].nterminal = false;
-	fragmentions[precursor_ion_co_loss_ammonia_loss].cterminal = false;
-	fragmentions[precursor_ion_co_loss_ammonia_loss].name = "[M+zH]+ x-CO";
-	fragmentions[precursor_ion_co_loss_ammonia_loss].massdifference = PRECURSOR_ION - CO - NH3 + nterminusshift  + cterminusshift;
-	fragmentions[precursor_ion_co_loss_ammonia_loss].parent = precursor_ion_co_loss;
+	fragmentions[precursor_ion_co_loss_and_deamidated].nterminal = false;
+	fragmentions[precursor_ion_co_loss_and_deamidated].cterminal = false;
+	fragmentions[precursor_ion_co_loss_and_deamidated].name = "[M+zH]+ x-CO";
+	fragmentions[precursor_ion_co_loss_and_deamidated].massdifference = PRECURSOR_ION - CO - NH3 + nterminusshift + cterminusshift + adductshift;
+	fragmentions[precursor_ion_co_loss_and_deamidated].parent = precursor_ion_co_loss;
 
 	// initialize precursor ion - CO - H2O - NH3
-	fragmentions[precursor_ion_co_loss_water_and_ammonia_loss].nterminal = false;
-	fragmentions[precursor_ion_co_loss_water_and_ammonia_loss].cterminal = false;
-	fragmentions[precursor_ion_co_loss_water_and_ammonia_loss].name = "[M+zH]+ *x-CO";
-	fragmentions[precursor_ion_co_loss_water_and_ammonia_loss].massdifference = PRECURSOR_ION - CO - H2O - NH3 + nterminusshift  + cterminusshift;
-	fragmentions[precursor_ion_co_loss_water_and_ammonia_loss].parent = precursor_ion_co_loss;
+	fragmentions[precursor_ion_co_loss_and_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[precursor_ion_co_loss_and_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[precursor_ion_co_loss_and_dehydrated_and_deamidated].name = "[M+zH]+ *x-CO";
+	fragmentions[precursor_ion_co_loss_and_dehydrated_and_deamidated].massdifference = PRECURSOR_ION - CO - H2O - NH3 + nterminusshift + cterminusshift + adductshift;
+	fragmentions[precursor_ion_co_loss_and_dehydrated_and_deamidated].parent = precursor_ion_co_loss;
 
 	// initialize cyclic precursor ion
 	fragmentions[cyclic_precursor_ion].nterminal = false;
 	fragmentions[cyclic_precursor_ion].cterminal = false;
 	fragmentions[cyclic_precursor_ion].name = "[M+zH]+";
-	fragmentions[cyclic_precursor_ion].massdifference = PRECURSOR_ION_CYCLIC;
+	fragmentions[cyclic_precursor_ion].massdifference = PRECURSOR_ION_CYCLIC + adductshift;
 	fragmentions[cyclic_precursor_ion].parent = cyclic_precursor_ion;
 
 	// initialize cyclic precursor ion - H2O
-	fragmentions[cyclic_precursor_ion_water_loss].nterminal = false;
-	fragmentions[cyclic_precursor_ion_water_loss].cterminal = false;
-	fragmentions[cyclic_precursor_ion_water_loss].name = "[M+zH]+ *";
-	fragmentions[cyclic_precursor_ion_water_loss].massdifference = PRECURSOR_ION_CYCLIC - H2O;
-	fragmentions[cyclic_precursor_ion_water_loss].parent = cyclic_precursor_ion;
+	fragmentions[cyclic_precursor_ion_dehydrated].nterminal = false;
+	fragmentions[cyclic_precursor_ion_dehydrated].cterminal = false;
+	fragmentions[cyclic_precursor_ion_dehydrated].name = "[M+zH]+ *";
+	fragmentions[cyclic_precursor_ion_dehydrated].massdifference = PRECURSOR_ION_CYCLIC - H2O + adductshift;
+	fragmentions[cyclic_precursor_ion_dehydrated].parent = cyclic_precursor_ion;
 
 	// initialize cyclic precursor ion - NH3
-	fragmentions[cyclic_precursor_ion_ammonia_loss].nterminal = false;
-	fragmentions[cyclic_precursor_ion_ammonia_loss].cterminal = false;
-	fragmentions[cyclic_precursor_ion_ammonia_loss].name = "[M+zH]+ x";
-	fragmentions[cyclic_precursor_ion_ammonia_loss].massdifference = PRECURSOR_ION_CYCLIC - NH3;
-	fragmentions[cyclic_precursor_ion_ammonia_loss].parent = cyclic_precursor_ion;
+	fragmentions[cyclic_precursor_ion_deamidated].nterminal = false;
+	fragmentions[cyclic_precursor_ion_deamidated].cterminal = false;
+	fragmentions[cyclic_precursor_ion_deamidated].name = "[M+zH]+ x";
+	fragmentions[cyclic_precursor_ion_deamidated].massdifference = PRECURSOR_ION_CYCLIC - NH3 + adductshift;
+	fragmentions[cyclic_precursor_ion_deamidated].parent = cyclic_precursor_ion;
 
 	// initialize cyclic precursor ion - H2O - NH3
-	fragmentions[cyclic_precursor_ion_water_and_ammonia_loss].nterminal = false;
-	fragmentions[cyclic_precursor_ion_water_and_ammonia_loss].cterminal = false;
-	fragmentions[cyclic_precursor_ion_water_and_ammonia_loss].name = "[M+zH]+ *x";
-	fragmentions[cyclic_precursor_ion_water_and_ammonia_loss].massdifference = PRECURSOR_ION_CYCLIC - H2O - NH3;
-	fragmentions[cyclic_precursor_ion_water_and_ammonia_loss].parent = cyclic_precursor_ion;
+	fragmentions[cyclic_precursor_ion_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[cyclic_precursor_ion_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[cyclic_precursor_ion_dehydrated_and_deamidated].name = "[M+zH]+ *x";
+	fragmentions[cyclic_precursor_ion_dehydrated_and_deamidated].massdifference = PRECURSOR_ION_CYCLIC - H2O - NH3 + adductshift;
+	fragmentions[cyclic_precursor_ion_dehydrated_and_deamidated].parent = cyclic_precursor_ion;
 
 	// initialize cyclic precursor ion - CO
 	fragmentions[cyclic_precursor_ion_co_loss].nterminal = false;
 	fragmentions[cyclic_precursor_ion_co_loss].cterminal = false;
 	fragmentions[cyclic_precursor_ion_co_loss].name = "[M+zH]+ -CO";
-	fragmentions[cyclic_precursor_ion_co_loss].massdifference = PRECURSOR_ION_CYCLIC - CO;
+	fragmentions[cyclic_precursor_ion_co_loss].massdifference = PRECURSOR_ION_CYCLIC - CO + adductshift;
 	fragmentions[cyclic_precursor_ion_co_loss].parent = cyclic_precursor_ion;
 
 	// initialize cyclic precursor ion - CO - H2O
-	fragmentions[cyclic_precursor_ion_co_loss_water_loss].nterminal = false;
-	fragmentions[cyclic_precursor_ion_co_loss_water_loss].cterminal = false;
-	fragmentions[cyclic_precursor_ion_co_loss_water_loss].name = "[M+zH]+ *-CO";
-	fragmentions[cyclic_precursor_ion_co_loss_water_loss].massdifference = PRECURSOR_ION_CYCLIC - CO - H2O;
-	fragmentions[cyclic_precursor_ion_co_loss_water_loss].parent = cyclic_precursor_ion_co_loss;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated].nterminal = false;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated].cterminal = false;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated].name = "[M+zH]+ *-CO";
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated].massdifference = PRECURSOR_ION_CYCLIC - CO - H2O + adductshift;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated].parent = cyclic_precursor_ion_co_loss;
 
 	// initialize cyclic precursor ion - CO - NH3
-	fragmentions[cyclic_precursor_ion_co_loss_ammonia_loss].nterminal = false;
-	fragmentions[cyclic_precursor_ion_co_loss_ammonia_loss].cterminal = false;
-	fragmentions[cyclic_precursor_ion_co_loss_ammonia_loss].name = "[M+zH]+ x-CO";
-	fragmentions[cyclic_precursor_ion_co_loss_ammonia_loss].massdifference = PRECURSOR_ION_CYCLIC - CO - NH3;
-	fragmentions[cyclic_precursor_ion_co_loss_ammonia_loss].parent = cyclic_precursor_ion_co_loss;
+	fragmentions[cyclic_precursor_ion_co_loss_and_deamidated].nterminal = false;
+	fragmentions[cyclic_precursor_ion_co_loss_and_deamidated].cterminal = false;
+	fragmentions[cyclic_precursor_ion_co_loss_and_deamidated].name = "[M+zH]+ x-CO";
+	fragmentions[cyclic_precursor_ion_co_loss_and_deamidated].massdifference = PRECURSOR_ION_CYCLIC - CO - NH3 + adductshift;
+	fragmentions[cyclic_precursor_ion_co_loss_and_deamidated].parent = cyclic_precursor_ion_co_loss;
 
 	// initialize cyclic precursor ion - CO - H2O - NH3
-	fragmentions[cyclic_precursor_ion_co_loss_water_and_ammonia_loss].nterminal = false;
-	fragmentions[cyclic_precursor_ion_co_loss_water_and_ammonia_loss].cterminal = false;
-	fragmentions[cyclic_precursor_ion_co_loss_water_and_ammonia_loss].name = "[M+zH]+ *x-CO";
-	fragmentions[cyclic_precursor_ion_co_loss_water_and_ammonia_loss].massdifference = PRECURSOR_ION_CYCLIC - CO - H2O - NH3;
-	fragmentions[cyclic_precursor_ion_co_loss_water_and_ammonia_loss].parent = cyclic_precursor_ion_co_loss;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated].nterminal = false;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated].cterminal = false;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated].name = "[M+zH]+ *x-CO";
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated].massdifference = PRECURSOR_ION_CYCLIC - CO - H2O - NH3 + adductshift;
+	fragmentions[cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated].parent = cyclic_precursor_ion_co_loss;
 
 	// initialize MS N-terminal ion H+
 	fragmentions[ms_nterminal_ion_hplus].nterminal = true;
@@ -554,7 +594,7 @@ void cFragmentIons::store(ofstream& os) {
 	os.write((char *)&size, sizeof(int));
 	for (map<fragmentIonType,fragmentDescription>::iterator it = fragmentions.begin(); it != fragmentions.end(); ++it) {
 		os.write((char *)&it->first, sizeof(fragmentIonType));
-		os.write((char *)&it->second, sizeof(fragmentDescription));
+		it->second.store(os);
 	}
 }
 
@@ -568,7 +608,7 @@ void cFragmentIons::load(ifstream& is) {
 	fragmentions.clear();
 	for (int i = 0; i < size; i++) {
 		is.read((char *)&iontype, sizeof(fragmentIonType));
-		is.read((char *)&description, sizeof(fragmentDescription));
+		description.load(is);
 		fragmentions[iontype] = description;
 	}
 }
@@ -605,3 +645,130 @@ void initializeFragmentIonsForDeNovoGraphOfLinearPolysaccharide(vector<fragmentI
 	fragmentions.push_back(precursor_ion);
 }
 
+
+int loadModificationsFromPlainTextStream(ifstream &stream, vector<fragmentDescription>& modifications, string& errormessage, bool ignoreerrors) {
+	string s;
+	fragmentDescription modification;
+	size_t pos;
+	double mass;
+
+	bool error = false;
+	errormessage = "";
+	cSummaryFormula formula;
+	
+	modifications.clear();
+	while (stream.good()) {
+		getline(stream,s);
+
+		// skip a comment
+		if ((s.length() > 0) && (s[0] == '#')) {
+			continue;
+		}
+
+		// replaces commas with dots
+		pos = s.find(',');
+		while (pos != string::npos) {
+			s.replace(pos, 1, ".");
+			pos = s.find(',');
+		}
+
+		modification.clear();
+
+		// load the name
+		pos = s.find('\t');
+		if (pos != string::npos) {
+			modification.name = s.substr(0, pos);
+			s = s.substr(pos + 1);
+		}
+		else {
+			break;
+		}
+
+		// load summary
+		pos = s.find('\t');
+		if (pos != string::npos) {
+			modification.summary = s.substr(0, pos);
+			s = s.substr(pos + 1);
+		}
+		else {
+			break;
+		}
+
+		// load the mass (unused !)
+		pos = s.find('\t');
+		if (pos != string::npos) {
+			sscanf_s(s.substr(0, pos).c_str(), "%lf", &mass);
+			s = s.substr(pos + 1);
+		}
+		else {
+			break;
+		}
+
+
+		// load N-terminal flag
+		pos = s.find('\t');
+		if (pos != string::npos) {
+			modification.nterminal = (s.substr(0, pos).compare("0") == 0)?false:true;
+			s = s.substr(pos + 1);
+		}
+		else {
+			break;
+		}
+
+
+		// load C-terminal flag
+		#if OS_TYPE == UNX
+			if ((s.size() > 0) && (s.back() == '\r')) {
+				s = s.substr(0, s.size() - 1);
+			}
+		#endif
+		modification.cterminal = (s.compare("0") == 0)?false:true;
+
+
+		// calculate mass from the summary
+		formula.clear();
+		formula.setFormula(modification.summary);
+		if (formula.isValid(errormessage)) {
+			modification.massdifference = formula.getMass();
+		}
+		else {
+			if (!ignoreerrors) {
+				error = true;
+				break;
+			}
+		}
+
+		modifications.push_back(modification);
+
+	}
+
+	if (!ignoreerrors && error) {
+		return -1;
+	}
+
+	return 0;
+}
+
+
+void storeModificationsToPlainTextStream(ofstream &stream, vector<fragmentDescription>& modifications) {
+	for (int i = 0; i < (int)modifications.size(); i++) {
+		stream << removeWhiteSpacesExceptSpaces(modifications[i].name) << "\t";
+		stream << removeWhiteSpacesExceptSpaces(modifications[i].summary) << "\t";
+		stream << std::fixed << std::setprecision(10) << modifications[i].massdifference << "\t";
+
+		if (modifications[i].nterminal) {
+			stream << 1 << "\t";
+		}
+		else {
+			stream << 0 << "\t";
+		}
+
+		if (modifications[i].cterminal) {
+			stream << 1 << endl;
+		}
+		else {
+			stream << 0 << endl;
+		}
+	}
+}
+
diff --git a/CycloBranch/core/cFragmentIons.h b/CycloBranch/core/cFragmentIons.h
index 66cda9b..aab7545 100644
--- a/CycloBranch/core/cFragmentIons.h
+++ b/CycloBranch/core/cFragmentIons.h
@@ -9,8 +9,8 @@
 
 #include <string>
 #include <iostream>
+#include <iomanip>
 #include <fstream>
-#include <regex>
 #include <map>
 #include <vector>
 #include <QMetaType>
@@ -108,35 +108,6 @@ const double PRECURSOR_ION = Hplus + H2O;
 const double PRECURSOR_ION_CYCLIC = Hplus;
 
 
-/**
-	\brief The types of peptides supported by the application.
-*/
-enum peptideType {
-	linear = 0,
-	cyclic = 1,
-	branched = 2,
-	lasso = 3,
-	linearpolysaccharide = 4,
-	other = 5
-};
-
-
-/**
-	\brief Convert a string to peptide type.
-	\param s string
-	\retval peptideType type of peptide
-*/
-peptideType getPeptideTypeFromString(string s);
-
-
-/**
-	\brief Convert the peptide type to a string.
-	\param peptidetype type of peptide
-	\retval string string
-*/
-string getStringFromPeptideType(peptideType peptidetype);
-
-
 /**
 	\brief Register peptideType by Qt.
 */
@@ -144,78 +115,90 @@ Q_DECLARE_METATYPE(peptideType);
 
 
 /**
-	\brief Convert single charged mz ratio to multiple charged mz ratio.
-	\param mass single charged mz ratio
-	\param charge new charge
-	\retval double multiple charged mzratio
+	\brief Get mzratio from neutral mass.
+	\param neutralmass neutral mass
+	\param charge charge
+	\retval double mzratio
 */ 
-double charge(double mass, int charge);
+double charge(double neutralmass, int charge);
 
 
 /**
-	\brief Convert multiple charged mz ratio to single charged mz ratio.
-	\param mass multiple charged mz ratio
-	\param charge old charge
-	\retval double single charged mzratio
+	\brief Get neutral mass from mzratio.
+	\param mzratio mzratio
+	\param charge charge
+	\retval double neutral mass
 */ 
-double uncharge(double mass, int charge);
+double uncharge(double mzratio, int charge);
 
 
 /**
 	\brief The types of supported fragment ions.
 */
 enum fragmentIonType {
-	b_ion = 0,
-	b_ion_water_loss = 1,
-	b_ion_ammonia_loss = 2,
-	b_ion_water_and_ammonia_loss = 3,
-	a_ion = 4,
-	a_ion_water_loss = 5,
-	a_ion_ammonia_loss = 6,
-	a_ion_water_and_ammonia_loss = 7,
-	y_ion = 8,
-	y_ion_water_loss = 9,
-	y_ion_ammonia_loss = 10,
-	y_ion_water_and_ammonia_loss = 11,
-	precursor_ion = 12,
-	precursor_ion_water_loss = 13,
-	precursor_ion_ammonia_loss = 14,
-	precursor_ion_water_and_ammonia_loss = 15,
-	precursor_ion_co_loss = 16,
-	precursor_ion_co_loss_water_loss = 17,
-	precursor_ion_co_loss_ammonia_loss = 18,
-	precursor_ion_co_loss_water_and_ammonia_loss = 19,
-	cyclic_precursor_ion = 20,
-	cyclic_precursor_ion_water_loss = 21,
-	cyclic_precursor_ion_ammonia_loss = 22,
-	cyclic_precursor_ion_water_and_ammonia_loss = 23,
-	cyclic_precursor_ion_co_loss = 24,
-	cyclic_precursor_ion_co_loss_water_loss = 25,
-	cyclic_precursor_ion_co_loss_ammonia_loss = 26,
-	cyclic_precursor_ion_co_loss_water_and_ammonia_loss = 27,
-	ms_nterminal_ion_hplus = 28,
-	ms_nterminal_ion_naplus = 29,
-	ms_nterminal_ion_kplus = 30,
-	ms_cterminal_ion_hplus = 31,
-	ms_cterminal_ion_naplus = 32,
-	ms_cterminal_ion_kplus = 33,
-	ms_hplus = 34,
-	ms_naplus = 35,
-	ms_kplus = 36,
-	ms_hminus = 37,
-	ms_3M2Fe5H = 38,
-	ms_2MFe2H = 39,
-	ms_3MFe2H = 40,
-	ms_MFe2H = 41,
-	ms_3M2Fe6HNa = 42,
-	ms_2MFe3HNa = 43,
-	ms_3MFe3HNa = 44,
-	ms_MFe3HNa = 45,
-	ms_3M2Fe7H = 46,
-	ms_2MFe4H = 47,
-	ms_3MFe4H = 48,
-	ms_MFe4H = 49,
-	//b_ion_2H_loss = 34,
+	a_ion = 1,
+	a_ion_dehydrated = 2,
+	a_ion_deamidated = 3,
+	a_ion_dehydrated_and_deamidated = 4,
+	b_ion = 5,
+	b_ion_dehydrated = 6,
+	b_ion_deamidated = 7,
+	b_ion_dehydrated_and_deamidated = 8,
+	c_ion = 9,
+	c_ion_dehydrated = 10,
+	c_ion_deamidated = 11,
+	c_ion_dehydrated_and_deamidated = 12,
+	x_ion = 13,
+	x_ion_dehydrated = 14,
+	x_ion_deamidated = 15,
+	x_ion_dehydrated_and_deamidated = 16,
+	y_ion = 17,
+	y_ion_dehydrated = 18,
+	y_ion_deamidated = 19,
+	y_ion_dehydrated_and_deamidated = 20,
+	z_ion = 21,
+	z_ion_dehydrated = 22,
+	z_ion_deamidated = 23,
+	z_ion_dehydrated_and_deamidated = 24,
+	precursor_ion = 25,
+	precursor_ion_dehydrated = 26,
+	precursor_ion_deamidated = 27,
+	precursor_ion_dehydrated_and_deamidated = 28,
+	precursor_ion_co_loss = 29,
+	precursor_ion_co_loss_and_dehydrated = 30,
+	precursor_ion_co_loss_and_deamidated = 31,
+	precursor_ion_co_loss_and_dehydrated_and_deamidated = 32,
+	cyclic_precursor_ion = 33,
+	cyclic_precursor_ion_dehydrated = 34,
+	cyclic_precursor_ion_deamidated = 35,
+	cyclic_precursor_ion_dehydrated_and_deamidated = 36,
+	cyclic_precursor_ion_co_loss = 37,
+	cyclic_precursor_ion_co_loss_and_dehydrated = 38,
+	cyclic_precursor_ion_co_loss_and_deamidated = 39,
+	cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated = 40,
+	ms_nterminal_ion_hplus = 41,
+	ms_nterminal_ion_naplus = 42,
+	ms_nterminal_ion_kplus = 43,
+	ms_cterminal_ion_hplus = 44,
+	ms_cterminal_ion_naplus = 45,
+	ms_cterminal_ion_kplus = 46,
+	ms_hplus = 47,
+	ms_naplus = 48,
+	ms_kplus = 49,
+	ms_hminus = 50,
+	ms_3M2Fe5H = 51,
+	ms_2MFe2H = 52,
+	ms_3MFe2H = 53,
+	ms_MFe2H = 54,
+	ms_3M2Fe6HNa = 55,
+	ms_2MFe3HNa = 56,
+	ms_3MFe3HNa = 57,
+	ms_MFe3HNa = 58,
+	ms_3M2Fe7H = 59,
+	ms_2MFe4H = 60,
+	ms_3MFe4H = 61,
+	ms_MFe4H = 62,
+	//b_ion_2H_loss = 63,
 	fragmentIonTypeEnd
 };
 
@@ -283,6 +266,14 @@ struct fragmentDescription {
 		\brief The default constructor.
 	*/ 
 	fragmentDescription() {
+		clear();
+	}
+
+
+	/**
+		\brief Clear the structure.
+	*/ 
+	void clear() {
 		name = "";
 		summary = "";
 		massdifference = 0;
@@ -359,8 +350,9 @@ class cFragmentIons {
 		\brief The constructor.
 		\param cyclicnterminus true when the N-terminus of a linear peptide is cyclized
 		\param cycliccterminus true when the C-terminus of a linear peptide is cyclized
+		\param precursoradduct an adduct of a precursor ion
 	*/ 
-	cFragmentIons(bool cyclicnterminus, bool cycliccterminus);
+	cFragmentIons(bool cyclicnterminus, bool cycliccterminus, string& precursoradduct);
 
 
 	/**
@@ -375,8 +367,9 @@ class cFragmentIons {
 		\brief Recalculate all fragment ion types.
 		\param cyclicnterminus true when the N-terminus of a linear peptide is cyclized
 		\param cycliccterminus true when the C-terminus of a linear peptide is cyclized
+		\param precursoradduct an adduct of a precursor ion
 	*/ 
-	void recalculateFragments(bool cyclicnterminus, bool cycliccterminus);
+	void recalculateFragments(bool cyclicnterminus, bool cycliccterminus, string& precursoradduct);
 
 
 	/**
@@ -423,7 +416,7 @@ void initializeFragmentIonsForDeNovoGraphOfTPeptides(vector<fragmentIonType>& fr
 
 
 /**
-	\brief Initialize fragment ion types for the de novo graph of lasso peptides.
+	\brief Initialize fragment ion types for the de novo graph of branch-cyclic peptides.
 	\param fragmentions reference to a vector of fragment ion types
 */ 
 void initializeFragmentIonsForDeNovoGraphOfLassoPeptides(vector<fragmentIonType>& fragmentions);
@@ -436,4 +429,24 @@ void initializeFragmentIonsForDeNovoGraphOfLassoPeptides(vector<fragmentIonType>
 void initializeFragmentIonsForDeNovoGraphOfLinearPolysaccharide(vector<fragmentIonType>& fragmentions);
 
 
-#endif
\ No newline at end of file
+/**
+	\brief Load modifications from a plain text stream.
+	\param stream reference to an input file stream
+	\param modifications reference to a vector where modifications will be placed
+	\param errormessage reference to a string where an error message might be stored
+	\param ignoreerrors if true errors are ignored
+	\retval int 0 when modifications were successfully loaded, -1 when an error occurred (\a errormessage is filled up)
+*/ 
+int loadModificationsFromPlainTextStream(ifstream &stream, vector<fragmentDescription>& modifications, string& errormessage, bool ignoreerrors);
+
+
+/**
+	\brief Store modifications into a plain text stream.
+	\param stream reference to an output file stream
+	\param modifications reference to a vector of modifications which will be stored
+*/ 
+void storeModificationsToPlainTextStream(ofstream &stream, vector<fragmentDescription>& modifications);
+
+
+#endif
+
diff --git a/CycloBranch/core/cParameters.cpp b/CycloBranch/core/cParameters.cpp
index a6ee67f..40c8b26 100644
--- a/CycloBranch/core/cParameters.cpp
+++ b/CycloBranch/core/cParameters.cpp
@@ -9,12 +9,14 @@ cParameters::cParameters() {
 
 
 void cParameters::clear() {
+	string s = "";
 	os = 0;
-	fragmentdefinitions.recalculateFragments(false, false);
+	fragmentdefinitions.recalculateFragments(false, false, s);
 	peptidetype = linear;
 	peaklistfilename = "";
 	peaklist.clear();
 	precursormass = 0;
+	precursoradduct = "";
 	precursormasserrortolerance = 5;
 	precursorcharge = 1;
 	fragmentmasserrortolerance = 5;
@@ -29,6 +31,8 @@ void cParameters::clear() {
 	maximumbricksincombination = max(max(maximumbricksincombinationbegin, maximumbricksincombinationmiddle), maximumbricksincombinationend);
 	maximumcumulativemass = 0;
 	generatebrickspermutations = true;
+	modificationsfilename = "";
+	searchedmodifications.clear();
 	maximumnumberofthreads = 1;
 	mode = denovoengine;
 	scoretype = b_ions;
@@ -49,9 +53,6 @@ void cParameters::clear() {
 	sequencedatabase.clear();
 	sequencedatabasefilename = "";
 
-	searchedmodifications.clear();
-	searchedmodifications.push_back(fragmentDescription("", 0, "", true, true));
-
 	fragmentionsfordenovograph.clear();
 	fragmentionsfortheoreticalspectra.clear();
 }
@@ -63,11 +64,17 @@ int cParameters::checkAndPrepare() {
 	string errormessage = "";
 	ifstream peakliststream;
 	ifstream bricksdatabasestream;
+	ifstream modificationsstream;
 	ifstream sequencedatabasestream;
 	regex rx;
 	ePeakListFileFormat peaklistfileformat;
 	string s;
+	int i;
 
+	if (peaklistfilename.empty()) {
+		error = true;
+		errormessage = "A peaklist is not specified. Have you configured the engine (Search -> Settings...) ?\n";
+	}
 
 	// peaklist check
 	if (!error) {
@@ -94,14 +101,16 @@ int cParameters::checkAndPrepare() {
 				peaklistfileformat = mzXML;
 			}
 			
-			rx = "\\.[bB][aA][fF]$";
-			// Bruker Analysis File
-			if (regex_search(peaklistfilename, rx)) {
-				peaklistfileformat = baf;
-			}
+			#if OS_TYPE == WIN
+				rx = "\\.[bB][aA][fF]$";
+				// Bruker Analysis File
+				if (regex_search(peaklistfilename, rx)) {
+					peaklistfileformat = baf;
+				}
+			#endif
 
 		}
-		catch (std::regex_error& e) {
+		catch (regex_error& e) {
 			error = true;
 			errormessage = "cParameters::checkAndPrepare: regex_search failed, error no. " + to_string((int)e.code()) + "\n";
 		}
@@ -118,17 +127,31 @@ int cParameters::checkAndPrepare() {
 				break;
 			case mzML:
 			case mzXML:
-				*os << "Converting the file " + peaklistfilename + " to .mgf ... ";
-				s = "External\\any2mgf.bat \"" + peaklistfilename + "\"";
-				if (system(s.c_str()) != 0) {
-					error = true;
-					errormessage = "The file cannot be converted.\n";
-					errormessage += "Does the file '" + peaklistfilename + "' exist ?\n";
-					errormessage += "Do you have OpenMS installed ?\n";
-					errormessage += "Do you have path to the OpenMS/bin/FileConverter.exe in your PATH variable ?\n";
-					errormessage += "Is the directory with the file '" + peaklistfilename + "' writable ?\n";
-					errormessage += "Do you have 'any2mgf.bat' file located in the 'External' folder ?\n";
-				}
+				*os << "Converting the file " + peaklistfilename + " to mgf ... ";
+				
+				#if OS_TYPE == UNX
+					s = linuxinstalldir.toStdString() + "External/linux/any2mgf.sh " + peaklistfilename;
+					if (system(s.c_str()) != 0) {
+						error = true;
+						errormessage = "The file cannot be converted.\n";
+						errormessage += "Does the file '" + peaklistfilename + "' exist ?\n";
+						errormessage += "Is the directory with the file '" + peaklistfilename + "' writable ?\n";
+						errormessage += "Do you have FileConverter installed (sudo apt-get install topp) ?\n";
+						errormessage += "Do you have 'any2mgf.sh' file located in '" + linuxinstalldir.toStdString() + "External/linux' folder ?\n";
+						errormessage += "Is the file 'any2mgf.sh' executable (sudo chmod +x " + linuxinstalldir.toStdString() + "External/linux/any2mgf.sh) ? \n";
+					}
+				#else
+					s = "External\\windows\\any2mgf.bat \"" + peaklistfilename + "\"";
+					if (system(s.c_str()) != 0) {
+						error = true;
+						errormessage = "The file cannot be converted.\n";
+						errormessage += "Does the file '" + peaklistfilename + "' exist ?\n";
+						errormessage += "Is the directory with the file '" + peaklistfilename + "' writable ?\n";
+						errormessage += "Do you have FileConverter installed (OpenMS 1.11) ?\n";
+						errormessage += "Do you have a path to FileConverter in your PATH variable (e.g., 'C:/Program Files/OpenMS-1.11/bin') ?\n";
+						errormessage += "Do you have 'any2mgf.bat' file located in the '" + appname.toStdString() + "/External/windows' folder ?\n";
+					}
+				#endif
 
 				if (!error) {
 					*os << "ok" << endl << endl;
@@ -136,22 +159,24 @@ int cParameters::checkAndPrepare() {
 				}
 				break;
 			case baf:
-				*os << "Converting the file " + peaklistfilename + " ... ";
-				s = "External\\baf2csv.bat \"" + peaklistfilename + "\"";
-				if (system(s.c_str()) != 0) {
-					error = true;
-					errormessage = "The file cannot be converted.\n";
-					errormessage += "Does the file '" + peaklistfilename + "' exist ?\n";
-					errormessage += "Do you have Bruker Daltonik's CompassXport installed ?\n";
-					errormessage += "Do you have path to the CompassXport.exe in your PATH variable ?\n";
-					errormessage += "Is the directory with the file '" + peaklistfilename + "' writable ?\n";
-					errormessage += "Do you have 'baf2csv.bat' file located in the 'External' folder ?\n";
-				}
+				#if OS_TYPE == WIN
+					*os << "Converting the file " + peaklistfilename + " ... ";
+					s = "External\\windows\\baf2csv.bat \"" + peaklistfilename + "\"";
+					if (system(s.c_str()) != 0) {
+						error = true;
+						errormessage = "The file cannot be converted.\n";
+						errormessage += "Does the file '" + peaklistfilename + "' exist ?\n";
+						errormessage += "Do you have Bruker Daltonik's CompassXport installed ?\n";
+						errormessage += "Do you have path to the CompassXport.exe in your PATH variable ?\n";
+						errormessage += "Is the directory with the file '" + peaklistfilename + "' writable ?\n";
+						errormessage += "Do you have 'baf2csv.bat' file located in the 'External/windows' folder ?\n";
+					}
 
-				if (!error) {
-					*os << "ok" << endl << endl;
-					peakliststream.open(peaklistfilename + ".csv");
-				}
+					if (!error) {
+						*os << "ok" << endl << endl;
+						peakliststream.open(peaklistfilename + ".csv");
+					}
+				#endif
 				break;
 			default:
 				break;
@@ -179,7 +204,9 @@ int cParameters::checkAndPrepare() {
 					peaklist.loadFromMGFStream(peakliststream);
 					break;
 				case baf:
-					peaklist.loadFromBAFStream(peakliststream);
+					#if OS_TYPE == WIN
+						peaklist.loadFromBAFStream(peakliststream);
+					#endif
 					break;
 				default:
 					break;
@@ -206,7 +233,7 @@ int cParameters::checkAndPrepare() {
 			if (os) {
 				*os << "Loading the database of bricks... ";
 			}
-			if (bricksdatabase.loadFromPlainTextStream(bricksdatabasestream, errormessage) == -1) {
+			if (bricksdatabase.loadFromPlainTextStream(bricksdatabasestream, errormessage, false) == -1) {
 				error = true;
 			}
 			else {
@@ -245,6 +272,53 @@ int cParameters::checkAndPrepare() {
 	}
 
 
+	// modifications check
+	if (!error && ((mode == denovoengine) || (mode == singlecomparison) || (mode == databasesearch))) {
+
+		searchedmodifications.clear();
+
+		if ((peptidetype != cyclic) && (modificationsfilename.compare("") != 0)) {
+			modificationsstream.open(modificationsfilename);
+			if (!modificationsstream.good()) {
+				error = true;
+				errormessage = "Cannot open the file '" + modificationsfilename + "'.";
+			}
+			else {
+				if (os) {
+					*os << "Loading modifications... ";
+				}
+				if (loadModificationsFromPlainTextStream(modificationsstream, searchedmodifications, errormessage, false) == -1) {
+					error = true;
+				}
+				else {
+					if (os) {
+						*os << "ok" << endl << endl;
+					}
+				}
+			}
+			modificationsstream.close();
+		}
+
+		fragmentDescription fd;
+		fd.nterminal = true;
+		fd.cterminal = true;
+		searchedmodifications.insert(searchedmodifications.begin(), fd);
+
+	}
+
+
+	// precursor adduct check
+	if (!error && ((mode == denovoengine) || (mode == singlecomparison) || (mode == databasesearch))) {
+		cSummaryFormula formula;
+		formula.clear();
+		formula.setFormula(precursoradduct);
+		if (!formula.isValid(errormessage)) {
+			error = true;
+			errormessage = "Precursor Ion Adduct: " + errormessage;
+		}
+	}
+
+
 	// sequencedatabase check
 	if (!error && ((mode == databasesearch) || (mode == dereplication))) {
 
@@ -298,6 +372,20 @@ int cParameters::checkAndPrepare() {
 		}
 	}
 
+
+	// check theoretical fragments in positive/negative mode
+	if (!error && (mode == dereplication)) {
+		i = 0;
+		while (i < (int)fragmentionsfortheoreticalspectra.size()) {
+			if (fragmentdefinitions[fragmentionsfortheoreticalspectra[i]].positive != (precursorcharge > 0)) {
+				fragmentionsfortheoreticalspectra.erase(fragmentionsfortheoreticalspectra.begin() + i);
+			}
+			else {
+				i++;
+			}
+		}
+	}
+
 	
 	// report errors and return
 	if (error) {
@@ -329,7 +417,7 @@ string cParameters::printToString() {
 		s += "Branched\n";
 		break;
 	case lasso:
-		s += "Lasso\n";
+		s += "Branch-cyclic\n";
 		break;
 	case linearpolysaccharide:
 		s += "Linear polysaccharide (beta version)\n";
@@ -342,7 +430,8 @@ string cParameters::printToString() {
 	}
 	s += "Peaklist File: " + peaklistfilename + "\n";
 	s += "Precursor Mass: " + to_string(precursormass) + "\n";
-	s += "Precursor Charge: " + to_string(precursorcharge) + "\n";
+	s += "Precursor Ion Adduct: " + precursoradduct + "\n";
+	s += "Charge: " + to_string(precursorcharge) + "\n";
 	s += "Precursor Mass Error Tolerance: " + to_string(precursormasserrortolerance) + "\n";
 	s += "Fragment Mass Error Tolerance: " + to_string(fragmentmasserrortolerance) + "\n";
 	s += "Fragment Mass Error Tolerance for Deisotoping: " + to_string(masserrortolerancefordeisotoping) + "\n";
@@ -356,13 +445,35 @@ string cParameters::printToString() {
 	s += generatebrickspermutations ? "on" : "off";
 	s += "\n";
 
-	s += "N-terminal and C-terminal Modifications:\n";
-	for (int i = 1; i < (int)searchedmodifications.size(); i++) {
-		s += searchedmodifications[i].name + ", " + to_string(searchedmodifications[i].massdifference) + ", ";
-		s += searchedmodifications[i].nterminal ? "N-terminal, " : "-, ";
-		s += searchedmodifications[i].cterminal ? "C-terminal" : "-";
-		s += "\n";
+	s += "N-/C-terminal Modifications File: " + modificationsfilename + "\n";
+
+	s += "Action with Blind Paths in De Novo Graph: ";
+	switch (blindedges) {
+	case 0:
+		s += "none (you can see a complete de novo graph)";
+		break;
+	case 1:
+		s += "remove (speed up the search)";
+		break;
+	case 2:
+		s += "connect (allow detection of sequence tags)";
+		break;
+	default:
+		break;
 	}
+	s += "\n";
+
+	s += "Cyclic N-terminus: ";
+	s += cyclicnterminus ? "on" : "off";
+	s += "\n";
+
+	s += "Cyclic C-terminus: ";
+	s += cycliccterminus ? "on" : "off";
+	s += "\n";
+
+	s += "Enable Scrambling: ";
+	s += enablescrambling ? "on" : "off";
+	s += "\n";
 
 	s += "Mode: ";
 	switch ((modeType)mode) {
@@ -383,6 +494,8 @@ string cParameters::printToString() {
 	}
 	s += "\n";
 
+	s += "Sequence Database File: " + sequencedatabasefilename + "\n";
+
 	s += "Maximum Number of Threads: " + to_string(maximumnumberofthreads) + "\n";
 
 	s += "Score Type: ";
@@ -390,10 +503,10 @@ string cParameters::printToString() {
 	case b_ions:
 		s += "Number of b-ions";
 		break;
-	case b_ions_and_b_water_loss_ions:
+	case b_ions_and_b_dehydrated_ions:
 		s += "Number of b-ions + dehydrated b-ions";
 		break;
-	case b_ions_and_b_ammonia_loss_ions:
+	case b_ions_and_b_deamidated_ions:
 		s += "Number of b-ions + deamidated b-ions";
 		break;
 	case y_ions_and_b_ions:
@@ -433,36 +546,6 @@ string cParameters::printToString() {
 	s += clearhitswithoutparent ? "on" : "off";
 	s += "\n";
 
-	s += "Cyclic N-terminus: ";
-	s += cyclicnterminus ? "on" : "off";
-	s += "\n";
-
-	s += "Cyclic C-terminus: ";
-	s += cycliccterminus ? "on" : "off";
-	s += "\n";
-
-	s += "Enable Scrambling: ";
-	s += enablescrambling ? "on" : "off";
-	s += "\n";
-
-	s += "Action with Edges Forming Blind Paths: ";
-	switch (blindedges) {
-	case 0:
-		s += "none (you can see a complete de novo graph)";
-		break;
-	case 1:
-		s += "remove (speed up the search)";
-		break;
-	case 2:
-		s += "connect (allow detection of sequence tags)";
-		break;
-	default:
-		break;
-	}
-	s += "\n";
-
-	s += "Sequence Database File: " + sequencedatabasefilename + "\n";
-
 	s += "Searched Peptide Sequence: " + originalsearchedsequence + "\n";
 	s += "N-terminal Modification of Searched Peptide Sequence: " + searchedsequenceNtermmodif + "\n";
 	s += "C-terminal Modification of Searched Peptide Sequence: " + searchedsequenceCtermmodif + "\n";
@@ -481,10 +564,10 @@ void cParameters::setOutputStream(cMainThread& os) {
 
 void cParameters::updateFragmentDefinitions() {
 	if (peptidetype == linear) {
-		fragmentdefinitions.recalculateFragments(cyclicnterminus, cycliccterminus);
+		fragmentdefinitions.recalculateFragments(cyclicnterminus, cycliccterminus, precursoradduct);
 	}
 	else {
-		fragmentdefinitions.recalculateFragments(false, false);
+		fragmentdefinitions.recalculateFragments(false, false, precursoradduct);
 	}
 }
 
@@ -500,6 +583,9 @@ void cParameters::store(ofstream& os) {
 	peaklist.store(os);
 
 	os.write((char *)&precursormass, sizeof(double));
+
+	storeString(precursoradduct, os);
+
 	os.write((char *)&precursormasserrortolerance, sizeof(double));
 	os.write((char *)&precursorcharge, sizeof(int));
 	os.write((char *)&fragmentmasserrortolerance, sizeof(double));
@@ -516,6 +602,14 @@ void cParameters::store(ofstream& os) {
 	os.write((char *)&maximumbricksincombination, sizeof(int));
 	os.write((char *)&maximumcumulativemass, sizeof(double));
 	os.write((char *)&generatebrickspermutations, sizeof(bool));
+	storeString(modificationsfilename, os);
+
+	size = (int)searchedmodifications.size();
+	os.write((char *)&size, sizeof(int));
+	for (int i = 0; i < (int)searchedmodifications.size(); i++) {
+		searchedmodifications[i].store(os);
+	}
+
 	os.write((char *)&maximumnumberofthreads, sizeof(int));
 	os.write((char *)&mode, sizeof(modeType));
 	os.write((char *)&scoretype, sizeof(scoreType));
@@ -539,12 +633,6 @@ void cParameters::store(ofstream& os) {
 	storeString(sequencedatabasefilename, os);
 	sequencedatabase.store(os);
 
-	size = (int)searchedmodifications.size();
-	os.write((char *)&size, sizeof(int));
-	for (int i = 0; i < (int)searchedmodifications.size(); i++) {
-		searchedmodifications[i].store(os);
-	}
-
 	size = (int)fragmentionsfordenovograph.size();
 	os.write((char *)&size, sizeof(int));
 	for (int i = 0; i < (int)fragmentionsfordenovograph.size(); i++) {
@@ -572,6 +660,9 @@ void cParameters::load(ifstream& is) {
 	peaklist.load(is);
 
 	is.read((char *)&precursormass, sizeof(double));
+
+	loadString(precursoradduct, is);
+
 	is.read((char *)&precursormasserrortolerance, sizeof(double));
 	is.read((char *)&precursorcharge, sizeof(int));
 	is.read((char *)&fragmentmasserrortolerance, sizeof(double));
@@ -588,6 +679,14 @@ void cParameters::load(ifstream& is) {
 	is.read((char *)&maximumbricksincombination, sizeof(int));
 	is.read((char *)&maximumcumulativemass, sizeof(double));
 	is.read((char *)&generatebrickspermutations, sizeof(bool));
+	loadString(modificationsfilename, is);
+
+	is.read((char *)&size, sizeof(int));
+	searchedmodifications.resize(size);
+	for (int i = 0; i < (int)searchedmodifications.size(); i++) {
+		searchedmodifications[i].load(is);
+	}
+
 	is.read((char *)&maximumnumberofthreads, sizeof(int));
 	is.read((char *)&mode, sizeof(modeType));
 	is.read((char *)&scoretype, sizeof(scoreType));
@@ -611,12 +710,6 @@ void cParameters::load(ifstream& is) {
 	loadString(sequencedatabasefilename, is);
 	sequencedatabase.load(is);
 
-	is.read((char *)&size, sizeof(int));
-	searchedmodifications.resize(size);
-	for (int i = 0; i < (int)searchedmodifications.size(); i++) {
-		searchedmodifications[i].load(is);
-	}
-
 	is.read((char *)&size, sizeof(int));
 	fragmentionsfordenovograph.resize(size);
 	for (int i = 0; i < (int)fragmentionsfordenovograph.size(); i++) {
diff --git a/CycloBranch/core/cParameters.h b/CycloBranch/core/cParameters.h
index 119a10d..923b1d1 100644
--- a/CycloBranch/core/cParameters.h
+++ b/CycloBranch/core/cParameters.h
@@ -9,6 +9,7 @@
 
 #include <iostream>
 #include <fstream>
+#include "core/utilities.h"
 #include "core/cPeaksList.h"
 #include "core/cBricksDatabase.h"
 #include "core/cSequenceDatabase.h"
@@ -16,6 +17,7 @@
 class cMainThread;
 
 using namespace std;
+using namespace boost;
 
 
 /**
@@ -81,6 +83,12 @@ class cParameters {
     double precursormass;
 
 
+	/**
+		\brief An adduct of a precursor ion.
+    */
+    string precursoradduct;
+
+
 	/**
 		\brief Precursor mass error tolerance (ppm).
     */
@@ -165,6 +173,12 @@ class cParameters {
     bool generatebrickspermutations;
 
 
+	/**
+		\brief A file with modifications.
+    */
+    string modificationsfilename;
+
+
 	/**
 		\brief Maximum number of threads.
     */
@@ -331,7 +345,7 @@ class cParameters {
 
 
 	/**
-		\brief Update definitions of fragment ions when \a cyclicnterminus or \a cycliccterminus have been changed.
+		\brief Update definitions of fragment ions when \a cyclicnterminus, \a cycliccterminus or \a precursoradduct have been changed.
 	*/ 
 	void updateFragmentDefinitions();
 
diff --git a/CycloBranch/core/cPeak.h b/CycloBranch/core/cPeak.h
index 478e33c..cf38944 100644
--- a/CycloBranch/core/cPeak.h
+++ b/CycloBranch/core/cPeak.h
@@ -20,8 +20,8 @@ using namespace std;
 */
 enum scoreType {
 	b_ions = 0,
-	b_ions_and_b_water_loss_ions = 1,
-	b_ions_and_b_ammonia_loss_ions = 2,
+	b_ions_and_b_dehydrated_ions = 1,
+	b_ions_and_b_deamidated_ions = 2,
 	y_ions_and_b_ions = 3,
 	y_ions = 4,
 	weighted_intensity = 5,
diff --git a/CycloBranch/core/cPeaksList.cpp b/CycloBranch/core/cPeaksList.cpp
index 55431ef..bef1b46 100644
--- a/CycloBranch/core/cPeaksList.cpp
+++ b/CycloBranch/core/cPeaksList.cpp
@@ -2,16 +2,21 @@
 #include "gui/cMainThread.h"
 
 
-bool comparePeakMasses(cPeak& a, cPeak& b) {
+bool comparePeakMasses(const cPeak& a, const cPeak& b) {
 	return (a.mzratio < b.mzratio);
 }
 
 
-bool comparePeakIntensitiesDesc(cPeak& a, cPeak& b) {
+bool comparePeakIntensitiesDesc(const cPeak& a, const cPeak& b) {
 	return (a.intensity > b.intensity);
 }
 
 
+bool comparePeakRemoveMeFlag(const cPeak& a, const cPeak& b) {
+	return (a.removeme < b.removeme);
+}
+
+
 bool isInPpmMassErrorTolerance(double experimentalmass, double theoreticalmass, double tolerance) {
 	double errortolerance = experimentalmass*tolerance*0.000001f;
 	return abs(experimentalmass - theoreticalmass) <= errortolerance;
@@ -28,6 +33,17 @@ cPeaksList::cPeaksList() {
 }
 
 
+cPeaksList::cPeaksList(const cPeaksList& peakslist) {
+	*this = peakslist;
+}
+
+
+cPeaksList& cPeaksList::operator=(const cPeaksList& peakslist) {
+	peaks = peakslist.peaks;
+	return *this;
+}
+
+
 void cPeaksList::clear() {
 	peaks.clear();
 }
@@ -201,6 +217,11 @@ void cPeaksList::sortbyMass(int limit) {
 }
 
 
+void cPeaksList::sortbyIntensityDesc() {
+	sort(peaks.begin(), peaks.end(), comparePeakIntensitiesDesc);
+}
+
+
 int cPeaksList::normalizeIntenzity() {
 	double maximum = 0.0f;
 	for (int i = 0; i < (int)peaks.size(); i++) {
@@ -234,9 +255,9 @@ void cPeaksList::cropIntenzity(double minimumrelativeintensitythreshold) {
 }
 
 
-void cPeaksList::cropMinimumMZRatio(double minimummz) {
+void cPeaksList::cropMinimumMZRatio(double minimummz, double errortolerance) {
 	while ((int)peaks.size() > 0) {
-		if (peaks[0].mzratio < minimummz) {
+		if ((peaks[0].mzratio < minimummz) && (!isInPpmMassErrorTolerance(peaks[0].mzratio, minimummz, errortolerance))) {
 			peaks.erase(peaks.begin());
 		}
 		else {
@@ -246,9 +267,9 @@ void cPeaksList::cropMinimumMZRatio(double minimummz) {
 }
 
 
-void cPeaksList::cropMaximumMZRatio(double maximummz) {
+void cPeaksList::cropMaximumMZRatio(double maximummz, double errortolerance) {
 	while ((int)peaks.size() > 0) {
-		if (peaks.back().mzratio > maximummz) {
+		if ((peaks.back().mzratio > maximummz) && (!isInPpmMassErrorTolerance(peaks.back().mzratio, maximummz, errortolerance))) {
 			peaks.erase(peaks.begin() + peaks.size() - 1);
 		}
 		else {
@@ -269,8 +290,12 @@ void cPeaksList::resize(int size) {
 
 
 double cPeaksList::getMinimumMZRatio() {
-	double minimum = DBL_MAX;
-	for (int i = 0; i < (int)peaks.size(); i++) {
+	if (peaks.size() == 0) {
+		return 0;	
+	}
+
+	double minimum = peaks[0].mzratio;
+	for (int i = 1; i < (int)peaks.size(); i++) {
 		if (peaks[i].mzratio < minimum) {
 			minimum = peaks[i].mzratio;
 		}
@@ -301,8 +326,8 @@ void cPeaksList::removeIsotopes(int maximumcharge, double fragmentmasserrortoler
 		peaks[i].isotope = false;
 	}
 	for (i = 0; i < (int)peaks.size(); i++) {
-		for (int j = 1; j <= maximumcharge; j++) {
-			pos = find(charge(peaks[i].mzratio + Hplus, j), fragmentmasserrortolerance);
+		for (int j = 1; j <= abs(maximumcharge); j++) {
+			pos = find(charge(peaks[i].mzratio, (maximumcharge > 0)?j:-j), fragmentmasserrortolerance);
 			if (pos != -1) {
 				if (peaks[pos].intensity < peaks[i].intensity) {
 					peaks[pos].isotope = true;
@@ -355,31 +380,31 @@ int cPeaksList::find(double mzratio, double fragmentmasserrortolerance) {
 }
 
 
-void cPeaksList::eraseAll(double mzratio) {
+void cPeaksList::findObsolete(double mzratio) {
 	int left, right, middle;
-	for (int i = 0; i < (int)peaks.size(); i++) {
-		left = 0;
-		right = (int)peaks.size() - 1;
-		while (left <= right) {
-			middle = (left + right) / 2;
-			if (abs(mzratio - peaks[middle].mzratio) < 0.00000001) {
-				while ((middle > 0) && (abs(mzratio - peaks[middle - 1].mzratio) < 0.00000001)) {
-					middle--;
-				}
-				while ((peaks.size() > 0) && (middle < (int)peaks.size()) && (abs(mzratio - peaks[middle].mzratio) < 0.00000001)) {
-					peaks.erase(peaks.begin()+middle);
-				}
-				return;
-			}
-			if (mzratio < peaks[middle].mzratio) {
-				right = middle - 1;
+
+	left = 0;
+	right = (int)peaks.size() - 1;
+	while (left <= right) {
+		middle = (left + right) / 2;
+		if (abs(mzratio - peaks[middle].mzratio) < 0.00000001) {
+			while ((middle > 0) && (abs(mzratio - peaks[middle - 1].mzratio) < 0.00000001)) {
+				middle--;
 			}
-			else {
-				left = middle + 1;
+			while ((middle < (int)peaks.size()) && (abs(mzratio - peaks[middle].mzratio) < 0.00000001)) {
+				peaks[middle].removeme = true;
+				middle++;
 			}
+			return;
+		}
+		if (mzratio < peaks[middle].mzratio) {
+			right = middle - 1;
+		}
+		else {
+			left = middle + 1;
 		}
 	}
-	return;
+
 }
 
 
@@ -391,22 +416,21 @@ void cPeaksList::remove(int position) {
 
 
 void cPeaksList::removeChargeVariants(int maximumcharge, double fragmentmasserrortolerance) {
-	if (maximumcharge == 1) {
+	if (abs(maximumcharge) == 1) {
 		return;
 	}
 
 	sortbyMass();
 
-	double uncharged, charged;
-	for (int i = maximumcharge; i > 1; i--) {
+	double charged;
+	for (int i = abs(maximumcharge); i > 1; i--) {
 		for (int j = i - 1; j >= 1; j--) {
 			for (int k = 0; k < (int)peaks.size(); k++) {
 				if (peaks[k].removeme) {
 					continue;
 				}
 
-				uncharged = uncharge(peaks[k].mzratio, i);
-				charged = charge(uncharged, j);
+				charged = charge(uncharge(peaks[k].mzratio, (maximumcharge > 0)?i:-i), (maximumcharge > 0)?j:-j);
 
 				for (int m = k + 1; m < (int)peaks.size(); m++) {
 					if (peaks[m].removeme) {
@@ -428,37 +452,36 @@ void cPeaksList::removeChargeVariants(int maximumcharge, double fragmentmasserro
 
 
 void cPeaksList::removeNeutralLoss(double loss, int maximumcharge, double fragmentmasserrortolerance) {
-
 	sortbyMass();
 
 	int found = -1;
-	for (int i = 1; i <= maximumcharge; i++) {
+	//for (int i = 1; i <= maximumcharge; i++) {
 		for (int j = 0; j < (int)peaks.size(); j++) {
 			found = find(peaks[j].mzratio + loss, fragmentmasserrortolerance);
 			if ((found != -1) && (peaks[found].intensity < peaks[j].intensity)) {
 				peaks[found].removeme = true;
 			}
 		}
-	}
+	//}
 
 	removeObsolete();
-
 }
 
 
 void cPeaksList::removeObsolete() {
+	sort(peaks.begin(), peaks.end(), comparePeakRemoveMeFlag);
 
-	int i = 0;
-	while (i < (int)peaks.size()) {
-		if (peaks[i].removeme) {
-			//cout << peaks[i].mzratio << endl;
-			peaks.erase(peaks.begin()+i);
-		}
-		else {
-			i++;
-		}
+	int items = 0;
+	int size = (int)peaks.size();
+	while ((items < size) && (peaks[size - items - 1].removeme)) {
+		items++;
 	}
 
+	if (items > 0) {
+		peaks.erase(peaks.begin() + size - items, peaks.end());
+	}
+
+	sortbyMass();
 }
 
 
diff --git a/CycloBranch/core/cPeaksList.h b/CycloBranch/core/cPeaksList.h
index 1726347..2fbb41e 100644
--- a/CycloBranch/core/cPeaksList.h
+++ b/CycloBranch/core/cPeaksList.h
@@ -27,7 +27,7 @@ class cMainThread;
 	\param b second peak
 	\retval bool true when the mz ratio of the peak \a a is lower than the mz ratio of the peak \a b
 */
-bool comparePeakMasses(cPeak& a, cPeak& b);
+bool comparePeakMasses(const cPeak& a, const cPeak& b);
 
 
 /**
@@ -36,7 +36,16 @@ bool comparePeakMasses(cPeak& a, cPeak& b);
 	\param b second peak
 	\retval bool true when the intensity of the peak \a a is bigger than the intensity of the peak \a b
 */
-bool comparePeakIntensitiesDesc(cPeak& a, cPeak& b);
+bool comparePeakIntensitiesDesc(const cPeak& a, const cPeak& b);
+
+
+/**
+	\brief Compare two peaks by \a removeme flag.
+	\param a first peak
+	\param b second peak
+	\retval bool true when the \a removeme flag of the peak \a a is lower than the \a removeme flag of the peak \a b
+*/
+bool comparePeakRemoveMeFlag(const cPeak& a, const cPeak& b);
 
 
 /**
@@ -74,6 +83,20 @@ class cPeaksList {
 	cPeaksList();
 
 
+	/**
+		\brief The copy constructor.
+		\param peakslist reference to a cPeaksList
+	*/ 
+	cPeaksList(const cPeaksList& peakslist);
+
+
+	/**
+		\brief Overloaded operator=.
+		\param peakslist reference to a cPeaksList
+	*/ 
+	cPeaksList& operator=(const cPeaksList& peakslist);
+
+
 	/**
 		\brief Clear the peak list.
 	*/ 
@@ -137,6 +160,12 @@ class cPeaksList {
 	void sortbyMass(int limit = -1);
 
 
+	/**
+		\brief Sort the peaks by intensity in the descending order.
+	*/ 
+	void sortbyIntensityDesc();
+
+
 	/**
 		\brief Normalize intensities of peaks.
 		\retval int 0 == success, -1 == maximum intensity <= 0
@@ -154,15 +183,17 @@ class cPeaksList {
 	/**
 		\brief Crop mz ratio lower than a threshold.
 		\param minimummz minimum threshold of mz ratio
+		\param errortolerance mz error tolerance in ppm
 	*/ 
-	void cropMinimumMZRatio(double minimummz);
+	void cropMinimumMZRatio(double minimummz, double errortolerance);
 
 
 	/**
 		\brief Crop mz ratio bigger than a threshold.
 		\param maximummz maximum threshold of mz ratio
+		\param errortolerance mz error tolerance in ppm
 	*/ 
-	void cropMaximumMZRatio(double maximummz);
+	void cropMaximumMZRatio(double maximummz, double errortolerance);
 
 
 	/**
@@ -213,10 +244,10 @@ class cPeaksList {
 
 
 	/**
-		\brief Erase all peaks having specified m/z ratio.
-		\param mzratio mz ratio of peaks which will be erased
+		\brief Find all peaks having a specified \a mzratio and mark them with the flag \a removeme == true.
+		\param mzratio mz ratio of peaks which will be marked
 	*/ 
-	void eraseAll(double mzratio);
+	void findObsolete(double mzratio);
 
 
 	/**
@@ -282,4 +313,4 @@ class cPeaksList {
 };
 
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/core/cSequence.cpp b/CycloBranch/core/cSequence.cpp
index b488a28..26dcbbb 100644
--- a/CycloBranch/core/cSequence.cpp
+++ b/CycloBranch/core/cSequence.cpp
@@ -67,32 +67,32 @@ void cSequence::setPeptideType(peptideType peptidetype) {
 }
 
 
-void cSequence::setSequence(string& sequence) {
+void cSequence::setSequence(const string& sequence) {
 	this->sequence = sequence;
 }
 
 
-void cSequence::setName(string& name) {
+void cSequence::setName(const string& name) {
 	this->name = name;
 }
 
 
-void cSequence::setReference(string& reference) {
+void cSequence::setReference(const string& reference) {
 	this->reference = reference;
 }
 
 
-void cSequence::setNTterminalModification(string& modification) {
+void cSequence::setNTterminalModification(const string& modification) {
 	nterminalmodification = modification;
 }
 
 
-void cSequence::setCTterminalModification(string& modification) {
+void cSequence::setCTterminalModification(const string& modification) {
 	cterminalmodification = modification;
 }
 
 
-void cSequence::setBranchModification(string& modification) {
+void cSequence::setBranchModification(const string& modification) {
 	branchmodification = modification;
 }
 
@@ -165,8 +165,7 @@ string cSequence::getNameWithReferenceAsHTMLString() {
 		}
 
 	}
-	catch (std::regex_error& e) {
-		e;
+	catch (regex_error& /*e*/) {
 		// nothing to do
 	}
 
@@ -178,7 +177,7 @@ string cSequence::getNameWithReferenceAsHTMLString() {
 }
 
 
-void cSequence::setSummaryFormula(string& formula) {
+void cSequence::setSummaryFormula(const string& formula) {
 	summary.setFormula(formula);
 }
 
diff --git a/CycloBranch/core/cSequence.h b/CycloBranch/core/cSequence.h
index d23d904..bd2d2df 100644
--- a/CycloBranch/core/cSequence.h
+++ b/CycloBranch/core/cSequence.h
@@ -17,6 +17,7 @@
 
 
 using namespace std;
+using namespace boost;
 
 
 /**
@@ -101,42 +102,42 @@ class cSequence {
 		\brief Set sequence.
 		\param sequence sequence
 	*/ 
-	void setSequence(string& sequence);
+	void setSequence(const string& sequence);
 
 
 	/**
 		\brief Set name.
 		\param name name
 	*/ 
-	void setName(string& name);
+	void setName(const string& name);
 
 
 	/**
 		\brief Set reference.
 		\param reference reference
 	*/ 
-	void setReference(string& reference);
+	void setReference(const string& reference);
 
 
 	/**
 		\brief Set N-terminal modification.
 		\param modification name of an N-terminal modification
 	*/ 
-	void setNTterminalModification(string& modification);
+	void setNTterminalModification(const string& modification);
 
 
 	/**
 		\brief Set C-terminal modification.
 		\param modification name of a C-terminal modification
 	*/ 
-	void setCTterminalModification(string& modification);
+	void setCTterminalModification(const string& modification);
 
 
 	/**
 		\brief Set branch modification.
 		\param modification name of a branch modification
 	*/ 
-	void setBranchModification(string& modification);
+	void setBranchModification(const string& modification);
 
 
 	/**
@@ -171,7 +172,7 @@ class cSequence {
 		\brief Set the summary formula.
 		\param formula summary formula
 	*/ 
-	void setSummaryFormula(string& formula);
+	void setSummaryFormula(const string& formula);
 
 
 	/**
@@ -183,4 +184,4 @@ class cSequence {
 };
 
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/core/cSequenceDatabase.cpp b/CycloBranch/core/cSequenceDatabase.cpp
index 0f364d1..00a0748 100644
--- a/CycloBranch/core/cSequenceDatabase.cpp
+++ b/CycloBranch/core/cSequenceDatabase.cpp
@@ -38,7 +38,7 @@ void cSequenceDatabase::loadFromPlainTextStream(ifstream &stream) {
 			if (type.compare("branched") == 0) {
 				sequence.setPeptideType(branched);
 			}
-			if (type.compare("lasso") == 0) {
+			if (type.compare("branch-cyclic") == 0) {
 				sequence.setPeptideType(lasso);
 			}
 			if (type.compare("linearpolysaccharide") == 0) {
@@ -124,6 +124,11 @@ void cSequenceDatabase::loadFromPlainTextStream(ifstream &stream) {
 		}
 
 		// load reference
+		#if OS_TYPE == UNX
+			if ((s.size() > 0) && (s.back() == '\r')) {
+				s = s.substr(0, s.size() - 1);
+			}
+		#endif
 		sequence.setReference(s);
 
 		sequences.push_back(sequence);
diff --git a/CycloBranch/core/cSequenceDatabase.h b/CycloBranch/core/cSequenceDatabase.h
index 6937550..217f1b9 100644
--- a/CycloBranch/core/cSequenceDatabase.h
+++ b/CycloBranch/core/cSequenceDatabase.h
@@ -11,6 +11,7 @@
 #include <fstream>
 #include <vector>
 #include <string>
+#include "core/utilities.h"
 #include "core/cSequence.h"
 
 
diff --git a/CycloBranch/core/cSummaryFormula.cpp b/CycloBranch/core/cSummaryFormula.cpp
index fd90ed0..352643e 100644
--- a/CycloBranch/core/cSummaryFormula.cpp
+++ b/CycloBranch/core/cSummaryFormula.cpp
@@ -94,7 +94,7 @@ void cSummaryFormula::clear() {
 }
 
 
-void cSummaryFormula::setFormula(string& formula) {
+void cSummaryFormula::setFormula(const string& formula) {
 	this->formula = formula;
 }
 
@@ -140,7 +140,7 @@ bool cSummaryFormula::isValid(string& errormessage) {
 			return false;
 		}
 	}
-	catch (std::regex_error& e) {
+	catch (regex_error& e) {
 		errormessage = "getMassFromResidueSummary: regex_search failed, error no. " + to_string((int)e.code()) + "\n";
 		return false;
 	}
diff --git a/CycloBranch/core/cSummaryFormula.h b/CycloBranch/core/cSummaryFormula.h
index 7ac8de4..f6dc553 100644
--- a/CycloBranch/core/cSummaryFormula.h
+++ b/CycloBranch/core/cSummaryFormula.h
@@ -13,6 +13,7 @@
 
 
 using namespace std;
+using namespace boost;
 
 
 /**
@@ -50,7 +51,7 @@ class cSummaryFormula {
 		\brief Set the formula.
 		\param formula a chemical formula
 	*/
-	void setFormula(string& formula);
+	void setFormula(const string& formula);
 
 
 	/**
@@ -98,4 +99,4 @@ class cSummaryFormula {
 };
 
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/core/cTheoreticalSpectrum.cpp b/CycloBranch/core/cTheoreticalSpectrum.cpp
index 94432ab..7a53ba6 100644
--- a/CycloBranch/core/cTheoreticalSpectrum.cpp
+++ b/CycloBranch/core/cTheoreticalSpectrum.cpp
@@ -71,7 +71,7 @@ void cTheoreticalSpectrum::searchForPeakPairs(cPeaksList& theoreticalpeaks, int
 }
 
 
-void cTheoreticalSpectrum::computeSomeStatistics(bool writedescription) {
+void cTheoreticalSpectrum::computeStatistics(bool writedescription) {
 	experimentalpeaksmatched = 0;
 	scrambledpeaksmatched = 0;
 	if (writedescription) {
@@ -103,11 +103,90 @@ void cTheoreticalSpectrum::computeSomeStatistics(bool writedescription) {
 }
 
 
+void cTheoreticalSpectrum::generatePrecursorIon(vector<int>& intcomposition, cBricksDatabase& bricksdatabasewithcombinations, int& theoreticalpeaksrealsize, bool writedescription) {
+	cPeak peak;
+	int starttype, endtype;
+
+	switch (parameters->peptidetype)
+	{
+	case linear:
+		peak.mzratio = parameters->searchedmodifications[candidate.getStartModifID()].massdifference + parameters->searchedmodifications[candidate.getEndModifID()].massdifference;
+		peak.seriesid = 0;
+		starttype = (int)precursor_ion;
+		endtype = (int)precursor_ion_co_loss_and_dehydrated_and_deamidated;
+		break;
+	case cyclic:
+		peak.mzratio = 0;
+		peak.seriesid = (int)intcomposition.size() - 1;
+		starttype = (int)cyclic_precursor_ion;
+		endtype = (int)cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated;
+		break;
+	case branched:
+		peak.mzratio = parameters->searchedmodifications[candidate.getStartModifID()].massdifference + parameters->searchedmodifications[candidate.getEndModifID()].massdifference + parameters->searchedmodifications[candidate.getMiddleModifID()].massdifference;
+		peak.seriesid = 0;
+		starttype = (int)precursor_ion;
+		endtype = (int)precursor_ion_co_loss_and_dehydrated_and_deamidated;
+		break;
+	case lasso:
+		peak.mzratio = parameters->searchedmodifications[candidate.getMiddleModifID()].massdifference;
+		peak.seriesid = 0;
+		starttype = (int)cyclic_precursor_ion;
+		endtype = (int)cyclic_precursor_ion_co_loss_and_dehydrated_and_deamidated;
+		break;
+	case linearpolysaccharide:
+		peak.mzratio = parameters->searchedmodifications[candidate.getStartModifID()].massdifference + parameters->searchedmodifications[candidate.getEndModifID()].massdifference;
+		peak.seriesid = 0;
+		starttype = (int)precursor_ion;
+		endtype = (int)precursor_ion_co_loss_and_dehydrated_and_deamidated;
+		break;
+	case other:
+		break;
+	default:
+		break;
+	}
+
+	for (int i = 0; i < (int)intcomposition.size(); i++) {
+		peak.mzratio += bricksdatabasewithcombinations[intcomposition[i] - 1].getMass();
+	}
+	
+	double tempratio = peak.mzratio;
+	for (int i = starttype; i <= endtype; i++) {
+		for (int j = 1; j <= abs(parameters->precursorcharge); j++) {
+			peak.mzratio = tempratio + parameters->fragmentdefinitions[(fragmentIonType)i].massdifference;
+			peak.iontype = (fragmentIonType)i;
+
+			if (writedescription) {
+				if (parameters->precursorcharge > 0) {
+					peak.description = to_string(j) + "+ " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
+				}
+				else {
+					peak.description = to_string(j) + "- " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
+					peak.description.replace(peak.description.find("+z"), 2, "-z");
+					peak.description.replace(peak.description.find("]+"), 2, "]-");
+				}
+			}
+
+			peak.mzratio = charge(uncharge(peak.mzratio, 1), (parameters->precursorcharge > 0)?j:-j);
+			peak.charge = (parameters->precursorcharge > 0)?j:-j;
+
+			if (theoreticalpeaks.size() > theoreticalpeaksrealsize) {
+				theoreticalpeaks[theoreticalpeaksrealsize] = peak;
+			}
+			else {
+				theoreticalpeaks.add(peak);
+			}
+			theoreticalpeaksrealsize++;
+
+		}
+	}
+}
+
+
 void cTheoreticalSpectrum::generateScrambledIons(cBricksDatabase& bricksdatabase, bool writedescription, int& theoreticalpeaksrealsize) {
 	unordered_set<string> scrambledsequences, commonsequences;
 	vector<int> intcomposition;
 	scrambledsequences.clear();
-	int minimumsizeofscrambledsequences = 2;
+	//int minimumsizeofscrambledsequences = 2;
 	cBrick b;
 
 	b.setComposition(candidate.getComposition(), false);
@@ -122,7 +201,7 @@ void cTheoreticalSpectrum::generateScrambledIons(cBricksDatabase& bricksdatabase
 	int numberofbricks = (int)stringcomposition.size();
 	string subseq;
 	bool single;
-	// generate scrambled sequences
+	// generate all possible combinations of blocks
 	for (int i = 1; i < (int)pow(2, numberofbricks) - 1; i++) {
 			subseq = "";
 			single = true;
@@ -140,14 +219,14 @@ void cTheoreticalSpectrum::generateScrambledIons(cBricksDatabase& bricksdatabase
 			}
 	}
 
-	// normalize scrambled sequences
-	normalizeScrambledSequences(scrambledsequences);
+	// select and normalize scrambled sequences
+	selectAndNormalizeScrambledSequences(scrambledsequences);
 
 	cPeaksList scrambledpeaks;
 	scrambledpeaks.resize(5000);
 	int scrambledspeaksrealsize = 0;
 
-	// generate scrambled peaks
+	// generate scrambled peaks from sequences
 	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
 		for (unordered_set<string>::iterator it = scrambledsequences.begin(); it != scrambledsequences.end(); ++it) {
 			b.setComposition((string &)*it, false);
@@ -161,9 +240,21 @@ void cTheoreticalSpectrum::generateScrambledIons(cBricksDatabase& bricksdatabase
 			for (int i = 0; i < (int)intcomposition.size(); i++) {
 				peak.mzratio += bricksdatabase[intcomposition[i] - 1].getMass();
 			}
+			
+			if (parameters->precursorcharge < 0) {
+				peak.mzratio = charge(uncharge(peak.mzratio, 1), -1);
+			}
 
 			if (writedescription) {
-				peak.description = "scrambled ";
+
+				if (parameters->precursorcharge < 0) {
+					peak.description = "1- ";
+				}
+				else {
+					peak.description = "1+ ";
+				}
+
+				peak.description += "scrambled ";
 				peak.description += parameters->fragmentdefinitions[peak.iontype].name.substr(0, 1) + to_string((int)intcomposition.size());
 				if (parameters->fragmentdefinitions[peak.iontype].name.size() > 1) {
 					peak.description += parameters->fragmentdefinitions[peak.iontype].name.substr(1, parameters->fragmentdefinitions[peak.iontype].name.length() - 1);
@@ -188,12 +279,12 @@ void cTheoreticalSpectrum::generateScrambledIons(cBricksDatabase& bricksdatabase
 	}
 	scrambledpeaks.resize(scrambledspeaksrealsize);
 
-	// erase all scrambled peaks whose mz ratios collide with common fragment ions
-	// eraseAll - time consuming 55.8%
-	// scrambledpeaks.sortbyMass();
-	// for (int i = 0; i < theoreticalpeaksrealsize; i++) {
-	// 	scrambledpeaks.eraseAll(theoreticalpeaks[i].mzratio);
-	// }
+	// find and erase all scrambled peaks whose mz ratios collide with common fragment ions
+	scrambledpeaks.sortbyMass();
+	for (int i = 0; i < theoreticalpeaksrealsize; i++) {
+	 	scrambledpeaks.findObsolete(theoreticalpeaks[i].mzratio);
+	}
+	scrambledpeaks.removeObsolete();
 
 	// attach scrambled peaks to common peaks
 	for (int i = 0; i < (int)scrambledpeaks.size(); i++) {
@@ -209,7 +300,7 @@ void cTheoreticalSpectrum::generateScrambledIons(cBricksDatabase& bricksdatabase
 }
 
 
-void cTheoreticalSpectrum::normalizeScrambledSequences(unordered_set<string>& scrambledsequences) {
+void cTheoreticalSpectrum::selectAndNormalizeScrambledSequences(unordered_set<string>& scrambledsequences) {
 	unordered_set<string> temp = scrambledsequences;
 	scrambledsequences.clear();
 	
@@ -229,37 +320,69 @@ void cTheoreticalSpectrum::normalizeScrambledSequences(unordered_set<string>& sc
 }
 
 
-fragmentIonType cTheoreticalSpectrum::selectHigherPriorityIonType(fragmentIonType experimentalpeakiontype, fragmentIonType theoreticalpeakiontype) {
+fragmentIonType cTheoreticalSpectrum::selectHigherPriorityIonTypeCID(fragmentIonType experimentalpeakiontype, fragmentIonType theoreticalpeakiontype) {
 	if (experimentalpeakiontype != fragmentIonTypeEnd) {
 
 		switch (experimentalpeakiontype)
 		{
+		case a_ion:
+			if (theoreticalpeakiontype == b_ion) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case a_ion_dehydrated:
+		case a_ion_deamidated:
+			if ((theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == a_ion)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case a_ion_dehydrated_and_deamidated:
+			if ((theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == b_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
 		case b_ion:
 			break;
-		case b_ion_water_loss:
-		case b_ion_ammonia_loss:
+		case b_ion_dehydrated:
+		case b_ion_deamidated:
 			if (theoreticalpeakiontype == b_ion) {
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
-		case b_ion_water_and_ammonia_loss:
-			if ((theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_water_loss) || (theoreticalpeakiontype == b_ion_ammonia_loss)) {
+		case b_ion_dehydrated_and_deamidated:
+			if ((theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated)) {
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
-		case a_ion:
-			if (theoreticalpeakiontype == b_ion) {
+		case c_ion:
+			if ((theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == a_ion)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case c_ion_dehydrated:
+		case c_ion_deamidated:
+			if ((theoreticalpeakiontype == c_ion) || (theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == y_ion_dehydrated) || (theoreticalpeakiontype == y_ion_deamidated) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated)) {
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
-		case a_ion_water_loss:
-		case a_ion_ammonia_loss:
-			if ((theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_water_loss) || (theoreticalpeakiontype == b_ion_ammonia_loss) || (theoreticalpeakiontype == a_ion)) {
+		case c_ion_dehydrated_and_deamidated:
+			if ((theoreticalpeakiontype == c_ion) || (theoreticalpeakiontype == c_ion_dehydrated) || (theoreticalpeakiontype == c_ion_deamidated) || (theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == y_ion_dehydrated) || (theoreticalpeakiontype == y_ion_deamidated) || (theoreticalpeakiontype == y_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == b_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated) || (theoreticalpeakiontype == a_ion_dehydrated_and_deamidated)) {
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
-		case a_ion_water_and_ammonia_loss:
-			if ((theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_water_loss) || (theoreticalpeakiontype == b_ion_ammonia_loss) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_water_loss) || (theoreticalpeakiontype == a_ion_ammonia_loss)) {
+		case x_ion:
+			if ((theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == a_ion)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case x_ion_dehydrated:
+		case x_ion_deamidated:
+			if ((theoreticalpeakiontype == x_ion) || (theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == y_ion_dehydrated) || (theoreticalpeakiontype == y_ion_deamidated) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case x_ion_dehydrated_and_deamidated:
+			if ((theoreticalpeakiontype == x_ion) || (theoreticalpeakiontype == x_ion_dehydrated) || (theoreticalpeakiontype == x_ion_deamidated) || (theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == y_ion_dehydrated) || (theoreticalpeakiontype == y_ion_deamidated) || (theoreticalpeakiontype == y_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == b_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated) || (theoreticalpeakiontype == a_ion_dehydrated_and_deamidated)) {
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
@@ -268,14 +391,31 @@ fragmentIonType cTheoreticalSpectrum::selectHigherPriorityIonType(fragmentIonTyp
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
-		case y_ion_water_loss:
-		case y_ion_ammonia_loss:
-			if ((theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_water_loss) || (theoreticalpeakiontype == b_ion_ammonia_loss) || (theoreticalpeakiontype == a_ion)  || (theoreticalpeakiontype == a_ion_water_loss) || (theoreticalpeakiontype == a_ion_ammonia_loss)) {
+		case y_ion_dehydrated:
+		case y_ion_deamidated:
+			if ((theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == a_ion)  || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated)) {
 				experimentalpeakiontype = theoreticalpeakiontype;
 			}
 			break;
-		case y_ion_water_and_ammonia_loss:
+		case y_ion_dehydrated_and_deamidated:
 			experimentalpeakiontype = theoreticalpeakiontype;
+			break;
+		case z_ion:
+			if ((theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == a_ion)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case z_ion_dehydrated:
+		case z_ion_deamidated:
+			if ((theoreticalpeakiontype == z_ion) || (theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == y_ion_dehydrated) || (theoreticalpeakiontype == y_ion_deamidated) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
+		case z_ion_dehydrated_and_deamidated:
+			if ((theoreticalpeakiontype == z_ion) || (theoreticalpeakiontype == z_ion_dehydrated) || (theoreticalpeakiontype == z_ion_deamidated) || (theoreticalpeakiontype == y_ion) || (theoreticalpeakiontype == y_ion_dehydrated) || (theoreticalpeakiontype == y_ion_deamidated) || (theoreticalpeakiontype == y_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == b_ion) || (theoreticalpeakiontype == b_ion_dehydrated) || (theoreticalpeakiontype == b_ion_deamidated) || (theoreticalpeakiontype == b_ion_dehydrated_and_deamidated) || (theoreticalpeakiontype == a_ion) || (theoreticalpeakiontype == a_ion_dehydrated) || (theoreticalpeakiontype == a_ion_deamidated) || (theoreticalpeakiontype == a_ion_dehydrated_and_deamidated)) {
+				experimentalpeakiontype = theoreticalpeakiontype;
+			}
+			break;
 		default:
 			break;
 		}
@@ -328,12 +468,6 @@ void cTheoreticalSpectrum::clear(bool clearpeaklist) {
 	validposition = -1;
 	reversevalidposition = -1;
 	
-	realpeptidename = "";
-	acronympeptidename = "";
-	acronyms.clear();
-	backboneacronyms.clear();
-	branchacronyms.clear();
-	path = "";
 	seriescompleted = 1;
 }
 
@@ -351,7 +485,6 @@ void cTheoreticalSpectrum::setCandidate(cCandidate& candidate) {
 int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDatabase& bricksdatabasewithcombinations, bool writedescription, regex& sequencetag, regex& searchedsequence) {
 
 	cBrick brick;
-	vector<string> stringcomposition;
 	vector<splitSite> splittingsites;
 	int theoreticalpeaksrealsize = 0;
 
@@ -385,75 +518,31 @@ int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDat
 			}
 		}
 	} 
-	catch (std::regex_error& e) {
-		e;
+	catch (regex_error& /*e*/) {
 		return -2;
 	}
 
 	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
-		for (int j = 0; j < (int)trotations.size(); j++) {
 
-			if (writedescription) {
-				stringcomposition.clear();
-				for (int k = 0; k < (int)trotations[j].bricks.size(); k++) {
-					stringcomposition.push_back(to_string(trotations[j].bricks[k]));
-				}
-			}
+		for (int j = 0; j < (int)trotations.size(); j++) {
 
 			// we do not know whether the middle branch is n-terminal or c-terminal for an unmodified middle branch
-			// in this case the modifID is 0, and both n-terminal (*) and c-terminal (**) fragments are generated
-
-			// j == 2 and j == 5 have invalid n-terms
-			if ((parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) && (j != 2) && (j != 5)) {
-				// if the start modification for j == 1 or j == 4 is nterminal, generate n-terminal ions (*)
-				if (!(((j == 1) || (j == 4)) && (!parameters->searchedmodifications[trotations[j].startmodifID].nterminal))) {
-					generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, trotations[j].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, branched, &trotations[j]);
+			// in this case the modifID is 0, and both n-terminal and c-terminal fragments are generated
+			// j == 2, 4, 5 are invalid
+			if ((j == 0) || ((j == 1) && (parameters->searchedmodifications[trotations[j].startmodifID].nterminal)) || ((j == 3) && (parameters->searchedmodifications[trotations[j].endmodifID].cterminal))) {
+				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) {
+					generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, trotations[j].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, branched, &trotations[j]);
 				}
-			}
-
-			// j == 2 and j == 4 have invalid c-terms
-			if ((parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal) && (j != 2) && (j != 4)) {
-				// if the end modification for j == 3 or j == 5 is cterminal, generate c-terminal ions (**)
-				if (!(((j == 3) || (j == 5)) && (!parameters->searchedmodifications[trotations[j].endmodifID].cterminal))) {
-					generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, trotations[j].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, branched, &trotations[j]);
+				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal) {
+					generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, trotations[j].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, branched, &trotations[j]);
 				}
 			}
 
 		}	
-	}
 
-
-	// generate the precursor ion
-	cPeak peak;
-	peak.mzratio = parameters->searchedmodifications[candidate.getStartModifID()].massdifference + parameters->searchedmodifications[candidate.getEndModifID()].massdifference + parameters->searchedmodifications[candidate.getMiddleModifID()].massdifference;
-	for (int i = 0; i < (int)trotations[0].bricks.size(); i++) {
-		peak.mzratio += bricksdatabasewithcombinations[trotations[0].bricks[i] - 1].getMass();
-	}
-	peak.seriesid = 0;
-
-	double tempratio = peak.mzratio;
-	for (int i = (int)precursor_ion; i <= (int)precursor_ion_co_loss_water_and_ammonia_loss; i++) {
-		for (int j = 1; j <= parameters->precursorcharge; j++) {
-			peak.mzratio = tempratio + parameters->fragmentdefinitions[(fragmentIonType)i].massdifference;
-			peak.iontype = (fragmentIonType)i;
-
-			if (writedescription) {
-				peak.description = to_string(j) + "+ " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
-			}
-
-			peak.mzratio = charge(peak.mzratio, j);
-			peak.charge = j;
-
-			if (theoreticalpeaks.size() > theoreticalpeaksrealsize) {
-				theoreticalpeaks[theoreticalpeaksrealsize] = peak;
-			}
-			else {
-				theoreticalpeaks.add(peak);
-			}
-			theoreticalpeaksrealsize++;
-
-		}
 	}
+	
+	generatePrecursorIon(trotations[0].bricks, bricksdatabasewithcombinations, theoreticalpeaksrealsize, writedescription);
 
 
 	// search the theoretical peaks in the experimental peak list
@@ -466,7 +555,7 @@ int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDat
 	vector<map<fragmentIonType, vector<int> > > series;
 	series.resize(trotations.size());
 	for (int i = 0; i < (int)series.size(); i++) {
-		for (int j = 0; j < parameters->fragmentionsfortheoreticalspectra.size(); j++) {
+		for (int j = 0; j < (int)parameters->fragmentionsfortheoreticalspectra.size(); j++) {
 			series[i][parameters->fragmentionsfortheoreticalspectra[j]].resize(trotations[0].bricks.size());
 		}
 	}
@@ -507,7 +596,7 @@ int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDat
 				theoreticalpeaks[*it].matchdescription += ", measured mass " + to_string((long double)experimentalpeaks[i].mzratio) + " matched with " + to_string((long double)ppmError(experimentalpeaks[i].mzratio, theoreticalpeaks[*it].mzratio)) + " ppm error";
 			}
 
-			experimentalpeaks[i].iontype = selectHigherPriorityIonType(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
+			experimentalpeaks[i].iontype = selectHigherPriorityIonTypeCID(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
 		}
 	}
 
@@ -529,10 +618,10 @@ int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDat
 				tempseries.name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name;
 				coveragebyseries += tempseries.name + "  ";
 				tempseries.series.clear();
-				for (int k = 0; k < series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 1; k++) {
+				for (int k = 0; k < (int)series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 1; k++) {
 					coveragebyseries += to_string(series[i][parameters->fragmentionsfortheoreticalspectra[j]][k]);
 					tempseries.series.push_back(series[i][parameters->fragmentionsfortheoreticalspectra[j]][k]);
-					if (k < series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 2) {
+					if (k < (int)series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 2) {
 						coveragebyseries += " ";
 					}
 				}
@@ -543,7 +632,7 @@ int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDat
 
 	}
 
-	computeSomeStatistics(writedescription);
+	computeStatistics(writedescription);
 
 	return theoreticalpeaksrealsize;
 }
@@ -552,7 +641,6 @@ int cTheoreticalSpectrum::compareBranched(cPeaksList& sortedpeaklist, cBricksDat
 int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatabase& bricksdatabasewithcombinations, bool writedescription, regex& sequencetag, regex& searchedsequence) {
 	cBrick brick;
 	vector<int> intcomposition;
-	vector<string> stringcomposition;
 	vector<splitSite> splittingsites;
 	int theoreticalpeaksrealsize = 0;
 
@@ -570,8 +658,7 @@ int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatab
 			}	
 		}
 	} 
-	catch (std::regex_error& e) {
-		e;
+	catch (regex_error& /*e*/) {
 		return -2;
 	}
 
@@ -580,52 +667,16 @@ int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatab
 	brick.setComposition(candidate.getComposition(), false);
 	brick.explodeToIntComposition(intcomposition);
 
-	if (writedescription) {
-		stringcomposition.clear();
-		brick.explodeToStringComposition(stringcomposition);
-	}
-
 	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
 		if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) {
-			generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linear);
+			generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linear);
 		}
 		if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal) {
-			generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linear);
+			generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linear);
 		}
 	}
 
-
-	// generate the precursor ion
-	cPeak peak;
-	peak.mzratio = parameters->searchedmodifications[candidate.getStartModifID()].massdifference + parameters->searchedmodifications[candidate.getEndModifID()].massdifference;
-	for (int i = 0; i < (int)intcomposition.size(); i++) {
-		peak.mzratio += bricksdatabasewithcombinations[intcomposition[i] - 1].getMass();
-	}
-	peak.seriesid = 0;
-
-	double tempratio = peak.mzratio;
-	for (int i = (int)precursor_ion; i <= (int)precursor_ion_co_loss_water_and_ammonia_loss; i++) {
-		for (int j = 1; j <= parameters->precursorcharge; j++) {
-			peak.mzratio = tempratio + parameters->fragmentdefinitions[(fragmentIonType)i].massdifference;
-			peak.iontype = (fragmentIonType)i;
-
-			if (writedescription) {
-				peak.description = to_string(j) + "+ " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
-			}
-
-			peak.mzratio = charge(peak.mzratio, j);
-			peak.charge = j;
-
-			if (theoreticalpeaks.size() > theoreticalpeaksrealsize) {
-				theoreticalpeaks[theoreticalpeaksrealsize] = peak;
-			}
-			else {
-				theoreticalpeaks.add(peak);
-			}
-			theoreticalpeaksrealsize++;
-
-		}
-	}
+	generatePrecursorIon(intcomposition, bricksdatabasewithcombinations, theoreticalpeaksrealsize, writedescription);
 
 
 	// search the theoretical peaks in the experimental peak list
@@ -636,7 +687,7 @@ int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatab
 
 	// coverage of series
 	map<fragmentIonType, vector<int> > series;
-	for (int i = 0; i < parameters->fragmentionsfortheoreticalspectra.size(); i++) {
+	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
 		series[parameters->fragmentionsfortheoreticalspectra[i]].resize(intcomposition.size());
 	}
 
@@ -674,7 +725,7 @@ int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatab
 				theoreticalpeaks[*it].matchdescription += ", measured mass " + to_string((long double)experimentalpeaks[i].mzratio) + " matched with " + to_string((long double)ppmError(experimentalpeaks[i].mzratio, theoreticalpeaks[*it].mzratio)) + " ppm error";
 			}
 
-			experimentalpeaks[i].iontype = selectHigherPriorityIonType(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
+			experimentalpeaks[i].iontype = selectHigherPriorityIonTypeCID(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
 		}
 	}
 
@@ -689,10 +740,10 @@ int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatab
 			tempseries.name = parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name;
 			coveragebyseries += tempseries.name + "  ";
 			tempseries.series.clear();
-			for (int j = 0; j < series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 1; j++) {
+			for (int j = 0; j < (int)series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 1; j++) {
 				coveragebyseries += to_string(series[parameters->fragmentionsfortheoreticalspectra[i]][j]);
 				tempseries.series.push_back(series[parameters->fragmentionsfortheoreticalspectra[i]][j]);
-				if (j < series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 2) {
+				if (j < (int)series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 2) {
 					coveragebyseries += " ";
 				}
 			}
@@ -702,7 +753,7 @@ int cTheoreticalSpectrum::compareLinear(cPeaksList& sortedpeaklist, cBricksDatab
 
 	}
 
-	computeSomeStatistics(writedescription);
+	computeStatistics(writedescription);
 
 	return theoreticalpeaksrealsize;
 }
@@ -712,7 +763,6 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 
 	cBrick brick;
 	vector<int> intcomposition;
-	vector<string> stringcomposition;
 	vector<splitSite> splittingsites;
 	int theoreticalpeaksrealsize = 0;
 
@@ -799,8 +849,7 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 
 		}
 	}
-	catch (std::regex_error& e) {
-		e;
+	catch (regex_error& /*e*/) {
 		return -2;
 	}
 
@@ -812,13 +861,8 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 		brick.setComposition(rotations[i], false);
 		brick.explodeToIntComposition(intcomposition);
 
-		if (writedescription) {
-			stringcomposition.clear();
-			brick.explodeToStringComposition(stringcomposition);
-		}
-
 		for (int j = 0; j < (int)parameters->fragmentionsfortheoreticalspectra.size(); j++) {
-			generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, intcomposition, parameters->fragmentionsfortheoreticalspectra[j], bricksdatabasewithcombinations, writedescription, i, splittingsites, parameters->searchedmodifications, cyclic);
+			generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, intcomposition, parameters->fragmentionsfortheoreticalspectra[j], bricksdatabasewithcombinations, writedescription, i, splittingsites, parameters->searchedmodifications, cyclic);
 		}
 
 	}
@@ -827,38 +871,7 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 		generateScrambledIons(bricksdatabasewithcombinations, writedescription, theoreticalpeaksrealsize);
 	}
 
-	
-	// generate the precursor ion
-	cPeak peak;
-	peak.mzratio = 0;
-	for (int i = 0; i < (int)intcomposition.size(); i++) {
-		peak.mzratio += bricksdatabasewithcombinations[intcomposition[i] - 1].getMass();
-	}
-	peak.seriesid = (int)intcomposition.size() - 1;
-
-	double tempratio = peak.mzratio;
-	for (int i = (int)cyclic_precursor_ion; i <= (int)cyclic_precursor_ion_co_loss_water_and_ammonia_loss; i++) {
-		for (int j = 1; j <= parameters->precursorcharge; j++) {
-			peak.mzratio = tempratio + parameters->fragmentdefinitions[(fragmentIonType)i].massdifference;
-			peak.iontype = (fragmentIonType)i;
-
-			if (writedescription) {
-				peak.description = to_string(j) + "+ " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
-			}
-
-			peak.mzratio = charge(peak.mzratio, j);
-			peak.charge = j;
-
-			if (theoreticalpeaks.size() > theoreticalpeaksrealsize) {
-				theoreticalpeaks[theoreticalpeaksrealsize] = peak;
-			}
-			else {
-				theoreticalpeaks.add(peak);
-			}
-			theoreticalpeaksrealsize++;
-
-		}
-	}
+	generatePrecursorIon(intcomposition, bricksdatabasewithcombinations, theoreticalpeaksrealsize, writedescription);
 
 
 	// search the theoretical peaks in the experimental peak list
@@ -871,7 +884,7 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 	vector<map<fragmentIonType, vector<int> > > series;
 	series.resize(rotations.size());
 	for (int i = 0; i < (int)series.size(); i++) {
-		for (int j = 0; j < parameters->fragmentionsfortheoreticalspectra.size(); j++) {
+		for (int j = 0; j < (int)parameters->fragmentionsfortheoreticalspectra.size(); j++) {
 			series[i][parameters->fragmentionsfortheoreticalspectra[j]].resize(r);
 		}
 	}
@@ -967,52 +980,15 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 			}
 
 			if (experimentalpeaks[i].iontype != fragmentIonTypeEnd) {
-
 				if (theoreticalpeaks[*it].scrambled == experimentalpeaks[i].scrambled) {
-
-					switch (experimentalpeaks[i].iontype)
-					{
-					case b_ion:
-						break;
-					case b_ion_water_loss:
-					case b_ion_ammonia_loss:
-						if (theoreticalpeaks[*it].iontype == b_ion) {
-							experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
-						}
-						break;
-					case b_ion_water_and_ammonia_loss:
-						if ((theoreticalpeaks[*it].iontype == b_ion) || (theoreticalpeaks[*it].iontype == b_ion_water_loss) || (theoreticalpeaks[*it].iontype == b_ion_ammonia_loss)) {
-							experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
-						}
-						break;
-					case a_ion:
-						if (theoreticalpeaks[*it].iontype == b_ion) {
-							experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
-						}
-						break;
-					case a_ion_water_loss:
-					case a_ion_ammonia_loss:
-						if ((theoreticalpeaks[*it].iontype == b_ion) || (theoreticalpeaks[*it].iontype == b_ion_water_loss) || (theoreticalpeaks[*it].iontype == b_ion_ammonia_loss) || (theoreticalpeaks[*it].iontype == a_ion)) {
-							experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
-						}
-						break;
-					case a_ion_water_and_ammonia_loss:
-						experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
-						break;
-					default:
-						break;
-					}
-
+					experimentalpeaks[i].iontype = selectHigherPriorityIonTypeCID(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
 				}
 				else {
-				
 					if (experimentalpeaks[i].scrambled && !theoreticalpeaks[*it].scrambled) {
 						experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
 						experimentalpeaks[i].scrambled = theoreticalpeaks[*it].scrambled;
 					}
-				
 				}
-
 			}
 			else {
 				experimentalpeaks[i].iontype = theoreticalpeaks[*it].iontype;
@@ -1045,10 +1021,10 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 				tempseries.name = to_string(splittingsites[i].first + 1) + "-" + to_string(splittingsites[i].second + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name;
 				coveragebyseries += tempseries.name + "  ";
 				tempseries.series.clear();
-				for (int k = 0; k < series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 1; k++) {
+				for (int k = 0; k < (int)series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 1; k++) {
 					coveragebyseries += to_string(series[i][parameters->fragmentionsfortheoreticalspectra[j]][k]);
 					tempseries.series.push_back(series[i][parameters->fragmentionsfortheoreticalspectra[j]][k]);
-					if (k < series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 2) {
+					if (k < (int)series[i][parameters->fragmentionsfortheoreticalspectra[j]].size() - 2) {
 						coveragebyseries += " ";
 					}
 				}
@@ -1113,7 +1089,7 @@ int cTheoreticalSpectrum::compareCyclic(cPeaksList& sortedpeaklist, cBricksDatab
 		maskscore += mask[k];
 	}
 
-	computeSomeStatistics(writedescription);
+	computeStatistics(writedescription);
 
 	return theoreticalpeaksrealsize;
 }
@@ -1123,14 +1099,14 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 
 	vector<splitSite> splittingsites;
 	int theoreticalpeaksrealsize = 0;
-	vector<string> stringcomposition;
 	vector<cCandidate> lassorotations;
 
 
 	// normalize the candidate
 	candidate.getLassoRotations(lassorotations, false);
+	int numberofbricks = getNumberOfBricks(candidate.getComposition());
 	for (int i = 0; i < (int)lassorotations.size(); i++) {
-		if (lassorotations[i].getBranchEnd() == getNumberOfBricks(candidate.getComposition()) - 1) {
+		if (lassorotations[i].getBranchEnd() == numberofbricks - 1) {
 			vector<string> v;
 			v.push_back(lassorotations[i].getComposition());
 			candidate.setCandidate(v, candidate.getPath(), candidate.getStartModifID(), candidate.getEndModifID(), candidate.getMiddleModifID(), lassorotations[i].getBranchStart(), lassorotations[i].getBranchEnd());
@@ -1139,10 +1115,10 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 	}
 
 
-	// get lasso rotations
+	// get branch-cyclic rotations
 	candidate.getLassoRotations(lassorotations, true);
 
-	// get T-permutations of lasso rotations
+	// get T-permutations of branch-cyclic rotations
 	vector<vector<TRotationInfo> > trotationsoflassorotations;
 	trotationsoflassorotations.resize(lassorotations.size());
 	for (int i = 0; i < (int)lassorotations.size(); i++) {
@@ -1231,8 +1207,7 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 
 		}
 	} 
-	catch (std::regex_error& e) {
-		e;
+	catch (regex_error& /*e*/) {
 		return -2;
 	}
 
@@ -1243,21 +1218,13 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 
 			for (int k = 0; k < (int)trotationsoflassorotations[j].size(); k++) {
 
-				if (writedescription) {
-					// to do - performace issue, generated repeatedly
-					stringcomposition.clear();
-					for (int m = 0; m < (int)trotationsoflassorotations[j][k].bricks.size(); m++) {
-						stringcomposition.push_back(to_string(trotationsoflassorotations[j][k].bricks[m]));
-					}
-				}
-
 				// we do not know whether the middle branch is n-terminal or c-terminal for an unmodified middle branch
 				// in this case the modifID is 0, and both n-terminal (*) and c-terminal (**) fragments are generated
 
 				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) {
 					// if the start modification for k == 1 or k == 4 is nterminal, generate n-terminal ions (*)
 					if (!(((k == 1) || (k == 4)) && (!parameters->searchedmodifications[trotationsoflassorotations[j][k].startmodifID].nterminal))) {
-						generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, trotationsoflassorotations[j][k].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, j, splittingsites, parameters->searchedmodifications, lasso, &trotationsoflassorotations[j][k]);
+						generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, trotationsoflassorotations[j][k].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, j, splittingsites, parameters->searchedmodifications, lasso, &trotationsoflassorotations[j][k]);
 					}
 				}
 
@@ -1265,7 +1232,7 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal && ((k == 3) || (k == 5) /*|| ((k == 0) && (trotationsoflassorotations[j][k].endsWithBracket())) || ((k == 2) && (trotationsoflassorotations[j][k].startsWithBracket()))*/)) {
 					// if the end modification is cterminal, generate c-terminal ions (**)
 					if (parameters->searchedmodifications[trotationsoflassorotations[j][k].endmodifID].cterminal) {
-						generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, trotationsoflassorotations[j][k].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, j, splittingsites, parameters->searchedmodifications, lasso, &trotationsoflassorotations[j][k]);
+						generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, trotationsoflassorotations[j][k].bricks, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, j, splittingsites, parameters->searchedmodifications, lasso, &trotationsoflassorotations[j][k]);
 					}
 				}
 
@@ -1275,44 +1242,7 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 
 	}
 
-
-	// generate the precursor ion
-	// to do - performance
-	cBrick b;
-	b.setComposition(candidate.getComposition(), false);
-	vector<int> intcomposition;
-	b.explodeToIntComposition(intcomposition);
-
-	cPeak peak;
-	peak.mzratio = parameters->searchedmodifications[candidate.getMiddleModifID()].massdifference;
-	for (int i = 0; i < (int)intcomposition.size(); i++) {
-		peak.mzratio += bricksdatabasewithcombinations[intcomposition[i] - 1].getMass();
-	}
-	peak.seriesid = 0;
-
-	double tempratio = peak.mzratio;
-	for (int i = (int)cyclic_precursor_ion; i <= (int)cyclic_precursor_ion_co_loss_water_and_ammonia_loss; i++) {
-		for (int j = 1; j <= parameters->precursorcharge; j++) {
-			peak.mzratio = tempratio + parameters->fragmentdefinitions[(fragmentIonType)i].massdifference;
-			peak.iontype = (fragmentIonType)i;
-
-			if (writedescription) {
-				peak.description = to_string(j) + "+ " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
-			}
-
-			peak.mzratio = charge(peak.mzratio, j);
-			peak.charge = j;
-
-			if (theoreticalpeaks.size() > theoreticalpeaksrealsize) {
-				theoreticalpeaks[theoreticalpeaksrealsize] = peak;
-			}
-			else {
-				theoreticalpeaks.add(peak);
-			}
-			theoreticalpeaksrealsize++;
-
-		}
-	}
+	generatePrecursorIon(trotationsoflassorotations[0][0].bricks, bricksdatabasewithcombinations, theoreticalpeaksrealsize, writedescription);
 
 
 	// search the theoretical peaks in the experimental peak list
@@ -1329,7 +1259,7 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 		//series[i].resize(trotationsoflassorotations[i].size()); // to do - potential bug
 
 		for (int j = 0; j < (int)series[i].size(); j++) {
-			for (int k = 0; k < parameters->fragmentionsfortheoreticalspectra.size(); k++) {
+			for (int k = 0; k < (int)parameters->fragmentionsfortheoreticalspectra.size(); k++) {
 				series[i][j][parameters->fragmentionsfortheoreticalspectra[k]].resize(trotationsoflassorotations[i][0].bricks.size());
 			}
 		}
@@ -1375,7 +1305,7 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 				theoreticalpeaks[*it].matchdescription += ", measured mass " + to_string((long double)experimentalpeaks[i].mzratio) + " matched with " + to_string((long double)ppmError(experimentalpeaks[i].mzratio, theoreticalpeaks[*it].mzratio)) + " ppm error";
 			}
 
-			experimentalpeaks[i].iontype = selectHigherPriorityIonType(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
+			experimentalpeaks[i].iontype = selectHigherPriorityIonTypeCID(experimentalpeaks[i].iontype,theoreticalpeaks[*it].iontype);
 		}
 	}
 
@@ -1404,10 +1334,10 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 					tempseries.name += to_string(j + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[k]].name;
 					coveragebyseries += tempseries.name + "  ";
 					tempseries.series.clear();
-					for (int m = 0; m < series[i][j][parameters->fragmentionsfortheoreticalspectra[k]].size() - 1; m++) {
+					for (int m = 0; m < (int)series[i][j][parameters->fragmentionsfortheoreticalspectra[k]].size() - 1; m++) {
 						coveragebyseries += to_string(series[i][j][parameters->fragmentionsfortheoreticalspectra[k]][m]);
 						tempseries.series.push_back(series[i][j][parameters->fragmentionsfortheoreticalspectra[k]][m]);
-						if (m < series[i][j][parameters->fragmentionsfortheoreticalspectra[k]].size() - 2) {
+						if (m < (int)series[i][j][parameters->fragmentionsfortheoreticalspectra[k]].size() - 2) {
 							coveragebyseries += " ";
 						}
 					}
@@ -1420,7 +1350,7 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 	}
 
 
-	computeSomeStatistics(writedescription);
+	computeStatistics(writedescription);
 
 	return theoreticalpeaksrealsize;
 }
@@ -1429,7 +1359,6 @@ int cTheoreticalSpectrum::compareLasso(cPeaksList& sortedpeaklist, cBricksDataba
 int cTheoreticalSpectrum::compareLinearPolysaccharide(cPeaksList& sortedpeaklist, cBricksDatabase& bricksdatabasewithcombinations, bool writedescription, regex& sequencetag, regex& searchedsequence) {
 	cBrick brick;
 	vector<int> intcomposition;
-	vector<string> stringcomposition;
 	vector<splitSite> splittingsites;
 	int theoreticalpeaksrealsize = 0;
 
@@ -1447,8 +1376,7 @@ int cTheoreticalSpectrum::compareLinearPolysaccharide(cPeaksList& sortedpeaklist
 			}	
 		}
 	} 
-	catch (std::regex_error& e) {
-		e;
+	catch (regex_error& /*e*/) {
 		return -2;
 	}
 
@@ -1457,52 +1385,16 @@ int cTheoreticalSpectrum::compareLinearPolysaccharide(cPeaksList& sortedpeaklist
 	brick.setComposition(candidate.getComposition(), false);
 	brick.explodeToIntComposition(intcomposition);
 
-	if (writedescription) {
-		stringcomposition.clear();
-		brick.explodeToStringComposition(stringcomposition);
-	}
-
 	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
 		if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) {
-			generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linearpolysaccharide);
+			generateNTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linearpolysaccharide);
 		}
 		if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal) {
-			generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, stringcomposition, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linearpolysaccharide);
+			generateCTerminalFragmentIons(parameters->precursorcharge, theoreticalpeaksrealsize, intcomposition, parameters->fragmentionsfortheoreticalspectra[i], bricksdatabasewithcombinations, writedescription, 0, splittingsites, parameters->searchedmodifications, linearpolysaccharide);
 		}
 	}
 
-
-	// generate the precursor ion
-	cPeak peak;
-	peak.mzratio = parameters->searchedmodifications[candidate.getStartModifID()].massdifference + parameters->searchedmodifications[candidate.getEndModifID()].massdifference;
-	for (int i = 0; i < (int)intcomposition.size(); i++) {
-		peak.mzratio += bricksdatabasewithcombinations[intcomposition[i] - 1].getMass();
-	}
-	peak.seriesid = 0;
-
-	double tempratio = peak.mzratio;
-	for (int i = (int)precursor_ion; i <= (int)precursor_ion_co_loss_water_and_ammonia_loss; i++) {
-		for (int j = 1; j <= parameters->precursorcharge; j++) {
-			peak.mzratio = tempratio + parameters->fragmentdefinitions[(fragmentIonType)i].massdifference;
-			peak.iontype = (fragmentIonType)i;
-
-			if (writedescription) {
-				peak.description = to_string(j) + "+ " + parameters->fragmentdefinitions[(fragmentIonType)i].name + ":";
-			}
-
-			peak.mzratio = charge(peak.mzratio, j);
-			peak.charge = j;
-
-			if (theoreticalpeaks.size() > theoreticalpeaksrealsize) {
-				theoreticalpeaks[theoreticalpeaksrealsize] = peak;
-			}
-			else {
-				theoreticalpeaks.add(peak);
-			}
-			theoreticalpeaksrealsize++;
-
-		}
-	}
+	generatePrecursorIon(intcomposition, bricksdatabasewithcombinations, theoreticalpeaksrealsize, writedescription);
 
 
 	// search the theoretical peaks in the experimental peak list
@@ -1513,7 +1405,7 @@ int cTheoreticalSpectrum::compareLinearPolysaccharide(cPeaksList& sortedpeaklist
 
 	// coverage of series
 	map<fragmentIonType, vector<int> > series;
-	for (int i = 0; i < parameters->fragmentionsfortheoreticalspectra.size(); i++) {
+	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
 		series[parameters->fragmentionsfortheoreticalspectra[i]].resize(intcomposition.size());
 	}
 
@@ -1569,9 +1461,9 @@ int cTheoreticalSpectrum::compareLinearPolysaccharide(cPeaksList& sortedpeaklist
 		coveragebyseries = "Series of matched peaks:<br/>\n";
 		for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
 			coveragebyseries += parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name + "  ";
-			for (int j = 0; j < series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 1; j++) {
+			for (int j = 0; j < (int)series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 1; j++) {
 				coveragebyseries += to_string(series[parameters->fragmentionsfortheoreticalspectra[i]][j]);
-				if (j < series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 2) {
+				if (j < (int)series[parameters->fragmentionsfortheoreticalspectra[i]].size() - 2) {
 					coveragebyseries += " ";
 				}
 			}
@@ -1580,7 +1472,7 @@ int cTheoreticalSpectrum::compareLinearPolysaccharide(cPeaksList& sortedpeaklist
 
 	}
 
-	computeSomeStatistics(writedescription);
+	computeStatistics(writedescription);
 
 	return theoreticalpeaksrealsize;
 }
@@ -1592,7 +1484,7 @@ void cTheoreticalSpectrum::compareMSSpectrum(cParameters* parameters) {
 
 	cPeak peak;
 	cSummaryFormula formula;
-	theoreticalpeaks.resize((int)parameters->fragmentionsfortheoreticalspectra.size()*parameters->sequencedatabase.size()*parameters->precursorcharge);
+	theoreticalpeaks.resize((int)parameters->fragmentionsfortheoreticalspectra.size()*parameters->sequencedatabase.size()*abs(parameters->precursorcharge));
 	for (int i = 0; i < parameters->sequencedatabase.size(); i++) {
 		peak.clear();
 		formula.clear();
@@ -1600,7 +1492,8 @@ void cTheoreticalSpectrum::compareMSSpectrum(cParameters* parameters) {
 		formula.setFormula(parameters->sequencedatabase[i].getSummaryFormula());
 
 		for (int j = 0; j < (int)parameters->fragmentionsfortheoreticalspectra.size(); j++) {
-			for (int k = 0; k < parameters->precursorcharge; k++) {
+
+			for (int k = 0; k < abs(parameters->precursorcharge); k++) {
 				peak.mzratio = (double)parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].multiplier*formula.getMass() + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].massdifference;
 				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].positive) {
 					peak.mzratio += (double)k*Hplus;
@@ -1617,10 +1510,12 @@ void cTheoreticalSpectrum::compareMSSpectrum(cParameters* parameters) {
 				else {
 					peak.description += "-";
 				}
-				peak.description += " " + parameters->sequencedatabase[i].getName() + " (" + parameters->sequencedatabase[i].getSummaryFormula() + "): ";
+				//peak.description += " " + parameters->sequencedatabase[i].getName() + " (" + parameters->sequencedatabase[i].getSummaryFormula() + "): ";
+				peak.description += " " + parameters->sequencedatabase[i].getNameWithReferenceAsHTMLString() + " (" + parameters->sequencedatabase[i].getSummaryFormula() + "): ";
 
-				theoreticalpeaks[(i*(int)parameters->fragmentionsfortheoreticalspectra.size() + j)*parameters->precursorcharge + k] = peak;
+				theoreticalpeaks[(i*(int)parameters->fragmentionsfortheoreticalspectra.size() + j)*abs(parameters->precursorcharge) + k] = peak;
 			}
+
 		}
 	}
 	theoreticalpeaks.sortbyMass();
@@ -1635,12 +1530,12 @@ void cTheoreticalSpectrum::compareMSSpectrum(cParameters* parameters) {
 			if (experimentalpeaks[i].description.compare("") != 0) {
 				experimentalpeaks[i].description += ",";
 			}
-			experimentalpeaks[i].description += theoreticalpeaks[*it].description.substr(0,theoreticalpeaks[*it].description.find(':'));
+			experimentalpeaks[i].description += theoreticalpeaks[*it].description.substr(0,theoreticalpeaks[*it].description.rfind(':'));
 			theoreticalpeaks[*it].matchdescription += ", measured mass " + to_string((long double)experimentalpeaks[i].mzratio) + " matched with " + to_string((long double)ppmError(experimentalpeaks[i].mzratio, theoreticalpeaks[*it].mzratio)) + " ppm error";
 		}
 	}
 
-	computeSomeStatistics(true);
+	computeStatistics(true);
 }
 
 
@@ -1649,7 +1544,7 @@ int cTheoreticalSpectrum::getNumberOfPeaks() {
 }
 
 
-int cTheoreticalSpectrum::getNumberOfMatchedPeaks() {
+int cTheoreticalSpectrum::getNumberOfMatchedPeaks() const {
 	return experimentalpeaksmatched;
 }
 
@@ -1659,25 +1554,25 @@ int cTheoreticalSpectrum::getNumberOfScrambledPeaks() {
 }
 
 
-int cTheoreticalSpectrum::getNumberOfMatchedPeaks(fragmentIonType iontype) {
-	return matchedions[iontype];
+int cTheoreticalSpectrum::getNumberOfMatchedPeaks(fragmentIonType iontype) const {
+	return matchedions.at(iontype);
 }
 
 
-double cTheoreticalSpectrum::getRatioOfMatchedPeaks() {
-	return experimentalpeaksmatchedratio;
+int cTheoreticalSpectrum::getNumberOfMatchedPeaksYB() const {
+	return matchedions.at(y_ion)+matchedions.at(b_ion);
 }
 
 
-int cTheoreticalSpectrum::getNumberOfMatchedPeaksYB() {
-	return matchedions[y_ion]+matchedions[b_ion];
+double cTheoreticalSpectrum::getRatioOfMatchedPeaks() {
+	return experimentalpeaksmatchedratio;
 }
 
 
 void cTheoreticalSpectrum::printMatch(ofstream& os, peptideType peptidetype) {
 	vector<string> rotations;
 	
-	os << endl << "Peptide: " << realpeptidename << endl;
+	os << endl << "Peptide: " << candidate.getRealPeptideName() << endl;
 
 	switch (peptidetype)
 	{
@@ -1728,48 +1623,48 @@ void cTheoreticalSpectrum::printMatch(ofstream& os, peptideType peptidetype) {
 		os << "Matched y-ions: " << matchedions[y_ion] << endl;
 		os << "Matched b-ions: " << matchedions[b_ion] << endl;
 		os << "Matched a-ions: " << matchedions[a_ion] << endl;
-		os << "Matched y*-ions: " << matchedions[y_ion_water_loss] << endl;
-		os << "Matched b*-ions: " << matchedions[b_ion_water_loss] << endl;
-		os << "Matched a*-ions: " << matchedions[a_ion_water_loss] << endl;
-		os << "Matched yx-ions: " << matchedions[y_ion_ammonia_loss] << endl;
-		os << "Matched bx-ions: " << matchedions[b_ion_ammonia_loss] << endl;
-		os << "Matched ax-ions: " << matchedions[a_ion_ammonia_loss] << endl;
+		os << "Matched y*-ions: " << matchedions[y_ion_dehydrated] << endl;
+		os << "Matched b*-ions: " << matchedions[b_ion_dehydrated] << endl;
+		os << "Matched a*-ions: " << matchedions[a_ion_dehydrated] << endl;
+		os << "Matched yx-ions: " << matchedions[y_ion_deamidated] << endl;
+		os << "Matched bx-ions: " << matchedions[b_ion_deamidated] << endl;
+		os << "Matched ax-ions: " << matchedions[a_ion_deamidated] << endl;
 		break;
 	case cyclic:
 		os << "Matched b-ions: " << matchedions[b_ion] << endl;
 		os << "Matched a-ions: " << matchedions[a_ion] << endl;
-		os << "Matched b*-ions: " << matchedions[b_ion_water_loss] << endl;
-		os << "Matched a*-ions: " << matchedions[a_ion_water_loss] << endl;
-		os << "Matched bx-ions: " << matchedions[b_ion_ammonia_loss] << endl;
-		os << "Matched ax-ions: " << matchedions[a_ion_ammonia_loss] << endl;
-		os << "Matched b*x-ions: " << matchedions[b_ion_water_and_ammonia_loss] << endl;
-		os << "Matched a*x-ions: " << matchedions[a_ion_water_and_ammonia_loss] << endl;
-		os << "Matched b-ions and b*-ions: " << matchedions[b_ion] + matchedions[b_ion_water_loss] << endl;
-		os << "Matched b-ions and bx-ions: " << matchedions[b_ion] + matchedions[b_ion_ammonia_loss] << endl << endl;
+		os << "Matched b*-ions: " << matchedions[b_ion_dehydrated] << endl;
+		os << "Matched a*-ions: " << matchedions[a_ion_dehydrated] << endl;
+		os << "Matched bx-ions: " << matchedions[b_ion_deamidated] << endl;
+		os << "Matched ax-ions: " << matchedions[a_ion_deamidated] << endl;
+		os << "Matched b*x-ions: " << matchedions[b_ion_dehydrated_and_deamidated] << endl;
+		os << "Matched a*x-ions: " << matchedions[a_ion_dehydrated_and_deamidated] << endl;
+		os << "Matched b-ions and b*-ions: " << matchedions[b_ion] + matchedions[b_ion_dehydrated] << endl;
+		os << "Matched b-ions and bx-ions: " << matchedions[b_ion] + matchedions[b_ion_deamidated] << endl << endl;
 		break;
 	case branched:
 		os << "Matched y-ions and b-ions: " << matchedions[y_ion] + matchedions[b_ion] << endl;
 		os << "Matched y-ions: " << matchedions[y_ion] << endl;
 		os << "Matched b-ions: " << matchedions[b_ion] << endl;
 		os << "Matched a-ions: " << matchedions[a_ion] << endl;
-		os << "Matched y*-ions: " << matchedions[y_ion_water_loss] << endl;
-		os << "Matched b*-ions: " << matchedions[b_ion_water_loss] << endl;
-		os << "Matched a*-ions: " << matchedions[a_ion_water_loss] << endl;
-		os << "Matched yx-ions: " << matchedions[y_ion_ammonia_loss] << endl;
-		os << "Matched bx-ions: " << matchedions[b_ion_ammonia_loss] << endl;
-		os << "Matched ax-ions: " << matchedions[a_ion_ammonia_loss] << endl;
+		os << "Matched y*-ions: " << matchedions[y_ion_dehydrated] << endl;
+		os << "Matched b*-ions: " << matchedions[b_ion_dehydrated] << endl;
+		os << "Matched a*-ions: " << matchedions[a_ion_dehydrated] << endl;
+		os << "Matched yx-ions: " << matchedions[y_ion_deamidated] << endl;
+		os << "Matched bx-ions: " << matchedions[b_ion_deamidated] << endl;
+		os << "Matched ax-ions: " << matchedions[a_ion_deamidated] << endl;
 		break;
 	case lasso:
 		os << "Matched y-ions and b-ions: " << matchedions[y_ion] + matchedions[b_ion] << endl;
 		os << "Matched y-ions: " << matchedions[y_ion] << endl;
 		os << "Matched b-ions: " << matchedions[b_ion] << endl;
 		os << "Matched a-ions: " << matchedions[a_ion] << endl;
-		os << "Matched y*-ions: " << matchedions[y_ion_water_loss] << endl;
-		os << "Matched b*-ions: " << matchedions[b_ion_water_loss] << endl;
-		os << "Matched a*-ions: " << matchedions[a_ion_water_loss] << endl;
-		os << "Matched yx-ions: " << matchedions[y_ion_ammonia_loss] << endl;
-		os << "Matched bx-ions: " << matchedions[b_ion_ammonia_loss] << endl;
-		os << "Matched ax-ions: " << matchedions[a_ion_ammonia_loss] << endl;
+		os << "Matched y*-ions: " << matchedions[y_ion_dehydrated] << endl;
+		os << "Matched b*-ions: " << matchedions[b_ion_dehydrated] << endl;
+		os << "Matched a*-ions: " << matchedions[a_ion_dehydrated] << endl;
+		os << "Matched yx-ions: " << matchedions[y_ion_deamidated] << endl;
+		os << "Matched bx-ions: " << matchedions[b_ion_deamidated] << endl;
+		os << "Matched ax-ions: " << matchedions[a_ion_deamidated] << endl;
 		break;
 	case linearpolysaccharide:
 		break;
@@ -1791,7 +1686,7 @@ void cTheoreticalSpectrum::printMatch(ofstream& os, peptideType peptidetype) {
 }
 
 
-void cTheoreticalSpectrum::generateNTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<string>& stringcomposition, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation) {
+void cTheoreticalSpectrum::generateNTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation) {
 	cPeak peak;
 	double tempratio;
 	string tempdescription;
@@ -1889,12 +1784,17 @@ void cTheoreticalSpectrum::generateNTerminalFragmentIons(int maxcharge, int& pea
 			if (writedescription) {
 				tempdescription = peak.description;
 			}
-			for (int j = 1; j <= maxcharge; j++) {
+			for (int j = 1; j <= abs(maxcharge); j++) {
 
-				peak.mzratio = charge(tempratio, j);
-				peak.charge = j;
+				peak.mzratio = charge(uncharge(tempratio, 1), (parameters->precursorcharge > 0)?j:-j);
+				peak.charge = (parameters->precursorcharge > 0)?j:-j;
 				if (writedescription) {
-					peak.description = to_string(j) + "+ " + tempdescription;
+					if (parameters->precursorcharge > 0) {
+						peak.description = to_string(j) + "+ " + tempdescription;
+					}
+					else {
+						peak.description = to_string(j) + "- " + tempdescription;
+					}
 				}
 
 				if (theoreticalpeaks.size() > peaklistrealsize) {
@@ -1918,7 +1818,7 @@ void cTheoreticalSpectrum::generateNTerminalFragmentIons(int maxcharge, int& pea
 }
 
 
-void cTheoreticalSpectrum::generateCTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<string>& stringcomposition, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation) {
+void cTheoreticalSpectrum::generateCTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation) {
 	cPeak peak;
 	double tempratio;
 	string tempdescription;
@@ -2016,12 +1916,17 @@ void cTheoreticalSpectrum::generateCTerminalFragmentIons(int maxcharge, int& pea
 			if (writedescription) {
 				tempdescription = peak.description;
 			}
-			for (int j = 1; j <= maxcharge; j++) {
+			for (int j = 1; j <= abs(maxcharge); j++) {
 
-				peak.mzratio = charge(tempratio, j);
-				peak.charge = j;
+				peak.mzratio = charge(uncharge(tempratio, 1), (parameters->precursorcharge > 0)?j:-j);
+				peak.charge = (parameters->precursorcharge > 0)?j:-j;
 				if (writedescription) {
-					peak.description = to_string(j) + "+ " + tempdescription;
+					if (parameters->precursorcharge > 0) {
+						peak.description = to_string(j) + "+ " + tempdescription;
+					}
+					else {
+						peak.description = to_string(j) + "- " + tempdescription;
+					}
 				}
 
 				if (theoreticalpeaks.size() > peaklistrealsize) {
@@ -2060,61 +1965,11 @@ double cTheoreticalSpectrum::getPrecursorMass(cBricksDatabase& brickdatabasewith
 }
 
 
-double cTheoreticalSpectrum::getWeightedIntensityScore() {
+double cTheoreticalSpectrum::getWeightedIntensityScore() const {
 	return intensityweightedscore;
 }
 
 
-void cTheoreticalSpectrum::setRealPeptideName(cBricksDatabase& bricksdatabase, peptideType peptidetype) {
-	switch (peptidetype)
-	{
-	case linear:
-	case cyclic:
-	case linearpolysaccharide:
-		realpeptidename = bricksdatabase.getRealName(candidate.getComposition());
-		break;
-	case branched:
-	case lasso:
-		realpeptidename = candidate.getRealNameTComposition(bricksdatabase);
-		break;
-	case other:
-	default:
-		realpeptidename = "";
-		break;
-	}
-}
-
-
-void cTheoreticalSpectrum::setAcronymPeptideNameWithHTMLReferences(cBricksDatabase& bricksdatabase, peptideType peptidetype) {
-	switch (peptidetype)
-	{
-	case linear:
-	case cyclic:
-	case linearpolysaccharide:
-		acronympeptidename = bricksdatabase.getAcronymName(candidate.getComposition(), true);
-		break;
-	case branched:
-	case lasso:
-		acronympeptidename = candidate.getAcronymsTComposition(bricksdatabase);
-		break;
-	case other:
-	default:
-		acronympeptidename = "";
-		break;
-	}
-}
-
-
-string& cTheoreticalSpectrum::getRealPeptideName() {
-	return realpeptidename;
-}
-
-
-string& cTheoreticalSpectrum::getAcronymPeptideNameWithHTMLReferences() {
-	return acronympeptidename;
-}
-
-
 cPeak& cTheoreticalSpectrum::operator[](int position) {
 	return theoreticalpeaks[position];
 }
@@ -2155,7 +2010,7 @@ int cTheoreticalSpectrum::getReverseValidPosition() {
 }
 
 
-int cTheoreticalSpectrum::getNumberOfMatchedBricks() {
+int cTheoreticalSpectrum::getNumberOfMatchedBricks() const {
 	return maskscore;
 }
 
@@ -2165,115 +2020,6 @@ vector<visualSeries>& cTheoreticalSpectrum::getVisualCoverage() {
 }
 
 
-void cTheoreticalSpectrum::setAcronyms(cBricksDatabase& bricksdatabase) {
-	vector<int> bricks;
-	cBrick b;
-	b.clear();
-	b.setComposition(candidate.getComposition(), false);
-	b.explodeToIntComposition(bricks);
-
-	acronyms.clear();
-	for (int i = 0; i < (int)bricks.size(); i++) {
-		acronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
-	}
-}
-
-
-void cTheoreticalSpectrum::setBackboneAcronyms(cBricksDatabase& bricksdatabase) {
-	vector<int> bricks;
-	cBrick b;
-	b.clear();
-	b.setComposition(candidate.getComposition(), false);
-	b.explodeToIntComposition(bricks);
-
-	backboneacronyms.clear();
-	for (int i = 0; i < (int)bricks.size(); i++) {
-		if ((candidate.getBranchStart() >= 0) && (candidate.getBranchEnd() >= 0) && ((i <= candidate.getBranchStart()) || (i > candidate.getBranchEnd()))) {
-			backboneacronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
-		}
-	}
-}
-
-
-void cTheoreticalSpectrum::setBranchAcronyms(cBricksDatabase& bricksdatabase) {
-	vector<int> bricks;
-	cBrick b;
-	b.clear();
-	b.setComposition(candidate.getComposition(), false);
-	b.explodeToIntComposition(bricks);
-
-	branchacronyms.clear();
-	for (int i = 0; i < (int)bricks.size(); i++) {
-		if ((candidate.getBranchStart() >= 0) && (candidate.getBranchEnd() >= 0) && (i > candidate.getBranchStart()) && (i <= candidate.getBranchEnd())) {
-			branchacronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
-		}
-	}
-}
-
-
-vector<string>& cTheoreticalSpectrum::getAcronyms() {
-	return acronyms;
-}
-
-
-vector<string>& cTheoreticalSpectrum::getBackboneAcronyms() {
-	return backboneacronyms;
-}
-
-
-vector<string>& cTheoreticalSpectrum::getBranchAcronyms() {
-	return branchacronyms;
-}
-
-
-void cTheoreticalSpectrum::setPath(cDeNovoGraph& graph) {
-	cDeNovoGraphNode* currentnode;
-	cDeNovoGraphNode* targetnode;
-	cEdge* currentedge;
-	path = "";
-	for (int i = 0; i < (int)candidate.getPath().size(); i++) {
-		currentnode = &graph[candidate.getPath()[i].nodeid];
-		currentedge = &((*currentnode)[candidate.getPath()[i].edgeid]);
-		targetnode = &graph[currentedge->targetnode];
-
-		path += to_string(currentnode->getMZRatio());
-		path += " -> ";
-		path += to_string(targetnode->getMZRatio());
-		path += " using brick(s): ";
-		if (currentedge->composition.compare("0") == 0) {
-			path += "none";
-		}
-		else {
-			path += graph.getBrickDatabaseWithCombinations()->getAcronymName(currentedge->composition, true);
-		}
-
-		path += " (mass difference: " + to_string(currentedge->massdifference) + ", ";
-		path += "source intensity: " + to_string(currentnode->getIntensity()) + ", ";
-		path += "target intensity: " + to_string(targetnode->getIntensity()) + ", ";
-		path += "ppm error: " + to_string(currentedge->ppmerror) + ", ";
-		path += "source charge: " + to_string(currentedge->sourcecharge) + ", ";
-		path += "target charge: " + to_string(currentedge->targetcharge);
-		if ((parameters->peptidetype == branched) || (parameters->peptidetype == lasso)) {
-			if (currentedge->middlemodifID > 0) {
-				path += ", branch modification: " + parameters->searchedmodifications[currentedge->middlemodifID].name;
-			}
-		}
-		if (currentedge->endmodifID > 0) {
-			path += ", terminal modification: " + parameters->searchedmodifications[currentedge->endmodifID].name;
-		}
-		//path += currentedge->printSourceAnnotation(fragmentdefinitions);
-		//path += "->";
-		//path += currentedge->printTargetAnnotation(fragmentdefinitions);
-		path += ")<br/>";
-	}	
-}
-
-
-string& cTheoreticalSpectrum::getPath() {
-	return path;
-}
-
-
 int cTheoreticalSpectrum::getNumberOfCompletedSeries() {
 	return seriescompleted;
 }
@@ -2325,13 +2071,6 @@ void cTheoreticalSpectrum::store(ofstream& os) {
 	os.write((char *)&validposition, sizeof(int));
 	os.write((char *)&reversevalidposition, sizeof(int));
 	os.write((char *)&seriescompleted, sizeof(int));
-
-	storeString(realpeptidename, os);
-	storeString(acronympeptidename, os);
-	storeStringVector(acronyms, os);
-	storeStringVector(backboneacronyms, os);
-	storeStringVector(branchacronyms, os);
-	storeString(path, os);
 }
 
 
@@ -2376,12 +2115,5 @@ void cTheoreticalSpectrum::load(ifstream& is) {
 	is.read((char *)&validposition, sizeof(int));
 	is.read((char *)&reversevalidposition, sizeof(int));
 	is.read((char *)&seriescompleted, sizeof(int));
-
-	loadString(realpeptidename, is);
-	loadString(acronympeptidename, is);
-	loadStringVector(acronyms, is);
-	loadStringVector(backboneacronyms, is);
-	loadStringVector(branchacronyms, is);
-	loadString(path, is);
 }
 
diff --git a/CycloBranch/core/cTheoreticalSpectrum.h b/CycloBranch/core/cTheoreticalSpectrum.h
index 3c3100f..3f69e6e 100644
--- a/CycloBranch/core/cTheoreticalSpectrum.h
+++ b/CycloBranch/core/cTheoreticalSpectrum.h
@@ -11,7 +11,6 @@
 #include <set>
 #include <string>
 #include <map>
-#include <regex>
 #include <QMetaType>
 
 #include "core/cParameters.h"
@@ -113,30 +112,26 @@ class cTheoreticalSpectrum {
 	int reversevalidposition;
 	int seriescompleted;
 
-	string realpeptidename;
-	string acronympeptidename;
-	vector<string> acronyms;
-	vector<string> backboneacronyms;
-	vector<string> branchacronyms;
-	string path;
-
 	// remove false hits, i.e., b-H2O without existing b-ion
 	void clearFalseHits(map<fragmentIonType, vector<int> >& series, vector<fragmentIonType>& fragmentions);
 
 	// search for matches of experimental and theoretical peaks
 	void searchForPeakPairs(cPeaksList& theoreticalpeaks, int theoreticalpeaksrealsize, cPeaksList& experimentalpeaks, vector<set<int> >& experimentalpeakmatches, double fragmentmasserrortolerance);
 
-	// compute some scores, etc.
-	void computeSomeStatistics(bool writedescription);
+	// compute additional scores
+	void computeStatistics(bool writedescription);
+
+	// generate precursor ion and its variants
+	void generatePrecursorIon(vector<int>& intcomposition, cBricksDatabase& bricksdatabasewithcombinations, int& theoreticalpeaksrealsize, bool writedescription);
 
 	// generate scrambled sequences
 	void generateScrambledIons(cBricksDatabase& bricksdatabase, bool writedescription, int& theoreticalpeaksrealsize);
 
-	// normalize scrambled sequences
-	void normalizeScrambledSequences(unordered_set<string>& scrambledsequences);
+	// select and normalize scrambled sequences
+	void selectAndNormalizeScrambledSequences(unordered_set<string>& scrambledsequences);
 
 	// select a proper fragment ion type for an experimental peak when masses of more theoretical fragment ions collide
-	fragmentIonType selectHigherPriorityIonType(fragmentIonType experimentalpeakiontype, fragmentIonType theoreticalpeakiontype);
+	fragmentIonType selectHigherPriorityIonTypeCID(fragmentIonType experimentalpeakiontype, fragmentIonType theoreticalpeakiontype);
 
 public:
 
@@ -166,14 +161,14 @@ class cTheoreticalSpectrum {
 		\brief Get the peptide spectrum candidate.
 		\retval cCandidate reference to the peptide sequence candidate
 	*/ 
-	cCandidate& cTheoreticalSpectrum::getCandidate();
+	cCandidate& getCandidate();
 	
 
 	/**
 		\brief Set a peptide spectrum candidate.
 		\param candidate reference to the peptide sequence candidate
 	*/ 
-	void cTheoreticalSpectrum::setCandidate(cCandidate& candidate);
+	void setCandidate(cCandidate& candidate);
 
 
 	/**
@@ -220,7 +215,7 @@ class cTheoreticalSpectrum {
 
 
 	/**
-		\brief Compare the theoretical spectrum of a lasso peptide with an experimental spectrum.
+		\brief Compare the theoretical spectrum of a branch-cyclic peptide with an experimental spectrum.
 		\param sortedpeaklist reference to a peak list of an experimental spectrum
 		\param bricksdatabasewithcombinations reference to a database of bricks with combinations of bricks
 		\param writedescription if true then string descriptions of peaks are filled
@@ -254,7 +249,7 @@ class cTheoreticalSpectrum {
 		\brief Get the number of matched peaks between an experimental and a theoretical spectrum.
 		\retval int number of matched peaks
 	*/ 
-	int getNumberOfMatchedPeaks();
+	int getNumberOfMatchedPeaks() const;
 
 
 	/**
@@ -269,14 +264,14 @@ class cTheoreticalSpectrum {
 		\param iontype a fragment ion type
 		\retval int number of matched peaks
 	*/ 
-	int getNumberOfMatchedPeaks(fragmentIonType iontype);
+	int getNumberOfMatchedPeaks(fragmentIonType iontype) const;
 
 
 	/**
 		\brief Get the number of matched Y and B ions between an experimental and a theoretical spectrum.
 		\retval int number of matched peaks
 	*/ 
-	int getNumberOfMatchedPeaksYB();
+	int getNumberOfMatchedPeaksYB() const;
 
 
 	/**
@@ -298,7 +293,6 @@ class cTheoreticalSpectrum {
 		\brief Generate a N-terminal fragment ion series.
 		\param maxcharge a charge of precursor ion
 		\param peaklistrealsize real size of the peak list
-		\param stringcomposition reference to a vector of ids of bricks as strings
 		\param intcomposition reference to a vector of ids of bricks as integers
 		\param fragmentiontype fragment ion type which will be generated
 		\param bricksdatabase reference to a database of building blocks
@@ -309,14 +303,13 @@ class cTheoreticalSpectrum {
 		\param peptidetype the type of searched peptide
 		\param trotation a pointer to a T-permutation of a branched peptide
 	*/ 
-	void generateNTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<string>& stringcomposition, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation = 0);
+	void generateNTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation = 0);
 	
 
 	/**
 		\brief Generate a C-terminal fragment ion series.
 		\param maxcharge a charge of precursor ion
 		\param peaklistrealsize real size of the peak list
-		\param stringcomposition reference to a vector of ids of bricks as strings
 		\param intcomposition reference to a vector of ids of bricks as integers
 		\param fragmentiontype fragment ion type which will be generated
 		\param bricksdatabase reference to a database of building blocks
@@ -327,7 +320,7 @@ class cTheoreticalSpectrum {
 		\param peptidetype the type of searched peptide
 		\param trotation a pointer to a T-permutation of a branched peptide
 	*/ 
-	void generateCTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<string>& stringcomposition, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation = 0);
+	void generateCTerminalFragmentIons(int maxcharge, int& peaklistrealsize, vector<int>& intcomposition, fragmentIonType fragmentiontype, cBricksDatabase& bricksdatabase, bool writedescription, int rotationid, vector<splitSite>& splittingsites, vector<fragmentDescription>& searchedmodifications, peptideType peptidetype, TRotationInfo* trotation = 0);
 
 
 	/**
@@ -356,37 +349,7 @@ class cTheoreticalSpectrum {
 		\brief Get the sum of relative intensities of matched peaks.
 		\retval double sum of relative intensities of matched peaks
 	*/ 
-	double getWeightedIntensityScore();
-
-
-	/**
-		\brief Set a real peptide name.
-		\param bricksdatabase the database of building blocks
-		\param peptidetype the type of peptide
-	*/ 
-	void setRealPeptideName(cBricksDatabase& bricksdatabase, peptideType peptidetype);
-
-
-	/**
-		\brief Set an acronym peptide name.
-		\param bricksdatabase the database of building blocks
-		\param peptidetype the type of peptide
-	*/ 
-	void setAcronymPeptideNameWithHTMLReferences(cBricksDatabase& bricksdatabase, peptideType peptidetype);
-
-
-	/**
-		\brief Get a real peptide name.
-		\retval string reference to the real peptide name
-	*/ 
-	string& getRealPeptideName();
-
-
-	/**
-		\brief Get an acronym peptide name.
-		\retval string reference to the acronym peptide name
-	*/ 
-	string& getAcronymPeptideNameWithHTMLReferences();
+	double getWeightedIntensityScore() const;
 
 
 	/**
@@ -450,7 +413,7 @@ class cTheoreticalSpectrum {
 		\brief Get the number of matched bricks.
 		\retval int number of matched bricks
 	*/ 
-	int getNumberOfMatchedBricks();
+	int getNumberOfMatchedBricks() const;
 
 
 	/**
@@ -460,62 +423,6 @@ class cTheoreticalSpectrum {
 	vector<visualSeries>& getVisualCoverage();
 
 
-	/**
-		\brief Set a vector of acronyms corresponding to a peptide sequence candidate.
-		\param bricksdatabase a database of building blocks
-	*/ 
-	void setAcronyms(cBricksDatabase& bricksdatabase);
-
-
-	/**
-		\brief Set a vector of acronyms corresponding to a backbone of a peptide sequence candidate.
-		\param bricksdatabase a database of building blocks
-	*/ 
-	void setBackboneAcronyms(cBricksDatabase& bricksdatabase);
-
-
-	/**
-		\brief Set a vector of acronyms corresponding to a branch of a peptide sequence candidate.
-		\param bricksdatabase a database of building blocks
-	*/ 
-	void setBranchAcronyms(cBricksDatabase& bricksdatabase);
-
-
-	/**
-		\brief Get a vector of acronyms corresponding to a peptide sequence candidate.
-		\retval vector<string> a vector of acronyms
-	*/ 
-	vector<string>& getAcronyms();
-
-
-	/**
-		\brief Get a vector of acronyms corresponding to a backbone of a peptide sequence candidate.
-		\retval vector<string> a vector of acronyms
-	*/ 
-	vector<string>& getBackboneAcronyms();
-
-
-	/**
-		\brief Get a vector of acronyms corresponding to a branch of a peptide sequence candidate.
-		\retval vector<string> a vector of acronyms
-	*/ 
-	vector<string>& getBranchAcronyms();
-
-
-	/**
-		\brief Set a path in the de novo graph corresponding to the spectrum.
-		\param graph reference to the de novo graph
-	*/ 
-	void setPath(cDeNovoGraph& graph);
-
-
-	/**
-		\brief Get a path in the de novo graph corresponding to the spectrum.
-		\retval string reference to a path corresponding to the spectrum
-	*/ 
-	string& getPath();
-
-
 	/**
 		\brief Get a number of series which identify the peptide.
 		\retval int number of completed series
@@ -553,11 +460,5 @@ class cTheoreticalSpectrum {
 };
 
 
-/**
-	\brief Register cTheoreticalSpectrum by Qt.
-*/
-Q_DECLARE_METATYPE(cTheoreticalSpectrum);
-
-
 #endif
 
diff --git a/CycloBranch/core/cTheoreticalSpectrumList.cpp b/CycloBranch/core/cTheoreticalSpectrumList.cpp
index ad3a3ea..1addb34 100644
--- a/CycloBranch/core/cTheoreticalSpectrumList.cpp
+++ b/CycloBranch/core/cTheoreticalSpectrumList.cpp
@@ -48,6 +48,11 @@ void cTheoreticalSpectrumList::fixRegularExpression(string& s) {
 
 
 cTheoreticalSpectrumList::cTheoreticalSpectrumList() {
+	clear();
+}
+
+
+void cTheoreticalSpectrumList::clear() {
 	theoreticalspectra.clear();
 	os = 0;
 	parameters = 0;
@@ -55,6 +60,7 @@ cTheoreticalSpectrumList::cTheoreticalSpectrumList() {
 
 	worstScore = 0;
 	worstNumberOfMatchedPeaks = 0;
+	refreshlimit = 0;
 }
 
 
@@ -132,7 +138,7 @@ int cTheoreticalSpectrumList::parallelCompareAndStore(cCandidateSet& candidates,
 	try {
 		rxsequencetag = stmp;
 	}
-	catch (const std::regex_error& e) {
+	catch (regex_error& e) {
 		*os << endl << endl << "Error: Bad Regular Expression in Peptide Sequence Tag." << endl << e.what() << endl;
 		return -1;
 	}
@@ -154,7 +160,7 @@ int cTheoreticalSpectrumList::parallelCompareAndStore(cCandidateSet& candidates,
 	try {
 		rxsearchedsequence = stmp;
 	}
-	catch (const std::regex_error& e) {
+	catch (regex_error& e) {
 		*os << endl << endl << "Error: Bad Regular Expression in Searched Peptide Sequence." << endl << e.what() << endl;
 		return -1;
 	}
@@ -273,15 +279,15 @@ int cTheoreticalSpectrumList::parallelCompareAndStore(cCandidateSet& candidates,
 	// sort peaks in theoretical spectra by mass and set real names of peptides
 	for (int i = 0; i < (int)theoreticalspectra.size(); i++) {
 		theoreticalspectra[i].sortByMass();
-		theoreticalspectra[i].setRealPeptideName(*bricksdb, parameters->peptidetype);
-		theoreticalspectra[i].setAcronymPeptideNameWithHTMLReferences(*bricksdb, parameters->peptidetype);
-		theoreticalspectra[i].setAcronyms(*bricksdb);
+		theoreticalspectra[i].getCandidate().setRealPeptideName(*bricksdb, parameters->peptidetype);
+		theoreticalspectra[i].getCandidate().setAcronymPeptideNameWithHTMLReferences(*bricksdb, parameters->peptidetype);
+		theoreticalspectra[i].getCandidate().setAcronyms(*bricksdb);
 		if ((parameters->peptidetype == branched) || (parameters->peptidetype == lasso)) {
-			theoreticalspectra[i].setBackboneAcronyms(*bricksdb);
-			theoreticalspectra[i].setBranchAcronyms(*bricksdb);
+			theoreticalspectra[i].getCandidate().setBackboneAcronyms(*bricksdb);
+			theoreticalspectra[i].getCandidate().setBranchAcronyms(*bricksdb);
 		}
 		if (parameters->mode == denovoengine) {
-			theoreticalspectra[i].setPath(*graph);
+			theoreticalspectra[i].getCandidate().setPath(*graph, parameters);
 		}
 		// parameters must not be used by viewer, they are not stored/loaded
 		theoreticalspectra[i].setParameters(0);
@@ -316,13 +322,13 @@ void cTheoreticalSpectrumList::addButDoNotFitSize(cTheoreticalSpectrum& theoreti
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBandAllIonsDesc);
 				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion);
 				break;
-			case b_ions_and_b_water_loss_ions:
+			case b_ions_and_b_dehydrated_ions:
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBBwaterLossAndAllIonsDesc);
-				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_water_loss);
+				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_dehydrated);
 				break;
-			case b_ions_and_b_ammonia_loss_ions:
+			case b_ions_and_b_deamidated_ions:
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBBammoniaLossAndAllIonsDesc);
-				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_ammonia_loss);
+				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_deamidated);
 				break;
 			case y_ions_and_b_ions:
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareYBandAllIonsDesc);
@@ -358,14 +364,14 @@ void cTheoreticalSpectrumList::addButDoNotFitSize(cTheoreticalSpectrum& theoreti
 				theoreticalspectra.back().resizePeakList(theoreticalpeaksrealsize);
 			}
 			break;
-		case b_ions_and_b_water_loss_ions:
-			if ((worstScore < theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_water_loss)) || ((worstScore == theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_water_loss)) && (worstNumberOfMatchedPeaks < theoreticalspectrum.getNumberOfMatchedPeaks()))) {
+		case b_ions_and_b_dehydrated_ions:
+			if ((worstScore < theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_dehydrated)) || ((worstScore == theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_dehydrated)) && (worstNumberOfMatchedPeaks < theoreticalspectrum.getNumberOfMatchedPeaks()))) {
 				theoreticalspectra.push_back(theoreticalspectrum);
 				theoreticalspectra.back().resizePeakList(theoreticalpeaksrealsize);
 			}
 			break;
-		case b_ions_and_b_ammonia_loss_ions:
-			if ((worstScore < theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_ammonia_loss)) || ((worstScore == theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_ammonia_loss)) && (worstNumberOfMatchedPeaks < theoreticalspectrum.getNumberOfMatchedPeaks()))) {
+		case b_ions_and_b_deamidated_ions:
+			if ((worstScore < theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_deamidated)) || ((worstScore == theoreticalspectrum.getNumberOfMatchedPeaks(b_ion) + theoreticalspectrum.getNumberOfMatchedPeaks(b_ion_deamidated)) && (worstNumberOfMatchedPeaks < theoreticalspectrum.getNumberOfMatchedPeaks()))) {
 				theoreticalspectra.push_back(theoreticalspectrum);
 				theoreticalspectra.back().resizePeakList(theoreticalpeaksrealsize);
 			}
@@ -410,15 +416,15 @@ void cTheoreticalSpectrumList::addButDoNotFitSize(cTheoreticalSpectrum& theoreti
 				theoreticalspectra.resize(parameters->hitsreported);
 				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion);
 				break;
-			case b_ions_and_b_water_loss_ions:
+			case b_ions_and_b_dehydrated_ions:
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBBwaterLossAndAllIonsDesc);
 				theoreticalspectra.resize(parameters->hitsreported);
-				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_water_loss);
+				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_dehydrated);
 				break;
-			case b_ions_and_b_ammonia_loss_ions:
+			case b_ions_and_b_deamidated_ions:
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBBammoniaLossAndAllIonsDesc);
 				theoreticalspectra.resize(parameters->hitsreported);
-				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_ammonia_loss);
+				worstScore = theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion) + theoreticalspectra.back().getNumberOfMatchedPeaks(b_ion_deamidated);
 				break;
 			case y_ions_and_b_ions:
 				sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareYBandAllIonsDesc);
@@ -461,10 +467,10 @@ void cTheoreticalSpectrumList::sortAndFitSize() {
 	case b_ions:
 		sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBandAllIonsDesc);
 		break;
-	case b_ions_and_b_water_loss_ions:
+	case b_ions_and_b_dehydrated_ions:
 		sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBBwaterLossAndAllIonsDesc);
 		break;
-	case b_ions_and_b_ammonia_loss_ions:
+	case b_ions_and_b_deamidated_ions:
 		sort(theoreticalspectra.begin(), theoreticalspectra.end(), compareBBammoniaLossAndAllIonsDesc);
 		break;
 	case y_ions_and_b_ions:
diff --git a/CycloBranch/core/cTheoreticalSpectrumList.h b/CycloBranch/core/cTheoreticalSpectrumList.h
index 5d881a0..f0129ab 100644
--- a/CycloBranch/core/cTheoreticalSpectrumList.h
+++ b/CycloBranch/core/cTheoreticalSpectrumList.h
@@ -46,6 +46,12 @@ class cTheoreticalSpectrumList {
 	cTheoreticalSpectrumList();
 
 
+	/**
+		\brief Clear the class.
+	*/ 
+	void clear();
+
+
 	/**
 		\brief Initialize the list.
 		\param os reference to the main thread of the application
diff --git a/CycloBranch/core/utilities.cpp b/CycloBranch/core/utilities.cpp
index 9bf5d8f..f8868c3 100644
--- a/CycloBranch/core/utilities.cpp
+++ b/CycloBranch/core/utilities.cpp
@@ -1,5 +1,12 @@
 #include "core/utilities.h"
 
+#include "core/cBrick.h"
+
+
+QString appname = "CycloBranch";
+QString appversion = "v. 1.0.1106 (64-bit)";
+QString linuxinstalldir = "/usr/share/cyclobranch/";
+
 
 void storeString(string& s, ofstream& os) {
 	int size = (int)s.size();
@@ -34,3 +41,173 @@ void loadStringVector(vector<string>& v, ifstream& is) {
 	}
 }
 
+
+bool isWhiteSpaceExceptSpace(char c) {
+	return isspace(c) && (c != ' ');
+}
+
+
+string& removeWhiteSpacesExceptSpaces(string& s) {
+	s.erase(remove_if(begin(s), end(s), isWhiteSpaceExceptSpace), end(s));
+	return s;
+}
+
+
+bool checkRegex(peptideType peptidetype, string& sequence, string& errormessage) {
+	errormessage = "";
+
+	if (sequence.compare("") == 0) {
+		errormessage = "The sequence is empty.";
+		return false;
+	}
+
+	regex rx;
+	// [^\\[\\]]+ is used instead of .+ to prevent from a too complex regex error
+	switch (peptidetype)
+	{
+	case linear:
+	case linearpolysaccharide:
+		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
+		break;
+	case cyclic:
+		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+$";
+		break;
+	case branched:
+		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
+		break;
+	case lasso:
+		rx = "(^(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$|^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+\\\\\\)(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?$)";
+		break;
+	case other:
+	default:
+		rx = ".*";
+		break;
+	}
+
+	try {
+		if (!(regex_search(sequence, rx))) {
+			errormessage = "The format of sequence '" + sequence + "' does not correspond to the sequence type '" + getStringFromPeptideType(peptidetype) + "'.";
+			return false;
+		}
+	}
+	catch (regex_error& e) {
+		errormessage = "checkRegex: regex_search failed, error no. " + to_string(e.code());
+		return false;
+	}
+
+	return true;
+}
+
+
+void parseBranch(peptideType peptidetype, string& composition, vector<string>& vectorcomposition, int& branchstart, int& branchend) {
+	string s = composition;
+	cBrick b;
+	branchstart = -1;
+	branchend = -1;
+
+	if ((peptidetype == branched) || (peptidetype == lasso)) {
+		int i = 0;
+		while (i < (int)s.size()) {
+			if (s[i] == '\\') {
+				s.erase(s.begin() + i);
+			}
+			else {
+				i++;
+			}
+		}
+
+		for (int i = 0; i < (int)s.size(); i++) {
+			if (s[i] == '(') {
+				if (i > 0) {
+					b.clear();
+					b.setComposition(s.substr(0, i - 1), false);
+					branchstart = getNumberOfBricks(b.getComposition());
+					s[i] = '-';
+				}
+				else {
+					s.erase(s.begin());
+					branchstart = 0;
+				}
+				break;
+			}
+		}
+
+		for (int i = 0; i < (int)s.size(); i++) {
+			if (s[i] == ')') {
+				b.clear();
+				b.setComposition(s.substr(0, i - 1), false);
+				branchend = getNumberOfBricks(b.getComposition()) - 1;
+				if (i < (int)s.size() - 1) {
+					s[i] = '-';
+				}
+				else {
+					s.erase(s.begin() + i);
+				}
+				break;
+			}
+		}
+
+		if (branchend <= branchstart) {
+			branchstart = -1;
+			branchend = -1;
+		}
+	}
+
+	b.clear();
+	b.setComposition(s, false);
+	b.explodeToStringComposition(vectorcomposition);
+}
+
+
+peptideType getPeptideTypeFromString(string s) {
+	if (s.compare("linear") == 0) {
+		return linear;
+	}
+	if (s.compare("cyclic") == 0) {
+		return cyclic;
+	}
+	if (s.compare("branched") == 0) {
+		return branched;
+	}
+	if (s.compare("branch-cyclic") == 0) {
+		return lasso;
+	}
+	if (s.compare("linearpolysaccharide") == 0) {
+		return linearpolysaccharide;
+	}
+	if (s.compare("other") == 0) {
+		return other;
+	}
+
+	return other;
+}
+
+
+string getStringFromPeptideType(peptideType peptidetype) {
+	switch (peptidetype)
+	{
+	case linear:
+		return "linear";
+		break;
+	case cyclic:
+		return "cyclic";
+		break;
+	case branched:
+		return "branched";
+		break;
+	case lasso:
+		return "branch-cyclic";
+		break;
+	case linearpolysaccharide:
+		return "linearpolysaccharide";
+		break;
+	case other:
+		return "other";
+		break;
+	default:
+		break;
+	}
+
+	return "other";
+}
+
diff --git a/CycloBranch/core/utilities.h b/CycloBranch/core/utilities.h
index 21a3272..bdff4c4 100644
--- a/CycloBranch/core/utilities.h
+++ b/CycloBranch/core/utilities.h
@@ -10,9 +10,57 @@
 #include <fstream>
 #include <vector>
 #include <string>
+#include <QString>
+#include <boost/regex.hpp>
+
+class cBrick;
+
+
+#define WIN 0   // Windows
+#define UNX 1   // Linux/UNIX
+
+#ifdef UNIX
+	#define OS_TYPE UNX
+	#define sscanf_s sscanf
+	#define sprintf_s sprintf
+#else
+	#define OS_TYPE WIN
+#endif
 
 
 using namespace std;
+using namespace boost;
+
+
+/**
+	\brief The types of peptides supported by the application.
+*/
+enum peptideType {
+	linear = 0,
+	cyclic = 1,
+	branched = 2,
+	lasso = 3,
+	linearpolysaccharide = 4,
+	other = 5
+};
+
+
+/**
+	\brief The name of the application.
+*/
+extern QString appname;
+
+
+/**
+	\brief The version of the application.
+*/
+extern QString appversion;
+
+
+/**
+	\brief A directory where the application is installed in Linux.
+*/
+extern QString linuxinstalldir;
 
 
 /**
@@ -47,5 +95,58 @@ void storeStringVector(vector<string>& v, ofstream& os);
 void loadStringVector(vector<string>& v, ifstream& is);
 
 
+/**
+	\brief Check if \a c is a white space (except normal space).
+	\param c char
+	\retval bool true if \a c is a white space (except normal space); false otherwise.
+*/ 
+bool isWhiteSpaceExceptSpace(char c);
+
+
+/**
+	\brief Remove white spaces except normal spaces from a string.
+	\param s reference to a string
+	\retval string reference to the input string
+*/ 
+string& removeWhiteSpacesExceptSpaces(string& s);
+
+
+/**
+	\brief Check the syntax of a peptide sequence.
+	\param peptidetype peptide type
+	\param sequence peptide sequence
+	\param errormessage an error message if false is returned
+	\retval bool true when the syntax is correct, false otherwise
+*/ 
+bool checkRegex(peptideType peptidetype, string& sequence, string& errormessage);
+
+
+/**
+	\brief Parse a position of a branch from a peptide sequence.
+	\param peptidetype peptide type
+	\param composition a peptide sequence where all blocks "[blockX]-[blockY]" were replaced by ids "1-2"; but "\(" and "\)" are still included
+	\param vectorcomposition an output vector with ids of blocks represented as strings
+	\param branchstart start position of a branch (an output value)
+	\param branchend end position of a branch (an output value)
+*/ 
+void parseBranch(peptideType peptidetype, string& composition, vector<string>& vectorcomposition, int& branchstart, int& branchend);
+
+
+/**
+	\brief Convert a string to peptide type.
+	\param s string
+	\retval peptideType type of peptide
+*/
+peptideType getPeptideTypeFromString(string s);
+
+
+/**
+	\brief Convert the peptide type to a string.
+	\param peptidetype type of peptide
+	\retval string string
+*/
+string getStringFromPeptideType(peptideType peptidetype);
+
+
 #endif
 
diff --git a/CycloBranch/cyclobranch.rc b/CycloBranch/cyclobranch.rc
new file mode 100644
index 0000000..4fe2776
--- /dev/null
+++ b/CycloBranch/cyclobranch.rc
@@ -0,0 +1 @@
+IDI_ICON1               ICON    DISCARDABLE     "images/cb.ico"
\ No newline at end of file
diff --git a/CycloBranch/gui/cAboutWidget.cpp b/CycloBranch/gui/cAboutWidget.cpp
index 75401aa..0fc521d 100644
--- a/CycloBranch/gui/cAboutWidget.cpp
+++ b/CycloBranch/gui/cAboutWidget.cpp
@@ -4,21 +4,35 @@
 #include <QTextBrowser>
 #include <QVBoxLayout>
 #include <QDialogButtonBox>
-
+#include <QKeyEvent>
+#include <QIcon>
 
 
 cAboutWidget::cAboutWidget(QWidget* parent) {
 	this->parent = parent;
 
 	setWindowTitle("About...");
+	setWindowIcon(QIcon(":/images/icons/48.png"));
 
 	layout = new QVBoxLayout();
 
+	QString title = "A tool for <i>de novo</i> sequencing of nonribosomal peptides from accurate product ion mass spectra.<br/><hr/><br/>";
+
+	QString licence = "Licence:<br/><br/> This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.<br/><br/>";
+	licence += "This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.<br/><br/>";
+	licence += "You should have received a copy of the GNU General Public License along with this program. If not, see <a href=\"http://www.gnu.org/licenses/\">http://www.gnu.org/licenses/</a>.<br/><hr/><br/>";
+
+	QString developers = "Developers:<br/><br/>Jiri Novak<br/>Laboratory of Molecular Structure Characterization<br/>Institute of Microbiology<br/>Academy of Sciences of the Czech Republic<br/>Videnska 1083<br/>142 20 Prague<br/>Czech Republic<br/><a href=\"mailto:jiri.novak@biomed.cas.cz\">jiri.novak@biomed.cas.cz</a><br/><a href=\"http://ms.biomed.cas.cz/cyclobranch/\">http://ms.biomed.cas.cz/cyclobranch/</a><br/><a href=\"http://ms.biomed.cas.cz/staff-novak_jiri.php\">http://ms.biomed.cas.cz/staff-novak_jiri.php</a><br/><a href=\"https://cas-cz.academia.edu/JiriNovak\">https://cas-cz.academia.edu/JiriNovak</a><br/><br/>(C) 2013 - 2015<br/><hr/><br/>";
+
+	QString splash = "<div align=\"center\"><img src=\":/images/splash.png\"></div><br/><hr/><br/>";
+
+	QString acknowledgement = "Acknowledgements:<br/><br/><a href=\"http://www.aha-soft.com/\">http://www.aha-soft.com/</a><br/><hr/><br/>";
+
 	message = new QTextBrowser();
 	message->setReadOnly(true);
 	message->setAcceptRichText(true);
 	message->setOpenExternalLinks(true);
-	message->setHtml(appname + " " + appversion + "<br/><br/>Developers:<br/><br/>Jiri Novak<br/>Laboratory of Molecular Structure Characterization<br/>Institute of Microbiology<br/>Academy of Sciences of the Czech Republic<br/>Videnska 1083<br/>142 20 Prague<br/>Czech Republic<br/><a href=\"mailto:jiri.novak@biomed.cas.cz\">jiri.novak@biomed.cas.cz</a><br/><a href=\"http://ms.biomed.cas.cz/cyclobranch/\">http://ms.biomed.cas.cz/cyclobranch/</a><br/><a href=\"http://ms.biomed.cas.cz/staff-novak_jiri.php\">http://ms.biomed.cas.cz/staff-novak_jiri.php</a><br/><a href=\"https://cas-cz.academia.edu/JiriNovak\">https://cas-cz.academia.edu/JiriNovak</a><br/><br/>(C) 2013-2014");
+	message->setHtml("<br/>" + splash + "<b>" + appname + " " + appversion + "</b><br/><br/>" + title + developers /*+ licence*/ + acknowledgement);
 
 	buttonbox = new QDialogButtonBox(QDialogButtonBox::Ok);
 	//buttonBox = new QDialogButtonBox(QDialogButtonBox::Ok | QDialogButtonBox::Cancel);
@@ -31,7 +45,7 @@ cAboutWidget::cAboutWidget(QWidget* parent) {
 
 	setLayout(layout);
 
-	resize(600, 400);
+	resize(800, 600);
 }
 
 
@@ -47,6 +61,13 @@ void cAboutWidget::closeEvent(QCloseEvent *event) {
 }
 
 
+void cAboutWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+}
+
+
 void cAboutWidget::accept() {
 	hide();
 	//parent->setEnabled(true);
diff --git a/CycloBranch/gui/cAboutWidget.h b/CycloBranch/gui/cAboutWidget.h
index f787147..e8ef446 100644
--- a/CycloBranch/gui/cAboutWidget.h
+++ b/CycloBranch/gui/cAboutWidget.h
@@ -46,6 +46,16 @@ class cAboutWidget : public QWidget
 	void closeEvent(QCloseEvent *event);
 
 
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
+
 private:
 	QWidget* parent;
 	QVBoxLayout* layout;
diff --git a/CycloBranch/gui/cBranchedWidget.cpp b/CycloBranch/gui/cBranchedWidget.cpp
index 324f9d5..ea01478 100644
--- a/CycloBranch/gui/cBranchedWidget.cpp
+++ b/CycloBranch/gui/cBranchedWidget.cpp
@@ -4,6 +4,9 @@
 #include <QVBoxLayout>
 #include <QPainter>
 #include <QPaintEvent>
+#include <QMessageBox>
+#include <QPrinter>
+#include <QSvgGenerator>
 
 
 cBranchedWidget::cBranchedWidget() {
@@ -19,18 +22,97 @@ void cBranchedWidget::initialize(cParameters* parameters, cTheoreticalSpectrum*
 }
 
 
+void cBranchedWidget::exportToPDF(QString filename, bool postscript) {
+	QPrinter printer;
+	if (postscript) {
+		printer.setPaperSize(QSizeF(width() + 100, height() + 100), QPrinter::DevicePixel);
+		printer.setPageMargins (50, 50, 50, 50, QPrinter::DevicePixel);
+	}
+	else {
+		printer.setPaperSize(QSizeF(width(), height()), QPrinter::DevicePixel);
+		printer.setPageMargins (0, 0, 0, 0, QPrinter::DevicePixel);
+	}
+	printer.setOutputFormat(QPrinter::NativeFormat);
+	printer.setOutputFileName(filename);
+
+	QPainter painter;
+	if (!painter.begin(&printer)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		#if OS_TYPE == UNX
+			errstr += "\nDo you have a properly configured print server (sudo apt-get install cups-pdf) ?";
+			errstr += "\nIf you cannot create a ps file, you can create a pdf file and then use pdf2ps tool.";
+		#endif
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+}
+
+
+void cBranchedWidget::exportToPNG(QString filename) {
+	QImage image(width(), height(), QImage::Format_ARGB32);
+	image.fill(Qt::white);
+
+	QPainter painter;
+	if (!painter.begin(&image)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+	image.save(filename);
+}
+
+
+void cBranchedWidget::exportToSVG(QString filename) {
+	QSvgGenerator generator;
+	generator.setFileName(filename);
+	generator.setSize(QSize(width(), height()));
+	generator.setViewBox(QRect(0, 0, width(), height()));
+
+	QPainter painter;
+	if (!painter.begin(&generator)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	paint(painter);
+	painter.end();
+}
+
+
 void cBranchedWidget::paintEvent(QPaintEvent *event) {
+	QPainter painter;
+	painter.begin(this);
+	paint(painter);
+	painter.end();
+}
+
 
-	if (theoreticalspectrum->getVisualCoverage().size() == 0) {
+void cBranchedWidget::paint(QPainter& painter) {
+
+	if (!theoreticalspectrum) {
 		return;
 	}
 
 	vector<string> backboneacronyms;
 	vector<string> branchacronyms;
-	backboneacronyms = theoreticalspectrum->getBackboneAcronyms();
-	branchacronyms = theoreticalspectrum->getBranchAcronyms();
+	backboneacronyms = theoreticalspectrum->getCandidate().getBackboneAcronyms();
+	branchacronyms = theoreticalspectrum->getCandidate().getBranchAcronyms();
 
-	QPainter painter(this);
 	const int topmargin = 20;
 	const int leftmargin = 20;
 	const int bottommargin = 80;
@@ -46,11 +128,17 @@ void cBranchedWidget::paintEvent(QPaintEvent *event) {
 	const int verticalstep = (height() - topmargin - bottommargin)/std::max(branchsize, 1);
 
 	QFont myFont("Courier", 9);
+	QFontMetrics fm(myFont);
 	painter.setFont(myFont);
 
 	for (int i = 0; i < backbonesize; i++) {
 		painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-		painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*i, topmargin + verticalstep*branchsize, horizontalstep/2, 20, Qt::AlignCenter, backboneacronyms[i].c_str());
+		if (fm.width(backboneacronyms[i].c_str()) > horizontalstep/2) {
+			painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*i + 2, topmargin + verticalstep*branchsize, horizontalstep/2 - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, backboneacronyms[i].c_str());
+		}
+		else {
+			painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*i, topmargin + verticalstep*branchsize, horizontalstep/2, 20, Qt::AlignCenter, backboneacronyms[i].c_str());
+		}
 
 		painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 		painter.drawRect(leftmargin + horizontalstep/4 + horizontalstep*i, topmargin + verticalstep*branchsize, horizontalstep/2, 20);
@@ -58,231 +146,244 @@ void cBranchedWidget::paintEvent(QPaintEvent *event) {
 		if (i < backbonesize - 1) {
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 			painter.drawLine(leftmargin + horizontalstep/4 + horizontalstep*i + horizontalstep/2, topmargin + verticalstep*branchsize + 11, leftmargin + horizontalstep/4 + horizontalstep*(i + 1), topmargin + verticalstep*branchsize + 11);
-			painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
-			painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize - 10, leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize + 30);	
-			painter.drawLine(leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*i + horizontalstep/2, topmargin + verticalstep*branchsize - 10, leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize - 10);
-			painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize + 30, leftmargin + horizontalstep*(i + 1) + horizontalstep/8, topmargin + verticalstep*branchsize + 30);
+			if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+				painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+				painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize - 10, leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize + 30);	
+				painter.drawLine(leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*i + horizontalstep/2, topmargin + verticalstep*branchsize - 10, leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize - 10);
+				painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin + verticalstep*branchsize + 30, leftmargin + horizontalstep*(i + 1) + horizontalstep/8, topmargin + verticalstep*branchsize + 30);
+			}
 		}
 	}
 	
 	for (int i = 0; i < branchsize; i++) {
 		painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-		painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*tpermutations[0].middlebranchstart, topmargin + verticalstep*i, horizontalstep/2, 20, Qt::AlignCenter, branchacronyms[branchsize - i - 1].c_str());
+		if (fm.width(branchacronyms[branchsize - i - 1].c_str()) > horizontalstep/2) {
+			painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*tpermutations[0].middlebranchstart + 2, topmargin + verticalstep*i, horizontalstep/2 - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, branchacronyms[branchsize - i - 1].c_str());
+		}
+		else {
+			painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*tpermutations[0].middlebranchstart, topmargin + verticalstep*i, horizontalstep/2, 20, Qt::AlignCenter, branchacronyms[branchsize - i - 1].c_str());
+		}	
 
 		painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 		painter.drawRect(leftmargin + horizontalstep/4 + horizontalstep*tpermutations[0].middlebranchstart, topmargin + verticalstep*i, horizontalstep/2, 20);
 
 		painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 		painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart, topmargin + verticalstep*i + 20, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart, topmargin + verticalstep*i + verticalstep);
-		painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
-		painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);	
-		painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 20, topmargin + verticalstep*i + (verticalstep + 10)/2 + verticalstep/8);
-		painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 20, topmargin + verticalstep*i + (verticalstep + 10)/2 - verticalstep/8, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);
+		if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+			painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+			painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);	
+			painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 20, topmargin + verticalstep*i + (verticalstep + 10)/2 + verticalstep/8);
+			painter.drawLine(leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 20, topmargin + verticalstep*i + (verticalstep + 10)/2 - verticalstep/8, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);
+		}
 	}
 
-	unordered_set<cIonLabel, hash_cIonLabel> labels;
-	labels.clear();
+	if (parameters && (theoreticalspectrum->getVisualCoverage().size() > 0)) {
+	
+		unordered_set<cIonLabel, hash_cIonLabel> labels;
+		labels.clear();
 
-	int position;
-	string name;
-	int len = (int)theoreticalspectrum->getVisualCoverage()[0].series.size();
-	for (int i = 0; i < 6; i++) {
+		int position;
+		string name;
+		int len = (int)theoreticalspectrum->getVisualCoverage()[0].series.size();
+		for (int i = 0; i < 6; i++) {
 
-		if ((visibletrotationid != -1) && (visibletrotationid != i)) {
-			continue;
-		}
+			if ((visibletrotationid != -1) && (visibletrotationid != i)) {
+				continue;
+			}
 
-		for (int j = 0; j < (int)parameters->fragmentionsfortheoreticalspectra.size(); j++) {
+			for (int j = 0; j < (int)parameters->fragmentionsfortheoreticalspectra.size(); j++) {
 			
-			position = 0;
-			if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].nterminal) {
-				for (int k = 0; k < len; k++) {
-					switch (i)
-					{
-					case 0:
-						if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*position + horizontalstep/2, topmargin + verticalstep*branchsize - 35, name, false);
+				position = 0;
+				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].nterminal) {
+					for (int k = 0; k < len; k++) {
+						switch (i)
+						{
+						case 0:
+							if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*position + horizontalstep/2, topmargin + verticalstep*branchsize - 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 1:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*k + verticalstep/2 - verticalstep/8, name, false);
+							break;
+						case 1:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*k + verticalstep/2 - verticalstep/8, name, false);
+								}
 							}
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*(position + tpermutations[i].middlebranchend - tpermutations[i].middlebranchstart) + horizontalstep/2, topmargin + verticalstep*branchsize - 35, name, false);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*(position + tpermutations[i].middlebranchend - tpermutations[i].middlebranchstart) + horizontalstep/2, topmargin + verticalstep*branchsize - 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 2:
-						if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 2 + 1), topmargin + verticalstep*branchsize + 35, name, false);
+							break;
+						case 2:
+							if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 2 + 1), topmargin + verticalstep*branchsize + 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 3:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*position + horizontalstep/2, topmargin + verticalstep*branchsize - 35, name, false);
+							break;
+						case 3:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*position + horizontalstep/2, topmargin + verticalstep*branchsize - 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2, name, true);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2, name, true);
+								}
 							}
-						}
-						break;
-					case 4:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*k + verticalstep/2 - verticalstep/8, name, false);
+							break;
+						case 4:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*k + verticalstep/2 - verticalstep/8, name, false);
+								}
 							}
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(backbonesize - tpermutations[i].middlebranchend + tpermutations[i].middlebranchstart - position - 2 + 1), topmargin + verticalstep*branchsize + 35, name, false);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(backbonesize - tpermutations[i].middlebranchend + tpermutations[i].middlebranchstart - position - 2 + 1), topmargin + verticalstep*branchsize + 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 5:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 2 + 1), topmargin + verticalstep*branchsize + 35, name, false);
+							break;
+						case 5:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 2 + 1), topmargin + verticalstep*branchsize + 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2, name, true);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[k] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(k + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2, name, true);
+								}
 							}
+							break;
+						default:
+							break;
 						}
-						break;
-					default:
-						break;
 					}
 				}
-			}
 			
-			position = 0;
-			if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].cterminal) {
-				for (int k = len - 1; k >= 0; k--) {
-					switch (i)
-					{
-					case 0:
-						if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 1), topmargin + verticalstep*branchsize + 35, name, false);
+				position = 0;
+				if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].cterminal) {
+					for (int k = len - 1; k >= 0; k--) {
+						switch (i)
+						{
+						case 0:
+							if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 1), topmargin + verticalstep*branchsize + 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 1:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*k + verticalstep/2, name, true);
+							break;
+						case 1:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*k + verticalstep/2, name, true);
+								}
 							}
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 1), topmargin + verticalstep*branchsize + 35, name, false);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - 1), topmargin + verticalstep*branchsize + 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 2:
-						if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*position + horizontalstep/2 + horizontalstep/4 + horizontalstep/8, topmargin + verticalstep*branchsize - 35, name, false);
+							break;
+						case 2:
+							if ((k < tpermutations[i].middlebranchstart) || (k >= tpermutations[i].middlebranchend)) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*position + horizontalstep/2 + horizontalstep/4 + horizontalstep/8, topmargin + verticalstep*branchsize - 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 3:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - tpermutations[i].middlebranchend + tpermutations[i].middlebranchstart - 1), topmargin + verticalstep*branchsize + 35, name, false);
+							break;
+						case 3:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(backbonesize - position - tpermutations[i].middlebranchend + tpermutations[i].middlebranchstart - 1), topmargin + verticalstep*branchsize + 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2 - verticalstep/8, name, false);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2 - verticalstep/8, name, false);
+								}
 							}
-						}
-						break;
-					case 4:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*k + verticalstep/2, name, true);
+							break;
+						case 4:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart - 25, topmargin + verticalstep*k + verticalstep/2, name, true);
+								}
 							}
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*position + horizontalstep/2 + horizontalstep/4 + horizontalstep/8, topmargin + verticalstep*branchsize - 35, name, false);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*position + horizontalstep/2 + horizontalstep/4 + horizontalstep/8, topmargin + verticalstep*branchsize - 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						break;
-					case 5:
-						if (k < tpermutations[i].middlebranchstart) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep*(position + tpermutations[i].middlebranchend - tpermutations[i].middlebranchstart) + horizontalstep/2 + horizontalstep/4 + horizontalstep/8, topmargin + verticalstep*branchsize - 35, name, false);
+							break;
+						case 5:
+							if (k < tpermutations[i].middlebranchstart) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep*(position + tpermutations[i].middlebranchend - tpermutations[i].middlebranchstart) + horizontalstep/2 + horizontalstep/4 + horizontalstep/8, topmargin + verticalstep*branchsize - 35, name, false);
+								}
+								position++;
 							}
-							position++;
-						}
-						if (k >= tpermutations[i].middlebranchend) {
-							if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
-								name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
-								insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2 - verticalstep/8, name, false);
+							if (k >= tpermutations[i].middlebranchend) {
+								if (theoreticalspectrum->getVisualCoverage()[i*parameters->fragmentionsfortheoreticalspectra.size() + j].series[len - k - 1] > 0) {
+									name = to_string(i + 1) + "_" + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name[0] + to_string(len - k) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[j]].name.substr(1);
+									insertLabel(labels, leftmargin + horizontalstep/2 + horizontalstep*tpermutations[0].middlebranchstart + 25, topmargin + verticalstep*(branchsize - k - 2 + backbonesize) + verticalstep/2 - verticalstep/8, name, false);
+								}
 							}
+							break;
+						default:
+							break;
 						}
-						break;
-					default:
-						break;
 					}
 				}
-			}
 
+			}
 		}
-	}
 
-	painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
-	for (auto it = labels.begin(); it != labels.end(); ++it) {
-		if (it->alignright) {
-			painter.drawText(it->x - (int)it->label.size()*7, it->y, (int)it->label.size()*7, 20, Qt::AlignLeft, it->label.c_str());
-		}
-		else {
-			painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+		painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
+		for (auto it = labels.begin(); it != labels.end(); ++it) {
+			if (it->alignright) {
+				painter.drawText(it->x - fm.width(it->label.c_str()), it->y, fm.width(it->label.c_str()), 20, Qt::AlignLeft, it->label.c_str());
+			}
+			else {
+				painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+			}
 		}
+
 	}
 	
 }
diff --git a/CycloBranch/gui/cBranchedWidget.h b/CycloBranch/gui/cBranchedWidget.h
index 1f8b9f2..74f27ae 100644
--- a/CycloBranch/gui/cBranchedWidget.h
+++ b/CycloBranch/gui/cBranchedWidget.h
@@ -40,6 +40,28 @@ class cBranchedWidget : public QWidget
 	void initialize(cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum);
 
 
+	/**
+		\brief Export peptide into a PDF or a PS file.
+		\param filename filename
+		\param postscript if true then PS file is generated instead of PDF
+	*/ 
+	void exportToPDF(QString filename, bool postscript);
+
+
+	/**
+		\brief Export peptide scene into a PNG file.
+		\param filename filename
+	*/ 
+	void exportToPNG(QString filename);
+
+
+	/**
+		\brief Export peptide scene into a SVG file.
+		\param filename filename
+	*/ 
+	void exportToSVG(QString filename);
+
+
 protected:
 
 
@@ -52,6 +74,8 @@ class cBranchedWidget : public QWidget
 
 private:
 
+	void paint(QPainter& painter);
+
 	cParameters* parameters;
 	cTheoreticalSpectrum* theoreticalspectrum;
 	int visibletrotationid;
diff --git a/CycloBranch/gui/cBricksDatabaseWidget.cpp b/CycloBranch/gui/cBricksDatabaseWidget.cpp
index bae78d0..81dec94 100644
--- a/CycloBranch/gui/cBricksDatabaseWidget.cpp
+++ b/CycloBranch/gui/cBricksDatabaseWidget.cpp
@@ -1,5 +1,6 @@
 #include "gui/cBricksDatabaseWidget.h"
 #include "gui/cMainThread.h"
+#include "gui/cEventFilter.h"
 
 #include <QTableWidget>
 #include <QTableWidgetItem>
@@ -12,9 +13,11 @@
 #include <QLabel>
 #include <QProgressDialog>
 #include <QCheckBox>
+#include <QKeyEvent>
+#include <QIcon>
 
 
-int numberOfOccurrences(string& s, char c) {
+int numberOfOccurrences(const string& s, char c) {
 	int count = 0;
 	for (int i = 0; i < (int)s.size(); i++) {
 		if (s[i] == c) {
@@ -29,6 +32,7 @@ cBricksDatabaseWidget::cBricksDatabaseWidget(QWidget* parent) {
 	this->parent = parent;
 
 	setWindowTitle("Building Blocks Editor");
+	setWindowIcon(QIcon(":/images/icons/68.png"));
 
 	insertrow = new QPushButton(tr("Add Row"));
 	insertrow->setToolTip("Add a new row.");
@@ -56,13 +60,20 @@ cBricksDatabaseWidget::cBricksDatabaseWidget(QWidget* parent) {
 
 	database = new QTableWidget(0, 0, this);
 	database->setColumnCount(7);
-	database->setHorizontalHeaderItem(0, new QTableWidgetItem(""));
-	database->setHorizontalHeaderItem(1, new QTableWidgetItem("Name(s)"));
-	database->setHorizontalHeaderItem(2, new QTableWidgetItem("Acronym(s)"));
-	database->setHorizontalHeaderItem(3, new QTableWidgetItem("Residue Summary"));
-	database->setHorizontalHeaderItem(4, new QTableWidgetItem("Monoisotopic Residue Mass"));
-	database->setHorizontalHeaderItem(5, new QTableWidgetItem("Reference(s)"));
-	database->setHorizontalHeaderItem(6, new QTableWidgetItem("Preview"));
+	database->setHorizontalHeaderItem(0, new QTableWidgetItem());
+	database->setHorizontalHeaderItem(1, new QTableWidgetItem());
+	database->horizontalHeaderItem(1)->setText("Name(s)");
+	database->setHorizontalHeaderItem(2, new QTableWidgetItem());
+	database->horizontalHeaderItem(2)->setText("Acronym(s)");
+	database->setHorizontalHeaderItem(3, new QTableWidgetItem());
+	database->horizontalHeaderItem(3)->setText("Residue Summary");
+	database->setHorizontalHeaderItem(4, new QTableWidgetItem());
+	database->horizontalHeaderItem(4)->setText("Monoisotopic Residue Mass");
+	database->setHorizontalHeaderItem(5, new QTableWidgetItem());
+	database->horizontalHeaderItem(5)->setText("Reference(s)");
+	database->setHorizontalHeaderItem(6, new QTableWidgetItem());
+	database->horizontalHeaderItem(6)->setText("Preview");
+
 	database->horizontalHeader()->setStretchLastSection(true);
 	for (int i = 0; i < database->columnCount(); i++) {
 		database->resizeColumnToContents(i);
@@ -77,11 +88,6 @@ cBricksDatabaseWidget::cBricksDatabaseWidget(QWidget* parent) {
 	mainlayout->addWidget(database);
 	mainlayout->addLayout(buttons);
 
-	progress = new QProgressDialog(this);
-	progress->setCancelButton(0);
-	progress->setMinimumDuration(1000);
-	progress->setWindowModality(Qt::WindowModal);
-
 	connect(database->horizontalHeader(), SIGNAL(sectionDoubleClicked(int)), this, SLOT(headerItemDoubleClicked(int)));
 	connect(database, SIGNAL(itemChanged(QTableWidgetItem *)), this, SLOT(itemChanged(QTableWidgetItem *)));
 	connect(insertrow, SIGNAL(released()), this, SLOT(addRow()));
@@ -96,7 +102,13 @@ cBricksDatabaseWidget::cBricksDatabaseWidget(QWidget* parent) {
 	resize(1280, 700);
 
 	databasefile = "";
-	lastdir = "./BrickDatabases/";
+
+	#if OS_TYPE == WIN
+		lastdir = "./BrickDatabases/";
+	#else
+		lastdir = linuxinstalldir + "BrickDatabases/";
+	#endif
+	
 	bricks.clear();
 }
 
@@ -119,7 +131,6 @@ cBricksDatabaseWidget::~cBricksDatabaseWidget() {
 	delete database;
 	delete buttons;
 	delete mainlayout;
-	delete progress;
 }
 
 
@@ -129,47 +140,51 @@ void cBricksDatabaseWidget::closeEvent(QCloseEvent *event) {
 
 
 void cBricksDatabaseWidget::deleteTable(bool enableprogress) {
+	QProgressDialog* progress;
+	cEventFilter filter;
+	int rowcount = database->rowCount();
+
 	if (enableprogress) {
-		progress->setLabelText("Clearing the table...");
-		progress->setMinimum(0);
-		progress->setValue(1);
-		progress->setMaximum(database->rowCount());
-		progress->show();
+		progress = new QProgressDialog("Clearing the table...", /*"Cancel"*/0, 0, rowcount, this);
+		progress->installEventFilter(&filter);
+		progress->setMinimumDuration(0);
+		progress->setWindowModality(Qt::WindowModal);
+		progress->setValue(0);
 	}
 
-	for (int i = 0; i < database->rowCount(); i++) {
-		for (int j = 0; j < database->columnCount(); j++) {
-			if ((j == 0) || (j == 6)) {
-				delete database->cellWidget(i, j);
-			}
-			else {
-				delete database->item(i, j);
-			}
-		}
+	widgetitemallocator.reset();
 
-		if (enableprogress && ((i == 0) || ((i - 1)/100 != i/100))) {
-			progress->setValue(i);
-		}
-	}
+	for (int i = 0; i < rowcount; i++) {
+		delete database->cellWidget(rowcount - i - 1, 0);
+		delete database->cellWidget(rowcount - i - 1, 6);
+
+        if (enableprogress) {
+            progress->setValue(i);
+            //if (progress->wasCanceled()) {
+            //    break;
+            //}
+        }
+    }
+	
+	database->setRowCount(0);
 
 	if (enableprogress) {
-		progress->setValue(database->rowCount());
-		progress->hide();
+		progress->setValue(rowcount);
+		delete progress;
 	}
-	database->setRowCount(0);
 }
 
 
 void cBricksDatabaseWidget::removeRow(int row) {
-	for (int i = 0; i < database->columnCount(); i++) {
-		if ((i == 0) || (i == 6)) {
-			delete database->cellWidget(row, i);
-		}
-		else {
-			delete database->item(row, i);
-		}
-	}
-	database->removeRow(row);
+   for (int i = 0; i < database->columnCount(); i++) {
+        if ((i == 0) || (i == 6)) {
+            delete database->cellWidget(row, i);
+        }
+        else {
+			database->takeItem(row, i);
+        }
+    }
+    database->removeRow(row);
 }
 
 
@@ -200,7 +215,7 @@ bool cBricksDatabaseWidget::checkTable() {
 }
 
 
-bool cBricksDatabaseWidget::checkFormula(int row, string& summary) {
+bool cBricksDatabaseWidget::checkFormula(int row, const string& summary) {
 	cSummaryFormula formula;
 	string errmsg;
 	formula.setFormula(summary);
@@ -221,6 +236,13 @@ bool cBricksDatabaseWidget::checkFormula(int row, string& summary) {
 }
 
 
+void cBricksDatabaseWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+}
+
+
 void cBricksDatabaseWidget::closeWindow() {
 	hide();
 }
@@ -228,11 +250,11 @@ void cBricksDatabaseWidget::closeWindow() {
 
 void cBricksDatabaseWidget::loadDatabase() {
 	QString filename = QFileDialog::getOpenFileName(this, tr("Load the Database of Building Blocks"), lastdir, tr("Database of Building Blocks (*.txt)"));
-	lastdir = filename;
-	string errormessage;
-
-	if (filename.toStdString().compare("") != 0) {
 
+	if (!filename.isEmpty()) {
+		lastdir = filename;
+		string errormessage;
+		
 		databasefile = filename;
 		save->setText(QString("  Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("'  "));
 		
@@ -246,46 +268,52 @@ void cBricksDatabaseWidget::loadDatabase() {
 		else {
 
 			bricks.clear();
-			bricks.loadFromPlainTextStream(inputstream, errormessage);
+			bricks.loadFromPlainTextStream(inputstream, errormessage, true);
 
 			deleteTable(true);
 
-			progress->setLabelText("Loading the Databatase of Building Blocks...");
-			progress->setMinimum(0);
-			progress->setValue(1);
-			progress->setMaximum(bricks.size());
-			progress->show();
+			QProgressDialog progress("Loading the Databatase of Building Blocks...", /*"Cancel"*/0, 0, bricks.size(), this);
+			cEventFilter filter;
+			progress.installEventFilter(&filter);
+			progress.setMinimumDuration(0);
+			progress.setWindowModality(Qt::WindowModal);
 
 			database->setRowCount(bricks.size());
 			for (int i = 0; i < bricks.size(); i++) {
 				QCheckBox* checkbox = new QCheckBox();
 				database->setCellWidget(i, 0, checkbox);
 
-				database->setItem(i, 1, new QTableWidgetItem(bricks[i].getName().c_str()));
-				database->setItem(i, 2, new QTableWidgetItem(bricks[i].getAcronymsAsString().c_str()));
-				database->setItem(i, 3, new QTableWidgetItem(bricks[i].getSummary().c_str()));
+				database->setItem(i, 1, widgetitemallocator.getNewItem());
+				database->item(i, 1)->setText(bricks[i].getName().c_str());
+
+				database->setItem(i, 2, widgetitemallocator.getNewItem());
+				database->item(i, 2)->setText(bricks[i].getAcronymsAsString().c_str());
+
+				database->setItem(i, 3, widgetitemallocator.getNewItem());
+				database->item(i, 3)->setText(bricks[i].getSummary().c_str());
 
-				database->setItem(i, 4, new QTableWidgetItem());
+				database->setItem(i, 4, widgetitemallocator.getNewItem());
 				database->item(i, 4)->setData(Qt::DisplayRole, bricks[i].getMass());
 				
-				database->setItem(i, 5, new QTableWidgetItem(bricks[i].getReferencesAsString().c_str()));
+				database->setItem(i, 5, widgetitemallocator.getNewItem());
+				database->item(i, 5)->setText(bricks[i].getReferencesAsString().c_str());
 				
 				database->setCellWidget(i, 6, new QLabel(bricks[i].getAcronymsWithReferencesAsHTMLString().c_str()));
 				((QLabel *)database->cellWidget(i, 6))->setTextFormat(Qt::RichText);
 				((QLabel *)database->cellWidget(i, 6))->setTextInteractionFlags(Qt::TextBrowserInteraction);
 				((QLabel *)database->cellWidget(i, 6))->setOpenExternalLinks(true);
 
-				if ((i == 0) || ((i - 1)/100 != i/100)) {
-					progress->setValue(i);
-				}
+				progress.setValue(i);
+				//if (progress.wasCanceled()) {
+				//	break;
+				//}
 			}
 
 			for (int i = 0; i < database->columnCount(); i++) {
 				database->resizeColumnToContents(i);
 			}
 
-			progress->setValue(bricks.size());
-			progress->hide();
+			progress.setValue(bricks.size());
 
 		}
 
@@ -314,19 +342,18 @@ void cBricksDatabaseWidget::saveDatabase() {
 	}
 	else {
 
-		progress->setLabelText("Saving the Databatase of Building Blocks...");
-		progress->setMinimum(0);
-		progress->setMaximum(100);
-		progress->setValue(1);
-		progress->show();
+		QProgressDialog progress("Saving the Databatase of Building Blocks...", /*"Cancel"*/0, 0, database->rowCount(), this);
+		cEventFilter filter;
+		progress.installEventFilter(&filter);
+		progress.setMinimumDuration(0);
+		progress.setWindowModality(Qt::WindowModal);
 
 		cBrick b;
 		bricks.clear();
+		string s;
 
 		removeEmptyRows();
 
-		progress->setMaximum(database->rowCount());
-
 		for (int i = 0; i < database->rowCount(); i++) {
 			b.clear();
 			for (int j = 0; j < database->columnCount(); j++) {
@@ -336,19 +363,23 @@ void cBricksDatabaseWidget::saveDatabase() {
 					// nothing to do
 					break;
 				case 1:
-					b.setName(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					b.setName(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 2:
-					b.setAcronyms(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					b.setAcronyms(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 3:
-					b.setSummary(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					b.setSummary(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 4:
 					b.setMass(database->item(i,j)->data(Qt::DisplayRole).toDouble());
 					break;
 				case 5:
-					b.setReferences(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					b.setReferences(removeWhiteSpacesExceptSpaces(s));
 					break;
 				default:
 					break;
@@ -356,15 +387,15 @@ void cBricksDatabaseWidget::saveDatabase() {
 			}
 			bricks.push_back(b);
 
-			if ((i == 0) || ((i - 1)/100 != i/100)) {
-				progress->setValue(i);
-			}
+			progress.setValue(i);
+			//if (progress.wasCanceled()) {
+			//	break;
+			//}
 		}
 
 		bricks.storeToPlainTextStream(outputstream);
 
-		progress->setValue(database->rowCount());
-		progress->hide();
+		progress.setValue(progress.maximum());
 
 	}
 	outputstream.close();
@@ -377,10 +408,11 @@ void cBricksDatabaseWidget::saveDatabaseAs() {
 		return;
 	}
 
-	QString filename = QFileDialog::getSaveFileName(this, tr("Save Settings As..."), lastdir, tr("Database of Building Blocks (*.txt)"));
-	lastdir = filename;
+	QString filename = QFileDialog::getSaveFileName(this, tr("Save the Database of Building Blocks As..."), lastdir, tr("Database of Building Blocks (*.txt)"));
 
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdir = filename;
+	
 		databasefile = filename;
 		save->setText(QString("  Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("'  "));
 		saveDatabase();
@@ -395,11 +427,11 @@ void cBricksDatabaseWidget::addRow() {
 	QCheckBox* checkbox = new QCheckBox();
 	database->setCellWidget(row, 0, checkbox);
 
-	database->setItem(row, 1, new QTableWidgetItem());
-	database->setItem(row, 2, new QTableWidgetItem());
-	database->setItem(row, 3, new QTableWidgetItem());
-	database->setItem(row, 4, new QTableWidgetItem());
-	database->setItem(row, 5, new QTableWidgetItem());
+	database->setItem(row, 1, widgetitemallocator.getNewItem());
+	database->setItem(row, 2, widgetitemallocator.getNewItem());
+	database->setItem(row, 3, widgetitemallocator.getNewItem());
+	database->setItem(row, 4, widgetitemallocator.getNewItem());
+	database->setItem(row, 5, widgetitemallocator.getNewItem());
 
 	database->setCellWidget(row, 6, new QLabel());
 	((QLabel *)database->cellWidget(row, 6))->setTextFormat(Qt::RichText);
diff --git a/CycloBranch/gui/cBricksDatabaseWidget.h b/CycloBranch/gui/cBricksDatabaseWidget.h
index ade57cc..673abe1 100644
--- a/CycloBranch/gui/cBricksDatabaseWidget.h
+++ b/CycloBranch/gui/cBricksDatabaseWidget.h
@@ -9,7 +9,9 @@
 
 #include <QWidget>
 #include <fstream>
+#include "core/utilities.h"
 #include "core/cBricksDatabase.h"
+#include "core/cAllocator.h"
 
 using namespace std;
 
@@ -19,10 +21,7 @@ class QHBoxLayout;
 class QVBoxLayout;
 class QTableWidget;
 class QTableWidgetItem;
-class QDialogButtonBox;
 class QPushButton;
-class QLabel;
-class QProgressDialog;
 
 
 /**
@@ -31,11 +30,11 @@ class QProgressDialog;
 	\param c char
 	\retval int number of occurrences of \a c in \a s
 */
-int numberOfOccurrences(string& s, char c);
+int numberOfOccurrences(const string& s, char c);
 
 
 /**
-	\brief The widget representing the dialog 'About'.
+	\brief Visualization of the database of building blocks.
 */
 class cBricksDatabaseWidget : public QWidget
 {
@@ -75,7 +74,6 @@ class cBricksDatabaseWidget : public QWidget
 	QTableWidget* database;
 	QHBoxLayout* buttons;
 	QVBoxLayout* mainlayout;
-	QProgressDialog* progress;
 
 	QString databasefile;
 	QString lastdir;
@@ -85,13 +83,26 @@ class cBricksDatabaseWidget : public QWidget
 
 	vector<int> headersort;
 
+	cAllocator<QTableWidgetItem> widgetitemallocator;
+
 	void deleteTable(bool enableprogress);
 
 	void removeRow(int row);
 
 	bool checkTable();
 
-	bool checkFormula(int row, string& summary);
+	bool checkFormula(int row, const string& summary);
+
+
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
 
 private slots:
 
@@ -113,4 +124,4 @@ private slots:
 
 };
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/gui/cCyclicWidget.cpp b/CycloBranch/gui/cCyclicWidget.cpp
index db7eede..491397e 100644
--- a/CycloBranch/gui/cCyclicWidget.cpp
+++ b/CycloBranch/gui/cCyclicWidget.cpp
@@ -4,11 +4,20 @@
 #include <QVBoxLayout>
 #include <QPainter>
 #include <QPaintEvent>
+#include <QMessageBox>
+#include <QPrinter>
+#include <QSvgGenerator>
 
 
-void paintCircle(QPainter& painter, QColor& brushcolor, vector<string>& acronymsofblocks, int centerx, int centery, int radius, double angle, int horizontalstep, int linesize, int cornerlinesize) {
+void paintCircle(QPainter& painter, vector<string>& acronymsofblocks, int centerx, int centery, int radius, double angle, int horizontalstep, int linesize, int cornerlinesize, bool drawdashlines, int visiblerotationid, unordered_set<cIonLabel, hash_cIonLabel>& labels) {
 	double cumulativeangle;
 
+	QFont myFont("Courier", 9);
+	QFontMetrics fm(myFont);
+
+	string nterm = "N-term";
+	string cterm = "C-term";
+
 	painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 	painter.drawEllipse(QPointF(centerx,centery), radius, radius);
 
@@ -18,86 +27,180 @@ void paintCircle(QPainter& painter, QColor& brushcolor, vector<string>& acronyms
 		cumulativeangle = angle*(double)(i + 1);
 		blockid = to_string(i + 1);
 		if (cumulativeangle < pi/2) {
-			painter.setBrush(QBrush(brushcolor, Qt::SolidPattern));
-			painter.drawRect(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 10, xsize, 20);
-			painter.setBrush(QBrush(brushcolor, Qt::NoBrush));
+			painter.eraseRect(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 10, xsize, 20);
 			painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-			painter.drawText(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
-			painter.drawText(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+
+			if (fm.width(acronymsofblocks[i].c_str()) > xsize) {
+				painter.drawText(centerx + sin(cumulativeangle)*radius - xsize/2 + 2, centery - sin(pi/2 - cumulativeangle)*radius - 10, xsize - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, acronymsofblocks[i].c_str());
+			}
+			else {
+				painter.drawText(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
+			}
+			
+			if (drawdashlines) {
+				painter.drawText(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+			}
+
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 			painter.drawRect(centerx + sin(cumulativeangle)*radius - xsize/2, centery - sin(pi/2 - cumulativeangle)*radius - 10, xsize, 20);
 		}
 		else if ((cumulativeangle >= pi/2) && (cumulativeangle <= pi)) {
-			painter.setBrush(QBrush(brushcolor, Qt::SolidPattern));
-			painter.drawRect(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 10, xsize, 20);
-			painter.setBrush(QBrush(brushcolor, Qt::NoBrush));
+			painter.eraseRect(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 10, xsize, 20);
 			painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-			painter.drawText(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
-			painter.drawText(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+						
+			if (fm.width(acronymsofblocks[i].c_str()) > xsize) {
+				painter.drawText(centerx + sin(pi - cumulativeangle)*radius - xsize/2 + 2, centery + sin(cumulativeangle - pi/2)*radius - 10, xsize - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, acronymsofblocks[i].c_str());
+			}
+			else {
+				painter.drawText(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
+			}
+
+			if (drawdashlines) {
+				painter.drawText(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+			}
+			
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 			painter.drawRect(centerx + sin(pi - cumulativeangle)*radius - xsize/2, centery + sin(cumulativeangle - pi/2)*radius - 10, xsize, 20);
 		}
 		else if ((cumulativeangle >= pi) && (cumulativeangle <= 3*pi/2)) {
-			painter.setBrush(QBrush(brushcolor, Qt::SolidPattern));
-			painter.drawRect(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 10, xsize, 20);
-			painter.setBrush(QBrush(brushcolor, Qt::NoBrush));
+			painter.eraseRect(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 10, xsize, 20);
 			painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-			painter.drawText(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
-			painter.drawText(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+						
+			if (fm.width(acronymsofblocks[i].c_str()) > xsize) {
+				painter.drawText(centerx - sin(cumulativeangle - pi)*radius - xsize/2 + 2, centery + sin(3*pi/2 - cumulativeangle)*radius - 10, xsize - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, acronymsofblocks[i].c_str());
+			}
+			else {
+				painter.drawText(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
+			}
+
+			if (drawdashlines) {
+				painter.drawText(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+			}
+			
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 			painter.drawRect(centerx - sin(cumulativeangle - pi)*radius - xsize/2, centery + sin(3*pi/2 - cumulativeangle)*radius - 10, xsize, 20);
 		}
 		else {
-			painter.setBrush(QBrush(brushcolor, Qt::SolidPattern));
-			painter.drawRect(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 10, xsize, 20);
-			painter.setBrush(QBrush(brushcolor, Qt::NoBrush));
+			painter.eraseRect(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 10, xsize, 20);
 			painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-			painter.drawText(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
-			painter.drawText(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+			
+			if (fm.width(acronymsofblocks[i].c_str()) > xsize) {
+				painter.drawText(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2 + 2, centery - sin(cumulativeangle - 3*pi/2)*radius - 10, xsize - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, acronymsofblocks[i].c_str());
+			}
+			else {
+				painter.drawText(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 10, xsize, 20, Qt::AlignCenter, acronymsofblocks[i].c_str());
+			}
+
+			if (drawdashlines) {
+				painter.drawText(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 30, xsize, 20, Qt::AlignLeft, blockid.c_str());
+			}
+			
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 			painter.drawRect(centerx - sin(2*pi - cumulativeangle)*radius - xsize/2, centery - sin(cumulativeangle - 3*pi/2)*radius - 10, xsize, 20);
 		}
 	}
 
-	painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
-	for (int i = 0; i < (int)acronymsofblocks.size(); i++) {
-		cumulativeangle = angle*(double)i + angle/(double)2;
-		if (cumulativeangle < pi/2) {
-			QPoint p1(centerx + sin(cumulativeangle)*(radius - linesize), centery - sin(pi/2 - cumulativeangle)*(radius - linesize));
-			QPoint p2(centerx + sin(cumulativeangle)*(radius + linesize), centery - sin(pi/2 - cumulativeangle)*(radius + linesize));
-			QPoint p3(centerx + sin(cumulativeangle)*(radius + linesize) - sin(pi/2 - cumulativeangle)*cornerlinesize, centery - sin(pi/2 - cumulativeangle)*(radius + linesize) - sin(cumulativeangle)*cornerlinesize);
-			QPoint p4(centerx + sin(cumulativeangle)*(radius - linesize) + sin(pi/2 - cumulativeangle)*cornerlinesize, centery - sin(pi/2 - cumulativeangle)*(radius - linesize) + sin(cumulativeangle)*cornerlinesize);
-			painter.drawLine(p1, p2); 
-			painter.drawLine(p3, p2); 
-			painter.drawLine(p1, p4); 
-		}
-		else if ((cumulativeangle >= pi/2) && (cumulativeangle <= pi)) {
-			QPoint p1(centerx + sin(pi - cumulativeangle)*(radius - linesize), centery + sin(cumulativeangle - pi/2)*(radius - linesize));
-			QPoint p2(centerx + sin(pi - cumulativeangle)*(radius + linesize), centery + sin(cumulativeangle - pi/2)*(radius + linesize));
-			QPoint p3(centerx + sin(pi - cumulativeangle)*(radius + linesize) + sin(cumulativeangle - pi/2)*cornerlinesize, centery + sin(cumulativeangle - pi/2)*(radius + linesize) - sin(pi - cumulativeangle)*cornerlinesize);
-			QPoint p4(centerx + sin(pi - cumulativeangle)*(radius - linesize) - sin(cumulativeangle - pi/2)*cornerlinesize, centery + sin(cumulativeangle - pi/2)*(radius - linesize) + sin(pi - cumulativeangle)*cornerlinesize);
-			painter.drawLine(p1, p2); 
-			painter.drawLine(p3, p2); 
-			painter.drawLine(p1, p4); 
-		}
-		else if ((cumulativeangle >= pi) && (cumulativeangle <= 3*pi/2)) {
-			QPoint p1(centerx - sin(cumulativeangle - pi)*(radius - linesize), centery + sin(3*pi/2 - cumulativeangle)*(radius - linesize));
-			QPoint p2(centerx - sin(cumulativeangle - pi)*(radius + linesize), centery + sin(3*pi/2 - cumulativeangle)*(radius + linesize));
-			QPoint p3(centerx - sin(cumulativeangle - pi)*(radius + linesize) + sin(3*pi/2 - cumulativeangle)*cornerlinesize, centery + sin(3*pi/2 - cumulativeangle)*(radius + linesize) + sin(cumulativeangle - pi)*cornerlinesize);
-			QPoint p4(centerx - sin(cumulativeangle - pi)*(radius - linesize) - sin(3*pi/2 - cumulativeangle)*cornerlinesize, centery + sin(3*pi/2 - cumulativeangle)*(radius - linesize) - sin(cumulativeangle - pi)*cornerlinesize);
-			painter.drawLine(p1, p2); 
-			painter.drawLine(p3, p2); 
-			painter.drawLine(p1, p4); 
+	int reddashid = visiblerotationid;
+	if (visiblerotationid >= (int)acronymsofblocks.size()) {
+		reddashid = (2*(int)acronymsofblocks.size() - visiblerotationid)%(int)acronymsofblocks.size();
+	}
+
+	if (drawdashlines) {
+		for (int i = 0; i < (int)acronymsofblocks.size(); i++) {
+			cumulativeangle = angle*(double)i + angle/(double)2;
+			if (cumulativeangle < pi/2) {
+				QPoint p1(centerx + sin(cumulativeangle)*(radius - linesize), centery - sin(pi/2 - cumulativeangle)*(radius - linesize));
+				QPoint p2(centerx + sin(cumulativeangle)*(radius + linesize), centery - sin(pi/2 - cumulativeangle)*(radius + linesize));
+				QPoint p3(centerx + sin(cumulativeangle)*(radius + linesize) - sin(pi/2 - cumulativeangle)*cornerlinesize, centery - sin(pi/2 - cumulativeangle)*(radius + linesize) - sin(cumulativeangle)*cornerlinesize);
+				QPoint p4(centerx + sin(cumulativeangle)*(radius - linesize) + sin(pi/2 - cumulativeangle)*cornerlinesize, centery - sin(pi/2 - cumulativeangle)*(radius - linesize) + sin(cumulativeangle)*cornerlinesize);
+				if (reddashid == i) {
+					painter.setPen(QPen(Qt::red, 2, Qt::DashLine));
+					if (visiblerotationid < (int)acronymsofblocks.size()) {
+						insertLabel(labels, p3.x() + 10, p3.y() - 10, cterm, false);
+						insertLabel(labels, p4.x() - 5, p4.y() - 5, nterm, true);
+					}
+					else {
+						insertLabel(labels, p3.x() + 10, p3.y() - 10, nterm, false);
+						insertLabel(labels, p4.x() - 5, p4.y() - 5, cterm, true);
+					}
+				}
+				else {
+					painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+				}
+				painter.drawLine(p1, p2);
+				painter.drawLine(p3, p2); 
+				painter.drawLine(p1, p4); 
+			}
+			else if ((cumulativeangle >= pi/2) && (cumulativeangle <= pi)) {
+				QPoint p1(centerx + sin(pi - cumulativeangle)*(radius - linesize), centery + sin(cumulativeangle - pi/2)*(radius - linesize));
+				QPoint p2(centerx + sin(pi - cumulativeangle)*(radius + linesize), centery + sin(cumulativeangle - pi/2)*(radius + linesize));
+				QPoint p3(centerx + sin(pi - cumulativeangle)*(radius + linesize) + sin(cumulativeangle - pi/2)*cornerlinesize, centery + sin(cumulativeangle - pi/2)*(radius + linesize) - sin(pi - cumulativeangle)*cornerlinesize);
+				QPoint p4(centerx + sin(pi - cumulativeangle)*(radius - linesize) - sin(cumulativeangle - pi/2)*cornerlinesize, centery + sin(cumulativeangle - pi/2)*(radius - linesize) + sin(pi - cumulativeangle)*cornerlinesize);
+				if (reddashid == i) {
+					painter.setPen(QPen(Qt::red, 2, Qt::DashLine));
+					if (visiblerotationid < (int)acronymsofblocks.size()) {
+						insertLabel(labels, p3.x() + 10, p3.y() - 10, cterm, false);
+						insertLabel(labels, p4.x() - 5, p4.y() - 5, nterm, true);
+					}
+					else {
+						insertLabel(labels, p3.x() + 10, p3.y() - 10, nterm, false);
+						insertLabel(labels, p4.x() - 5, p4.y() - 5, cterm, true);
+					}
+				}
+				else {
+					painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+				}
+				painter.drawLine(p1, p2);
+				painter.drawLine(p3, p2); 
+				painter.drawLine(p1, p4); 
+			}
+			else if ((cumulativeangle >= pi) && (cumulativeangle <= 3*pi/2)) {
+				QPoint p1(centerx - sin(cumulativeangle - pi)*(radius - linesize), centery + sin(3*pi/2 - cumulativeangle)*(radius - linesize));
+				QPoint p2(centerx - sin(cumulativeangle - pi)*(radius + linesize), centery + sin(3*pi/2 - cumulativeangle)*(radius + linesize));
+				QPoint p3(centerx - sin(cumulativeangle - pi)*(radius + linesize) + sin(3*pi/2 - cumulativeangle)*cornerlinesize, centery + sin(3*pi/2 - cumulativeangle)*(radius + linesize) + sin(cumulativeangle - pi)*cornerlinesize);
+				QPoint p4(centerx - sin(cumulativeangle - pi)*(radius - linesize) - sin(3*pi/2 - cumulativeangle)*cornerlinesize, centery + sin(3*pi/2 - cumulativeangle)*(radius - linesize) - sin(cumulativeangle - pi)*cornerlinesize);
+				if (reddashid == i) {
+					painter.setPen(QPen(Qt::red, 2, Qt::DashLine));
+					if (visiblerotationid < (int)acronymsofblocks.size()) {
+						insertLabel(labels, p3.x() - 10, p3.y() - 10, cterm, true);
+						insertLabel(labels, p4.x() + 10, p4.y() - 10, nterm, false);
+					}
+					else {
+						insertLabel(labels, p3.x() - 10, p3.y() - 10, nterm, true);
+						insertLabel(labels, p4.x() + 10, p4.y() - 10, cterm, false);
+					}
+				}
+				else {
+					painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+				}
+				painter.drawLine(p1, p2);
+				painter.drawLine(p3, p2); 
+				painter.drawLine(p1, p4); 
+			}
+			else {
+				QPoint p1(centerx - sin(2*pi - cumulativeangle)*(radius - linesize), centery - sin(cumulativeangle - 3*pi/2)*(radius - linesize));
+				QPoint p2(centerx - sin(2*pi - cumulativeangle)*(radius + linesize), centery - sin(cumulativeangle - 3*pi/2)*(radius + linesize));
+				QPoint p3(centerx - sin(2*pi - cumulativeangle)*(radius + linesize) - sin(cumulativeangle - 3*pi/2)*cornerlinesize, centery - sin(cumulativeangle - 3*pi/2)*(radius + linesize) + sin(2*pi - cumulativeangle)*cornerlinesize);
+				QPoint p4(centerx - sin(2*pi - cumulativeangle)*(radius - linesize) + sin(cumulativeangle - 3*pi/2)*cornerlinesize, centery - sin(cumulativeangle - 3*pi/2)*(radius - linesize) - sin(2*pi - cumulativeangle)*cornerlinesize);
+				if (reddashid == i) {
+					painter.setPen(QPen(Qt::red, 2, Qt::DashLine));
+					if (visiblerotationid < (int)acronymsofblocks.size()) {
+						insertLabel(labels, p3.x() - 10, p3.y() - 10, cterm, true);
+						insertLabel(labels, p4.x() + 10, p4.y() - 10, nterm, false);
+					}
+					else {
+						insertLabel(labels, p3.x() - 10, p3.y() - 10, nterm, true);
+						insertLabel(labels, p4.x() + 10, p4.y() - 10, cterm, false);
+					}
+				}
+				else {
+					painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+				}
+				painter.drawLine(p1, p2);
+				painter.drawLine(p3, p2); 
+				painter.drawLine(p1, p4); 
+			}
 		}
-		else {
-			QPoint p1(centerx - sin(2*pi - cumulativeangle)*(radius - linesize), centery - sin(cumulativeangle - 3*pi/2)*(radius - linesize));
-			QPoint p2(centerx - sin(2*pi - cumulativeangle)*(radius + linesize), centery - sin(cumulativeangle - 3*pi/2)*(radius + linesize));
-			QPoint p3(centerx - sin(2*pi - cumulativeangle)*(radius + linesize) - sin(cumulativeangle - 3*pi/2)*cornerlinesize, centery - sin(cumulativeangle - 3*pi/2)*(radius + linesize) + sin(2*pi - cumulativeangle)*cornerlinesize);
-			QPoint p4(centerx - sin(2*pi - cumulativeangle)*(radius - linesize) + sin(cumulativeangle - 3*pi/2)*cornerlinesize, centery - sin(cumulativeangle - 3*pi/2)*(radius - linesize) - sin(2*pi - cumulativeangle)*cornerlinesize);
-			painter.drawLine(p1, p2); 
-			painter.drawLine(p3, p2); 
-			painter.drawLine(p1, p4); 
-		}		
 	}
 }
 
@@ -195,19 +298,98 @@ void cCyclicWidget::initialize(cParameters* parameters, cTheoreticalSpectrum* th
 }
 
 
+void cCyclicWidget::exportToPDF(QString filename, bool postscript) {
+	QPrinter printer;
+	if (postscript) {
+		printer.setPaperSize(QSizeF(width() + 100, height() + 100), QPrinter::DevicePixel);
+		printer.setPageMargins (50, 50, 50, 50, QPrinter::DevicePixel);
+	}
+	else {
+		printer.setPaperSize(QSizeF(width(), height()), QPrinter::DevicePixel);
+		printer.setPageMargins (0, 0, 0, 0, QPrinter::DevicePixel);
+	}
+	printer.setOutputFormat(QPrinter::NativeFormat);
+	printer.setOutputFileName(filename);
+
+	QPainter painter;
+	if (!painter.begin(&printer)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		#if OS_TYPE == UNX
+			errstr += "\nDo you have a properly configured print server (sudo apt-get install cups-pdf) ?";
+			errstr += "\nIf you cannot create a ps file, you can create a pdf file and then use pdf2ps tool.";
+		#endif
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+}
+
+
+void cCyclicWidget::exportToPNG(QString filename) {
+	QImage image(width(), height(), QImage::Format_ARGB32);
+	image.fill(Qt::white);
+
+	QPainter painter;
+	if (!painter.begin(&image)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+	image.save(filename);
+}
+
+
+void cCyclicWidget::exportToSVG(QString filename) {
+	QSvgGenerator generator;
+	generator.setFileName(filename);
+	generator.setSize(QSize(width(), height()));
+	generator.setViewBox(QRect(0, 0, width(), height()));
+
+	QPainter painter;
+	if (!painter.begin(&generator)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	paint(painter);
+	painter.end();
+}
+
+
 void cCyclicWidget::paintEvent(QPaintEvent *event) {
+	QPainter painter;
+	painter.begin(this);
+	paint(painter);
+	painter.end();
+}
 
-	if (theoreticalspectrum->getVisualCoverage().size() == 0) {
+
+void cCyclicWidget::paint(QPainter& painter) {
+
+	if (!theoreticalspectrum) {
 		return;
 	}
 
-	QPainter painter(this);
 	const int topmargin = 20;//max(20,(height() - 80)/2);
 	const int leftmargin = 20;
 	const int bottommargin = 80;
 	const int rightmargin = 20;
 
-	int size = (int)theoreticalspectrum->getAcronyms().size();
+	int size = (int)theoreticalspectrum->getCandidate().getAcronyms().size();
 	double angle = 2*pi/(double)size;
 	int centerx = width()/2;
 	int centery = height()/2;
@@ -216,31 +398,37 @@ void cCyclicWidget::paintEvent(QPaintEvent *event) {
 	const int horizontalstep = (width() - leftmargin - rightmargin)/std::max(size, 1);
 
 	QFont myFont("Courier", 9);
+	QFontMetrics fm(myFont);
 	painter.setFont(myFont);
 
+	unordered_set<cIonLabel, hash_cIonLabel> labels;
+	labels.clear();
+
 	int linesize = 20;
 	int cornerlinesize = horizontalstep/8;
-	paintCircle(painter, (QColor &)(palette().color(QPalette::Background)), theoreticalspectrum->getAcronyms(), centerx, centery, radius, angle, horizontalstep, linesize, cornerlinesize);
+
+	paintCircle(painter, theoreticalspectrum->getCandidate().getAcronyms(), centerx, centery, radius, angle, horizontalstep, linesize, cornerlinesize, theoreticalspectrum->getVisualCoverage().size() > 0, visiblerotationid, labels);
 		
-	unordered_set<cIonLabel, hash_cIonLabel> labels;
-	labels.clear();
+	if (parameters && (theoreticalspectrum->getVisualCoverage().size() > 0)) {
 	
-	int half = (int)theoreticalspectrum->getVisualCoverage().size()/(int)parameters->fragmentionsfortheoreticalspectra.size()/2;
-	for (int i = 0; i < half; i++) {
-		generateCyclicLabelsToRight(true, i, i, 0, size - 1, size, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, -1, -1);
-	}
-	for (int i = half; i < 2*half; i++) {
-		generateCyclicLabelsToLeft(true, i, i, 0, size - 1, size, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, -1, -1);
-	}
-
-	painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
-	for (auto it = labels.begin(); it != labels.end(); ++it) {
-		if (it->alignright) {
-			painter.drawText(it->x - (int)it->label.size()*7, it->y, (int)it->label.size()*7, 20, Qt::AlignLeft, it->label.c_str());
+		int half = (int)theoreticalspectrum->getVisualCoverage().size()/(int)parameters->fragmentionsfortheoreticalspectra.size()/2;
+		for (int i = 0; i < half; i++) {
+			generateCyclicLabelsToRight(true, i, i, 0, size - 1, size, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, -1, -1);
 		}
-		else {
-			painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+		for (int i = half; i < 2*half; i++) {
+			generateCyclicLabelsToLeft(true, i, i, 0, size - 1, size, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, -1, -1);
 		}
+
+		painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
+		for (auto it = labels.begin(); it != labels.end(); ++it) {
+			if (it->alignright) {
+				painter.drawText(it->x - fm.width(it->label.c_str()), it->y, fm.width(it->label.c_str()), 20, Qt::AlignLeft, it->label.c_str());
+			}
+			else {
+				painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+			}
+		}
+
 	}
 	
 }
diff --git a/CycloBranch/gui/cCyclicWidget.h b/CycloBranch/gui/cCyclicWidget.h
index 03cac46..b7db166 100644
--- a/CycloBranch/gui/cCyclicWidget.h
+++ b/CycloBranch/gui/cCyclicWidget.h
@@ -23,9 +23,8 @@ const double pi = 3.141592653589793;
 
 
 /**
-	\brief Paint the circle of a cyclic or a lasso peptide.
+	\brief Paint the circle of a cyclic or a branch-cyclic peptide.
 	\param painter a reference to current QPainter
-	\param brushcolor a background color for rectangles with the acronyms of building blocks
 	\param acronymsofblocks acronyms of building blocks
 	\param centerx x coordinate of a center of the ring
 	\param centery y coordinate of a center of the ring
@@ -34,8 +33,11 @@ const double pi = 3.141592653589793;
 	\param horizontalstep determine width of rectangles with the acronyms of building blocks
 	\param linesize length of separators between building blocks
 	\param cornerlinesize length of endings of separators between building blocks
+	\param drawdashlines true when dashed lines between blocks and numbers of blocks are painted, false otherwise
+	\param visiblerotationid an identifier of a rotation of a cyclic peptide
+	\param labels labels of fragment ions
 */ 
-void paintCircle(QPainter& painter, QColor& brushcolor, vector<string>& acronymsofblocks, int centerx, int centery, int radius, double angle, int horizontalstep, int linesize, int cornerlinesize);
+void paintCircle(QPainter& painter, vector<string>& acronymsofblocks, int centerx, int centery, int radius, double angle, int horizontalstep, int linesize, int cornerlinesize, bool drawdashlines, int visiblerotationid, unordered_set<cIonLabel, hash_cIonLabel>& labels);
 
 
 /**
@@ -110,6 +112,28 @@ class cCyclicWidget : public QWidget
 	void initialize(cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum);
 
 
+	/**
+		\brief Export peptide into a PDF or a PS file.
+		\param filename filename
+		\param postscript if true then PS file is generated instead of PDF
+	*/ 
+	void exportToPDF(QString filename, bool postscript);
+
+
+	/**
+		\brief Export peptide scene into a PNG file.
+		\param filename filename
+	*/ 
+	void exportToPNG(QString filename);
+
+
+	/**
+		\brief Export peptide scene into a SVG file.
+		\param filename filename
+	*/ 
+	void exportToSVG(QString filename);
+
+
 protected:
 
 
@@ -122,6 +146,8 @@ class cCyclicWidget : public QWidget
 
 private:
 
+	void paint(QPainter& painter);
+
 	cParameters* parameters;
 	cTheoreticalSpectrum* theoreticalspectrum;
 	int visiblerotationid;
diff --git a/CycloBranch/gui/cDrawPeptideWidget.cpp b/CycloBranch/gui/cDrawPeptideWidget.cpp
new file mode 100644
index 0000000..9744319
--- /dev/null
+++ b/CycloBranch/gui/cDrawPeptideWidget.cpp
@@ -0,0 +1,665 @@
+#include "gui/cDrawPeptideWidget.h"
+
+#include <QTextEdit>
+#include <QTextBrowser>
+#include <QHBoxLayout>
+#include <QVBoxLayout>
+#include <QFormLayout>
+#include <QScrollArea>
+#include <QScrollBar>
+#include <QCheckBox>
+#include <QPushButton>
+#include <QSplitter>
+#include <QComboBox>
+#include <QDoubleSpinBox>
+#include <QLineEdit>
+#include <QSpinBox>
+#include <QMessageBox>
+#include <QFileDialog>
+#include <QClipboard>
+#include <QApplication>
+#include <QLabel>
+#include <QMenu>
+#include <QAction>
+#include <QToolButton>
+#include <QToolBar>
+#include <QKeyEvent>
+#include <QIcon>
+
+
+cDrawPeptideWidget::cDrawPeptideWidget(QWidget* parent) {
+	this->parent = parent;
+
+	setWindowTitle("Draw Peptide");
+	setWindowIcon(QIcon(":/images/icons/96.png"));
+
+	drawpeptideformlayout = new QFormLayout();
+
+	peptidetypecombobox = new QComboBox();
+	peptidetypecombobox->setToolTip("Select the type of peptide.");
+	peptidetypecombobox->setMaximumWidth(150);
+	peptidetypecombobox->addItem(tr("Linear"));
+	peptidetypecombobox->addItem(tr("Cyclic"));
+	peptidetypecombobox->addItem(tr("Branched"));
+	peptidetypecombobox->addItem(tr("Branch-cyclic"));
+	//peptidetypecombobox->addItem(tr("Linear polysaccharide (beta version)"));
+	//peptidetypecombobox->addItem(tr("Other"));
+	drawpeptideformlayout->addRow(tr("Peptide Type: "), peptidetypecombobox);
+
+	sequenceline = new QLineEdit();
+	sequenceline->setToolTip("A peptide sequence to be drawn.\nThe tool automatically checks if the syntax of an entered sequence corresponds to the selected peptide type.\nIf the syntax is correct then a green message \"correct\" is shown else a red message \"incorrect\" is shown at the end of the input line.");
+
+	sequencestatuslabel = new QLabel("");
+	sequencestatuslabel->setMinimumWidth(50);
+
+	sequenceactioncopy = new QAction("Copy to &Clipboard", this);
+	sequenceactionsetsequence = new QAction("Set as Searched &Sequence", this);
+	sequenceactionsettag = new QAction("Set as Sequence &Tag", this);
+	sequenceactioninsert = new QAction("Insert into Sequence &Database", this);
+	
+	sequencemenu = new QMenu();
+	sequencemenu->addAction(sequenceactioncopy);
+	sequencemenu->addSeparator();
+	sequencemenu->addAction(sequenceactionsetsequence);
+	sequencemenu->addAction(sequenceactionsettag);
+	sequencemenu->addAction(sequenceactioninsert);
+
+	sequencetoolbutton = new QToolButton();
+	sequencetoolbutton->setMenu(sequencemenu);
+	sequencetoolbutton->setPopupMode(QToolButton::MenuButtonPopup);
+	sequencetoolbutton->setDefaultAction(sequenceactioncopy);
+
+	sequencetoolbar = new QToolBar();
+	sequencetoolbar->addWidget(sequencetoolbutton);
+
+	sequencelayout = new QHBoxLayout();
+	sequencelayout->addWidget(sequenceline);
+	sequencelayout->addWidget(sequencestatuslabel);
+	sequencelayout->addWidget(sequencetoolbar);
+	drawpeptideformlayout->addRow(tr("Sequence: "), sequencelayout);
+
+	separateblocks = new QCheckBox();
+	separateblocks->setToolTip("If the box is checked, the sequence to be drawn is specified by the fields \"Number of Blocks at Backbone\", \"Number of Blocks at Branch\", \"Branch Connection Block No.\", \"Backbone Blocks\" and \"Branch Blocks\".\nIf the box is unchecked, the sequence to be drawn is specified in the field \"Sequence\".");
+	drawpeptideformlayout->addRow(tr("Define Blocks Separately: "), separateblocks);
+
+	numberofblocksbackbone = new QSpinBox();
+	numberofblocksbackbone->setToolTip("A number of blocks forming a backbone of a peptide.");
+	numberofblocksbackbone->setMaximumWidth(150);
+	numberofblocksbackbone->setSingleStep(1);
+	drawpeptideformlayout->addRow(tr("Number of Blocks at Backbone: "), numberofblocksbackbone);
+
+	numberofblocksbranch = new QSpinBox();
+	numberofblocksbranch->setToolTip("A number of blocks forming a branch of a branched or a branch-cyclic peptide.");
+	numberofblocksbranch->setMaximumWidth(150);
+	numberofblocksbranch->setRange(1, 100);
+	numberofblocksbranch->setSingleStep(1);
+	drawpeptideformlayout->addRow(tr("Number of Blocks at Branch: "), numberofblocksbranch);
+
+	branchposition = new QSpinBox();
+	branchposition->setToolTip("A number of a block where a backbone of a branched or a branch-cyclic peptide is connected to a branch.");
+	branchposition->setMaximumWidth(150);
+	branchposition->setSingleStep(1);
+	drawpeptideformlayout->addRow(tr("Branch Connection Block No.:"), branchposition);
+
+	backboneblocks = new QHBoxLayout();
+	backboneblocks->setContentsMargins(0, 0, 0, 0);
+	backboneblockswidget = new QWidget();
+	backboneblockswidget->setContentsMargins(0, 0, 0, 0);
+	backboneblockswidget->setLayout(backboneblocks);
+	backboneblockswidget->setToolTip("Names of building blocks forming a backbone of a peptide.\nThe number of fields is updated when the value of \"Number of Blocks at Backbone\" is changed.\nOne name of a building block per field must be entered.");
+	drawpeptideformlayout->addRow(tr("Backbone Blocks: "), backboneblockswidget);
+
+	branchblocks = new QHBoxLayout();
+	branchblocks->setContentsMargins(0, 0, 0, 0);
+	branchblockswidget = new QWidget();
+	branchblockswidget->setContentsMargins(0, 0, 0, 0);
+	branchblockswidget->setLayout(branchblocks);
+	branchblockswidget->setToolTip("Names of building blocks forming a branch of a branched or a branch-cyclic peptide.\nThe number of fields is updated when the value of \"Number of Blocks at Branch\" is changed.\nOne name of a building block per field must be entered.");
+	drawpeptideformlayout->addRow(tr("Branch Blocks: "), branchblockswidget);
+
+	drawpeptideformwidget = new QWidget();
+	drawpeptideformwidget->setLayout(drawpeptideformlayout);
+
+
+	linearwidget = new cLinearWidget();
+	linearwidget->initialize(0, 0);
+
+	cyclicwidget = new cCyclicWidget();
+	cyclicwidget->initialize(0, 0);
+
+	branchedwidget = new cBranchedWidget();
+	branchedwidget->initialize(0, 0);
+
+	lassowidget = new cLassoWidget();
+	lassowidget->initialize(0, 0);
+
+	vbox = new QVBoxLayout();
+	vbox->addWidget(drawpeptideformwidget);
+	vbox->addWidget(linearwidget);
+	vbox->addWidget(cyclicwidget);
+	vbox->addWidget(branchedwidget);
+	vbox->addWidget(lassowidget);
+
+	vbox->setStretchFactor(drawpeptideformwidget, 1);
+	vbox->setStretchFactor(linearwidget, 5);
+	vbox->setStretchFactor(cyclicwidget, 5);
+	vbox->setStretchFactor(branchedwidget, 5);
+	vbox->setStretchFactor(lassowidget, 5);
+
+	mainbox = new QHBoxLayout();
+	mainbox->addLayout(vbox);
+	setLayout(mainbox);
+
+	resize(1280, 700);
+
+	connect(sequenceline, SIGNAL(textEdited(const QString&)), this, SLOT(sequenceChanged()));
+	connect(sequenceactioncopy, SIGNAL(triggered()), this, SLOT(sequenceCopy()));
+	connect(sequenceactionsetsequence, SIGNAL(triggered()), this, SLOT(sequenceSetSequence()));
+	connect(sequenceactionsettag, SIGNAL(triggered()), this, SLOT(sequenceSetTag()));
+	connect(sequenceactioninsert, SIGNAL(triggered()), this, SLOT(sequenceInsert()));
+	connect(peptidetypecombobox, SIGNAL(currentIndexChanged(int)), this, SLOT(peptideTypeChanged(int)));
+	connect(separateblocks, SIGNAL(stateChanged(int)), this, SLOT(separateBlocksChanged(int)));
+	connect(numberofblocksbackbone, SIGNAL(valueChanged(int)), this, SLOT(numberOfBackboneBlocksChanged(int)));
+	connect(numberofblocksbranch, SIGNAL(valueChanged(int)), this, SLOT(numberOfBranchBlocksChanged(int)));
+	connect(branchposition, SIGNAL(valueChanged(int)), this, SLOT(blocksChanged()));
+	numberOfBackboneBlocksChanged(numberofblocksbackbone->value());
+	numberOfBranchBlocksChanged(numberofblocksbranch->value());
+	peptideTypeChanged(peptidetypecombobox->currentIndex());
+
+	connect(this, SIGNAL(sendSequence(int, QString)), parent, SLOT(setSequence(int, QString)));
+	connect(this, SIGNAL(sendTag(int, QString)), parent, SLOT(setTag(int, QString)));
+	connect(this, SIGNAL(sendInsert(int, QString)), parent, SLOT(insertSequence(int, QString)));
+}
+
+
+cDrawPeptideWidget::~cDrawPeptideWidget() {
+	delete linearwidget;
+	delete cyclicwidget;
+	delete branchedwidget;
+	delete lassowidget;
+
+	delete peptidetypecombobox;
+	
+	delete sequenceline;
+	delete sequencestatuslabel;
+	delete sequenceactioncopy;
+	delete sequenceactionsetsequence;
+	delete sequenceactionsettag;
+	delete sequenceactioninsert;
+	delete sequencemenu;
+	delete sequencetoolbutton;
+	delete sequencetoolbar;
+	delete sequencelayout;
+
+	delete separateblocks;
+
+	delete numberofblocksbackbone;
+	delete numberofblocksbranch;
+	delete branchposition;
+
+	QLayoutItem* item;
+
+	while (backboneblocks->count() > 0) {
+		item = backboneblocks->takeAt(0);
+		delete item->widget();
+	}
+
+	while (branchblocks->count() > 0) {
+		item = branchblocks->takeAt(0);
+		delete item->widget();
+	}
+
+	delete backboneblocks;
+	delete branchblocks;
+
+	delete backboneblockswidget;
+	delete branchblockswidget;
+
+	delete drawpeptideformlayout;
+	delete drawpeptideformwidget;
+
+	delete vbox;
+
+	delete mainbox;
+}
+
+
+void cDrawPeptideWidget::closeEvent(QCloseEvent *event) {
+	hide();
+}
+
+
+void cDrawPeptideWidget::setSequence(int peptidetypeindex, QString sequence) {
+	separateblocks->setChecked(false);
+	peptidetypecombobox->setCurrentIndex(peptidetypeindex);
+	sequenceline->setText(sequence);
+	sequenceChanged();
+	separateblocks->setChecked(true);
+}
+
+
+void cDrawPeptideWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+}
+
+
+void cDrawPeptideWidget::separateBlocksChanged(int state) {
+	if (state == Qt::Checked) {
+		sequenceline->setDisabled(true);
+		numberofblocksbackbone->setDisabled(false);
+		backboneblockswidget->setDisabled(false);
+		if (((peptideType)(peptidetypecombobox->currentIndex()) == branched) || ((peptideType)(peptidetypecombobox->currentIndex()) == lasso)) {
+			numberofblocksbranch->setDisabled(false);
+			branchblockswidget->setDisabled(false);
+			branchposition->setDisabled(false);
+		}
+		else {
+			numberofblocksbranch->setDisabled(true);
+			branchblockswidget->setDisabled(true);
+			branchposition->setDisabled(true);
+		}
+	}
+	else {
+		sequenceline->setDisabled(false);
+		numberofblocksbackbone->setDisabled(true);
+		backboneblockswidget->setDisabled(true);
+		numberofblocksbranch->setDisabled(true);
+		branchblockswidget->setDisabled(true);
+		branchposition->setDisabled(true);
+	}
+
+	blocksChanged();
+	sequenceChanged();
+}
+
+
+void cDrawPeptideWidget::numberOfBackboneBlocksChanged(int numberofblocks) {
+	switch ((peptideType)peptidetypecombobox->currentIndex()) {
+		case linear:
+			numberofblocksbackbone->setRange(1, 100);
+			branchposition->setRange(1, 1);
+			break;
+		case cyclic:
+			numberofblocksbackbone->setRange(2, 100);
+			branchposition->setRange(1, 1);
+			break;
+		case branched:
+			numberofblocksbackbone->setRange(3, 100);
+			branchposition->setRange(2, numberofblocks - 1);
+			break;
+		case lasso:
+			numberofblocksbackbone->setRange(2, 100);
+			branchposition->setRange(1, numberofblocks);
+			break;
+		case linearpolysaccharide:
+			break;
+		case other:
+			break;
+		default:
+			break;
+	}
+
+	if (numberofblocks > backboneblocks->count()) {
+		int itemscount = numberofblocks - backboneblocks->count();
+		QLineEdit* line;
+		for (int i = 0; i < itemscount; i++) {
+			line = new QLineEdit();
+			connect(line, SIGNAL(textEdited(const QString&)), this, SLOT(blocksChanged()));
+			backboneblocks->addWidget(line);
+		}
+	}
+	else if (numberofblocks < backboneblocks->count()) {
+		QLayoutItem* item;
+		while (numberofblocks < backboneblocks->count()) {
+			item = backboneblocks->takeAt(backboneblocks->count() - 1);
+			delete item->widget();
+		}
+	}
+
+	blocksChanged();
+}
+
+
+void cDrawPeptideWidget::numberOfBranchBlocksChanged(int numberofblocks) {
+	if (numberofblocks > branchblocks->count()) {
+		int itemscount = numberofblocks - branchblocks->count();
+		QLineEdit* line;
+		for (int i = 0; i < itemscount; i++) {
+			line = new QLineEdit();
+			connect(line, SIGNAL(textEdited(const QString&)), this, SLOT(blocksChanged()));
+			branchblocks->addWidget(line);
+		}
+	}
+	else if (numberofblocks < branchblocks->count()) {
+		QLayoutItem* item;
+		while (numberofblocks < branchblocks->count()) {
+			item = branchblocks->takeAt(branchblocks->count() - 1);
+			delete item->widget();
+		}
+	}
+
+	blocksChanged();
+}
+
+
+void cDrawPeptideWidget::peptideTypeChanged(int index) {
+
+	linearwidget->hide();
+	cyclicwidget->hide();
+	branchedwidget->hide();
+	lassowidget->hide();
+
+	switch ((peptideType)index) {
+		case linear:
+			linearwidget->show();
+			numberOfBackboneBlocksChanged(max(backboneblocks->count(), 1));
+			break;
+		case cyclic:
+			cyclicwidget->show();
+			numberOfBackboneBlocksChanged(max(backboneblocks->count(), 2));
+			break;
+		case branched:
+			branchedwidget->show();
+			numberOfBackboneBlocksChanged(max(backboneblocks->count(), 3));
+			break;
+		case lasso:
+			lassowidget->show();
+			numberOfBackboneBlocksChanged(max(backboneblocks->count(), 2));
+			break;
+		case linearpolysaccharide:
+			break;
+		case other:
+			break;
+		default:
+			break;
+	}
+
+	separateBlocksChanged(separateblocks->checkState());
+}
+
+
+void cDrawPeptideWidget::sequenceCopy() {
+	QApplication::clipboard()->setText(sequenceline->text());
+}
+
+
+void cDrawPeptideWidget::sequenceSetSequence() {
+	emit sendSequence(peptidetypecombobox->currentIndex(), sequenceline->text());
+}
+
+
+void cDrawPeptideWidget::sequenceSetTag() {
+	emit sendTag(peptidetypecombobox->currentIndex(), sequenceline->text());
+}
+
+
+void cDrawPeptideWidget::sequenceInsert() {
+	emit sendInsert(peptidetypecombobox->currentIndex(), sequenceline->text());
+}
+
+
+void cDrawPeptideWidget::blocksChanged() {
+	if (!separateblocks->isChecked()) {
+		return;
+	}
+
+	QString s = "";
+	string composition = "";
+	int compositioncount = 0;
+	cBricksDatabase bricksdb;
+	cBrick b;
+
+	int backbonecount = backboneblocks->count();
+	while ((backbonecount > 0) && (((QLineEdit *)(backboneblocks->itemAt(backbonecount - 1)->widget()))->text().toStdString().compare("") == 0)) {
+		backbonecount--;
+	}
+
+	int branchcount = branchblocks->count();
+	while ((branchcount > 1) && (((QLineEdit *)(branchblocks->itemAt(branchcount - 1)->widget()))->text().toStdString().compare("") == 0)) {
+		branchcount--;
+	}
+
+	peptideType peptidetype = (peptideType)peptidetypecombobox->currentIndex();
+
+	if ((peptidetype == linear) || (peptidetype == linearpolysaccharide) || ((backbonecount > 1) && (peptidetype == cyclic))) {
+		for (int i = 0; i < backbonecount; i++) {
+			if (i > 0) {
+				s += "-";
+				composition += "-";
+			}
+			s += "[";
+			s += ((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->text();
+			s += "]";
+			composition += to_string(++compositioncount);
+			b.clear();
+			b.setAcronyms(((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->text().toStdString());
+			bricksdb.push_back(b);
+		}
+	}
+
+	if (((backbonecount > branchposition->value()) && (peptidetype == branched)) || ((backbonecount >= branchposition->value()) && (peptidetype == lasso))) {
+		for (int i = 0; i < backbonecount; i++) {
+			if (i == branchposition->value() - 1) {
+				s += "\\([";
+				s += ((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->text();
+				s += "]";
+				if (composition.size() > 0) {
+					composition += "-";
+				}
+				composition += to_string(++compositioncount);
+				b.clear();
+				b.setAcronyms(((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->text().toStdString());
+				bricksdb.push_back(b);
+
+				for (int j = 0; j < branchcount; j++) {
+					s += "-[";
+					s += ((QLineEdit *)(branchblocks->itemAt(j)->widget()))->text();
+					s += "]";
+					if (composition.size() > 0) {
+						composition += "-";
+					}
+					composition += to_string(++compositioncount);
+					b.clear();
+					b.setAcronyms(((QLineEdit *)(branchblocks->itemAt(j)->widget()))->text().toStdString());
+					bricksdb.push_back(b);
+
+				}
+
+				s += "\\)";
+			}
+			else {
+				if ((i > 0) && (i != branchposition->value())) {
+					s += "-";
+				}
+				s += "[";
+				s += ((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->text();
+				s += "]";
+				if (composition.size() > 0) {
+					composition += "-";
+				}
+				composition += to_string(++compositioncount);
+				b.clear();
+				b.setAcronyms(((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->text().toStdString());
+				bricksdb.push_back(b);
+			}
+		}
+	}
+
+	sequenceline->setText(s);
+	
+	string errormessage = "";
+	string sequence = sequenceline->text().toStdString();
+	if (checkRegex(peptidetype, sequence, errormessage)) {
+		sequencestatuslabel->setText("<font color='green'>correct</font>");
+		vector<string> compositionvector;
+		compositionvector.push_back(composition);
+		drawPeptide(compositionvector, bricksdb, branchposition->value() - 1, branchposition->value() - 1 + branchcount);
+	}
+	else {
+		sequencestatuslabel->setText("<font color='red'>incorrect</font>");
+	}
+}
+
+
+void cDrawPeptideWidget::sequenceChanged() {
+	if (separateblocks->isChecked()) {
+		return;
+	}
+
+	string errormessage = "";
+	peptideType peptidetype = (peptideType)peptidetypecombobox->currentIndex();
+	string sequence = sequenceline->text().toStdString();
+	int start1, start2;
+
+	if (checkRegex(peptidetype, sequence, errormessage)) {
+
+		cBricksDatabase bricksdb;
+		cBrick b;
+		string s = "";
+		string acronym;
+		bool insidebrick = false;
+		bool found = false;
+
+		for (int i = 0; i < (int)sequence.size(); i++) {
+			if (sequence[i] == '[') {
+				acronym = "";
+				insidebrick = true;
+				continue;
+			}
+
+			if (sequence[i] == ']') {
+				b.clear();
+				b.setAcronyms(acronym);
+				bricksdb.push_back(b);
+				s += to_string(bricksdb.size());
+				insidebrick = false;
+				continue;
+			}
+
+			if (insidebrick) {
+				acronym += sequence[i];
+			}
+			else {
+				s += sequence[i];
+			}
+		}
+		sequence = s;
+
+		int branchstart, branchend;
+		vector<string> v;
+		parseBranch(peptidetype, sequence, v, branchstart, branchend);
+
+		sequencestatuslabel->setText("<font color='green'>correct</font>");
+		// the candidate is also initialized
+		drawPeptide(v, bricksdb, branchstart, branchend);
+
+		vector<int> intcomposition;
+		b.clear();
+		b.setComposition(theoreticalspectrum.getCandidate().getComposition(), false);
+		b.explodeToIntComposition(intcomposition);
+
+		if ((peptidetype == linear) || (peptidetype == linearpolysaccharide) || (peptidetype == cyclic)) {
+			numberofblocksbackbone->setValue((int)v.size());
+			for (int i = 0; i < backboneblocks->count(); i++) {
+				if (i < (int)v.size()) {
+					((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->setText(bricksdb[intcomposition[i] - 1].getAcronymsAsString().c_str());
+
+				}
+				else {
+					((QLineEdit *)(backboneblocks->itemAt(i)->widget()))->setText("");
+				}
+			}
+		}
+
+		if ((peptidetype == branched) || (peptidetype == lasso)) {
+			numberofblocksbackbone->setValue((int)v.size() - branchend + branchstart);
+			numberofblocksbranch->setValue(branchend - branchstart);
+			branchposition->setValue(branchstart + 1);
+
+			start1 = 0;
+			start2 = 0;
+			for (int i = 0; i < (int)v.size(); i++) {
+				if ((i > branchstart) && (i <= branchend)) {
+					((QLineEdit *)(branchblocks->itemAt(start1)->widget()))->setText(bricksdb[intcomposition[i] - 1].getAcronymsAsString().c_str());
+					start1++;
+				}
+				else {
+					((QLineEdit *)(backboneblocks->itemAt(start2)->widget()))->setText(bricksdb[intcomposition[i] - 1].getAcronymsAsString().c_str());
+					start2++;
+				}
+			}
+
+			while (start1 < branchblocks->count()) {
+				((QLineEdit *)(branchblocks->itemAt(start1)->widget()))->setText("");
+				start1++;
+			}
+
+			while (start2 < backboneblocks->count()) {
+				((QLineEdit *)(backboneblocks->itemAt(start2)->widget()))->setText("");
+				start2++;
+			}
+		}
+
+	}
+	else {
+		sequencestatuslabel->setText("<font color='red'>incorrect</font>");
+	}
+}
+
+
+void cDrawPeptideWidget::drawPeptide(vector<string>& composition, cBricksDatabase& bricksdb, int branchstart, int branchend) {
+	vector<nodeEdge> netmp;
+	vector<cCandidate> lassorotations;
+	int numberofbricks;
+
+	switch ((peptideType)peptidetypecombobox->currentIndex()) {
+		case linear:
+			theoreticalspectrum.getCandidate().setCandidate(composition, netmp, 0, 0, 0, -1, -1);
+			theoreticalspectrum.getCandidate().setAcronyms(bricksdb);
+			linearwidget->initialize(0, &theoreticalspectrum);
+			linearwidget->repaint();
+			break;
+		case cyclic:
+			theoreticalspectrum.getCandidate().setCandidate(composition, netmp, 0, 0, 0, -1, -1);
+			theoreticalspectrum.getCandidate().setAcronyms(bricksdb);
+			cyclicwidget->initialize(0, &theoreticalspectrum);
+			cyclicwidget->repaint();
+			break;
+		case branched:
+			theoreticalspectrum.getCandidate().setCandidate(composition, netmp, 0, 0, 0, branchstart, branchend);
+			theoreticalspectrum.getCandidate().setBackboneAcronyms(bricksdb);
+			theoreticalspectrum.getCandidate().setBranchAcronyms(bricksdb);
+			branchedwidget->initialize(0, &theoreticalspectrum);
+			branchedwidget->repaint();
+			break;
+		case lasso:
+			theoreticalspectrum.getCandidate().setCandidate(composition, netmp, 0, 0, 0, branchstart, branchend);
+
+			// normalize the candidate
+			theoreticalspectrum.getCandidate().getLassoRotations(lassorotations, false);
+			numberofbricks = getNumberOfBricks(theoreticalspectrum.getCandidate().getComposition());
+			for (int i = 0; i < (int)lassorotations.size(); i++) {
+				if (lassorotations[i].getBranchEnd() == numberofbricks - 1) {
+					vector<string> v;
+					v.push_back(lassorotations[i].getComposition());
+					theoreticalspectrum.getCandidate().setCandidate(v, theoreticalspectrum.getCandidate().getPath(), theoreticalspectrum.getCandidate().getStartModifID(), theoreticalspectrum.getCandidate().getEndModifID(), theoreticalspectrum.getCandidate().getMiddleModifID(), lassorotations[i].getBranchStart(), lassorotations[i].getBranchEnd());
+					break;
+				}
+			}
+
+			theoreticalspectrum.getCandidate().setBackboneAcronyms(bricksdb);
+			theoreticalspectrum.getCandidate().setBranchAcronyms(bricksdb);
+			lassowidget->initialize(0, &theoreticalspectrum);
+			lassowidget->repaint();
+			break;
+		case linearpolysaccharide:
+			break;
+		case other:
+			break;
+		default:
+			break;
+	}
+}
+
diff --git a/CycloBranch/gui/cDrawPeptideWidget.h b/CycloBranch/gui/cDrawPeptideWidget.h
new file mode 100644
index 0000000..e44ea87
--- /dev/null
+++ b/CycloBranch/gui/cDrawPeptideWidget.h
@@ -0,0 +1,176 @@
+/**
+	\file cDrawPeptideWidget.h
+	\brief Draw a peptide from a sequence of building blocks.
+*/
+
+
+#ifndef _CDRAWPEPTIDEWIDGET_H
+#define _CDRAWPEPTIDEWIDGET_H
+
+#include <QWidget>
+#include "gui/cLinearWidget.h"
+#include "gui/cCyclicWidget.h"
+#include "gui/cBranchedWidget.h"
+#include "gui/cLassoWidget.h"
+
+
+// forward declaration
+class QTextEdit;
+class QTextBrowser;
+class QHBoxLayout;
+class QVBoxLayout;
+class QFormLayout;
+class QScrollArea;
+class QCheckBox;
+class QPushButton;
+class QComboBox;
+class QDoubleSpinBox;
+class QLineEdit;
+class QSpinBox;
+class QLabel;
+class QAction;
+class QMenu;
+class QToolButton;
+class QToolBar;
+
+
+/**
+	\brief Draw a peptide from a sequence of building blocks.
+*/
+class cDrawPeptideWidget : public QWidget
+{
+	Q_OBJECT
+
+public:
+
+
+	/**
+		\brief The constructor.
+		\param parent pointer to a parent widget
+	*/ 
+	cDrawPeptideWidget(QWidget* parent = (QWidget *)0);
+
+
+	/**
+		\brief The destructor.
+	*/ 
+	~cDrawPeptideWidget();
+
+
+	/**
+		\brief Handle the window close event.
+		\param event pointer to QCloseEvent
+	*/ 
+	void closeEvent(QCloseEvent *event);
+
+
+	/**
+		\brief Set peptide sequence.
+		\param peptidetypeindex an index of current peptide type
+		\param sequence searched sequence
+	*/ 
+	void setSequence(int peptidetypeindex, QString sequence);
+
+
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
+
+private:
+
+	QWidget* parent;
+
+	QWidget* drawpeptideformwidget;
+	QFormLayout* drawpeptideformlayout;
+	QComboBox* peptidetypecombobox;
+
+	QLineEdit* sequenceline;
+	QLabel* sequencestatuslabel;
+	QAction *sequenceactioncopy;
+	QAction *sequenceactionsetsequence;
+	QAction *sequenceactionsettag;
+	QAction *sequenceactioninsert;
+	QMenu *sequencemenu;
+	QToolButton* sequencetoolbutton;
+	QToolBar *sequencetoolbar;
+	QHBoxLayout* sequencelayout;
+
+	QCheckBox* separateblocks;
+	QSpinBox* numberofblocksbackbone;
+	QSpinBox* numberofblocksbranch;
+	QSpinBox* branchposition;
+	QHBoxLayout* backboneblocks;
+	QWidget* backboneblockswidget;
+	QHBoxLayout* branchblocks;
+	QWidget* branchblockswidget;
+
+	cTheoreticalSpectrum theoreticalspectrum;
+	cLinearWidget* linearwidget;
+	cCyclicWidget* cyclicwidget;
+	cBranchedWidget* branchedwidget;
+	cLassoWidget* lassowidget;
+
+	QVBoxLayout* vbox;
+	QHBoxLayout* mainbox;
+
+
+	void drawPeptide(vector<string>& composition, cBricksDatabase& bricksdb, int branchstart, int branchend);
+
+
+private slots:
+
+	void separateBlocksChanged(int state);
+
+	void numberOfBackboneBlocksChanged(int numberofblocks);
+
+	void numberOfBranchBlocksChanged(int numberofblocks);
+
+	void peptideTypeChanged(int index);
+
+	void sequenceCopy();
+
+	void sequenceSetSequence();
+
+	void sequenceSetTag();
+
+	void sequenceInsert();
+
+	void blocksChanged();
+
+	void sequenceChanged();
+
+
+signals:
+
+	/**
+		\brief Send index of peptide type and searched sequence (a request for cParametersWidget).
+		\param peptidetypeindex an index of current peptide type
+		\param sequence searched sequence
+	*/ 
+	void sendSequence(int peptidetypeindex, QString sequence);
+
+
+	/**
+		\brief Send index of peptide type and sequence tag (a request for cParametersWidget).
+		\param peptidetypeindex an index of current peptide type
+		\param tag sequence tag
+	*/ 
+	void sendTag(int peptidetypeindex, QString tag);
+
+
+	/**
+		\brief Send index of peptide type and sequence (a request for cSequenceDatabaseWidget).
+		\param peptidetypeindex an index of current peptide type
+		\param sequence sequence
+	*/ 
+	void sendInsert(int peptidetypeindex, QString sequence);
+
+};
+
+#endif
\ No newline at end of file
diff --git a/CycloBranch/gui/cEventFilter.cpp b/CycloBranch/gui/cEventFilter.cpp
new file mode 100644
index 0000000..84a193c
--- /dev/null
+++ b/CycloBranch/gui/cEventFilter.cpp
@@ -0,0 +1,14 @@
+#include "gui/cEventFilter.h"
+
+
+bool cEventFilter::eventFilter(QObject *obj, QEvent *event) {
+	if (event->type() == QEvent::KeyPress) {
+		//QKeyEvent *keyEvent = static_cast<QKeyEvent *>(event);
+		//qDebug("Ate key press %d", keyEvent->key());
+		return true;
+	} 
+	else {
+		return QObject::eventFilter(obj, event);
+	}
+}
+
diff --git a/CycloBranch/gui/cEventFilter.h b/CycloBranch/gui/cEventFilter.h
new file mode 100644
index 0000000..e357b9a
--- /dev/null
+++ b/CycloBranch/gui/cEventFilter.h
@@ -0,0 +1,35 @@
+/**
+	\file cEventFilter.h
+	\brief An event filter.
+*/
+
+
+#ifndef _CEVENTFILTER_H
+#define _CEVENTFILTER_H
+
+#include <QObject>
+#include <QEvent>
+#include <QKeyEvent>
+
+
+/**
+	\brief An event filter.
+*/
+class cEventFilter : public QObject {
+
+	Q_OBJECT
+
+ protected:
+ 
+	/**
+		\brief Filter events.
+		\param obj pointer to QObject
+		\param event pointer to QKeyEvent
+	*/ 
+	bool eventFilter(QObject *obj, QEvent *event);
+ 
+};
+
+
+#endif
+
diff --git a/CycloBranch/gui/cGraphWidget.cpp b/CycloBranch/gui/cGraphWidget.cpp
index ba9ccfc..dde3d75 100644
--- a/CycloBranch/gui/cGraphWidget.cpp
+++ b/CycloBranch/gui/cGraphWidget.cpp
@@ -2,12 +2,15 @@
 
 #include <QTextBrowser>
 #include <QVBoxLayout>
+#include <QKeyEvent>
+#include <QIcon>
 
 
 cGraphWidget::cGraphWidget() {
 	htmlstring = "";
 
-	setWindowTitle("Graph");
+	setWindowTitle("De Novo Graph");
+	setWindowIcon(QIcon(":/images/icons/32.png"));
 
 	layout = new QVBoxLayout();
 
@@ -59,3 +62,10 @@ void cGraphWidget::load(ifstream& is) {
 	textbrowser->setHtml(htmlstring.c_str());
 }
 
+
+void cGraphWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+}
+
diff --git a/CycloBranch/gui/cGraphWidget.h b/CycloBranch/gui/cGraphWidget.h
index 4809917..08a04ba 100644
--- a/CycloBranch/gui/cGraphWidget.h
+++ b/CycloBranch/gui/cGraphWidget.h
@@ -83,6 +83,17 @@ class cGraphWidget : public QWidget
 	QTextBrowser* textbrowser;
 	string htmlstring;
 
+
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
+
 };
 
 #endif
\ No newline at end of file
diff --git a/CycloBranch/gui/cLassoWidget.cpp b/CycloBranch/gui/cLassoWidget.cpp
index 20874c1..3806b29 100644
--- a/CycloBranch/gui/cLassoWidget.cpp
+++ b/CycloBranch/gui/cLassoWidget.cpp
@@ -4,6 +4,9 @@
 #include <QVBoxLayout>
 #include <QPainter>
 #include <QPaintEvent>
+#include <QMessageBox>
+#include <QPrinter>
+#include <QSvgGenerator>
 
 
 void generateBranchLabelsDown(bool nterminal, int rotationid, unordered_set<cIonLabel, hash_cIonLabel>& labels, cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum, int centerx, int topmargin, int horizontalstep, int verticalstep, int visiblerotationid, int branchstart) {
@@ -64,18 +67,97 @@ void cLassoWidget::initialize(cParameters* parameters, cTheoreticalSpectrum* the
 }
 
 
+void cLassoWidget::exportToPDF(QString filename, bool postscript) {
+	QPrinter printer;
+	if (postscript) {
+		printer.setPaperSize(QSizeF(width() + 100, height() + 100), QPrinter::DevicePixel);
+		printer.setPageMargins (50, 50, 50, 50, QPrinter::DevicePixel);
+	}
+	else {
+		printer.setPaperSize(QSizeF(width(), height()), QPrinter::DevicePixel);
+		printer.setPageMargins (0, 0, 0, 0, QPrinter::DevicePixel);
+	}
+	printer.setOutputFormat(QPrinter::NativeFormat);
+	printer.setOutputFileName(filename);
+
+	QPainter painter;
+	if (!painter.begin(&printer)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		#if OS_TYPE == UNX
+			errstr += "\nDo you have a properly configured print server (sudo apt-get install cups-pdf) ?";
+			errstr += "\nIf you cannot create a ps file, you can create a pdf file and then use pdf2ps tool.";
+		#endif
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+}
+
+
+void cLassoWidget::exportToPNG(QString filename) {
+	QImage image(width(), height(), QImage::Format_ARGB32);
+	image.fill(Qt::white);
+
+	QPainter painter;
+	if (!painter.begin(&image)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+	image.save(filename);
+}
+
+
+void cLassoWidget::exportToSVG(QString filename) {
+	QSvgGenerator generator;
+	generator.setFileName(filename);
+	generator.setSize(QSize(width(), height()));
+	generator.setViewBox(QRect(0, 0, width(), height()));
+
+	QPainter painter;
+	if (!painter.begin(&generator)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	paint(painter);
+	painter.end();
+}
+
+
 void cLassoWidget::paintEvent(QPaintEvent *event) {
+	QPainter painter;
+	painter.begin(this);
+	paint(painter);
+	painter.end();
+}
+
 
-	if (theoreticalspectrum->getVisualCoverage().size() == 0) {
+void cLassoWidget::paint(QPainter& painter) {
+
+	if (!theoreticalspectrum) {
 		return;
 	}
 
 	vector<string> backboneacronyms;
 	vector<string> branchacronyms;
-	backboneacronyms = theoreticalspectrum->getBackboneAcronyms();
-	branchacronyms = theoreticalspectrum->getBranchAcronyms();
+	backboneacronyms = theoreticalspectrum->getCandidate().getBackboneAcronyms();
+	branchacronyms = theoreticalspectrum->getCandidate().getBranchAcronyms();
 
-	QPainter painter(this);
 	const int topmargin = 20;
 	const int leftmargin = 20;
 	const int bottommargin = 80;
@@ -83,6 +165,11 @@ void cLassoWidget::paintEvent(QPaintEvent *event) {
 
 	int backbonesize = (int)backboneacronyms.size();
 	int branchsize = (int)branchacronyms.size();
+
+	if (branchsize < 1) {
+		return;
+	}
+
 	double angle = 2*pi/(double)backbonesize;
 	int centerx = width()/2;
 	int centery = height()*3/4;
@@ -92,28 +179,44 @@ void cLassoWidget::paintEvent(QPaintEvent *event) {
 	const int verticalstep = (centery - radius - topmargin - 10)/std::max(branchsize, 1);
 
 	QFont myFont("Courier", 9);
+	QFontMetrics fm(myFont);
 	painter.setFont(myFont);
 
+	unordered_set<cIonLabel, hash_cIonLabel> labels;
+	labels.clear();
+
 	int linesize = 20;
 	int cornerlinesize = horizontalstep/8;
-	paintCircle(painter, (QColor &)(palette().color(QPalette::Background)), backboneacronyms, centerx, centery, radius, angle, horizontalstep, linesize, cornerlinesize);
+
+	paintCircle(painter, backboneacronyms, centerx, centery, radius, angle, horizontalstep, linesize, cornerlinesize, theoreticalspectrum->getVisualCoverage().size() > 0, visiblerotationid, labels);
 
 
 	// paint the branch
 	for (int i = 0; i < branchsize; i++) {
 		painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-		painter.drawText(centerx - horizontalstep/3, topmargin + verticalstep*i, horizontalstep*2/3, 20, Qt::AlignCenter, branchacronyms[branchsize - i - 1].c_str());
-		painter.drawText(centerx - horizontalstep/3, topmargin + verticalstep*i - 20, horizontalstep*2/3, 20, Qt::AlignLeft, to_string(backbonesize + branchsize - i).c_str());
+		if (fm.width(branchacronyms[branchsize - i - 1].c_str()) > horizontalstep*2/3) {
+			painter.drawText(centerx - horizontalstep/3 + 2, topmargin + verticalstep*i, horizontalstep*2/3 - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, branchacronyms[branchsize - i - 1].c_str());
+		}
+		else {
+			painter.drawText(centerx - horizontalstep/3, topmargin + verticalstep*i, horizontalstep*2/3, 20, Qt::AlignCenter, branchacronyms[branchsize - i - 1].c_str());
+		}	
+
+		if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+			painter.drawText(centerx - horizontalstep/3, topmargin + verticalstep*i - 20, horizontalstep*2/3, 20, Qt::AlignLeft, to_string(backbonesize + branchsize - i).c_str());
+		}
 
 		painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 		painter.drawRect(centerx - horizontalstep/3, topmargin + verticalstep*i, horizontalstep*2/3, 20);
 
 		painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 		painter.drawLine(centerx, topmargin + verticalstep*i + 20, centerx, topmargin + verticalstep*i + verticalstep);
-		painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
-		painter.drawLine(centerx - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, centerx + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);	
-		painter.drawLine(centerx - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, centerx - 20, topmargin + verticalstep*i + (verticalstep + 10)/2 + verticalstep/8);
-		painter.drawLine(centerx + 20, topmargin + verticalstep*i + (verticalstep + 10)/2 - verticalstep/8, centerx + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);
+
+		if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+			painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+			painter.drawLine(centerx - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, centerx + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);	
+			painter.drawLine(centerx - 20, topmargin + verticalstep*i + (verticalstep + 10)/2, centerx - 20, topmargin + verticalstep*i + (verticalstep + 10)/2 + verticalstep/8);
+			painter.drawLine(centerx + 20, topmargin + verticalstep*i + (verticalstep + 10)/2 - verticalstep/8, centerx + 20, topmargin + verticalstep*i + (verticalstep + 10)/2);
+		}
 
 		if (i == branchsize - 1) {
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
@@ -122,124 +225,125 @@ void cLassoWidget::paintEvent(QPaintEvent *event) {
 	}
 
 
-	// get lasso rotations
-	vector<cCandidate> lassorotations;
-	theoreticalspectrum->getCandidate().getLassoRotations(lassorotations, true);
+	if (parameters && (theoreticalspectrum->getVisualCoverage().size() > 0)) {
 
-	// get T-permutations of lasso rotations
-	vector<vector<TRotationInfo> > trotationsoflassorotations;
-	trotationsoflassorotations.resize(lassorotations.size());
-	for (int i = 0; i < (int)lassorotations.size(); i++) {
-		lassorotations[i].getPermutationsOfBranches(trotationsoflassorotations[i]);
-	}
+		// get branch-cyclic rotations
+		vector<cCandidate> lassorotations;
+		theoreticalspectrum->getCandidate().getLassoRotations(lassorotations, true);
 
-	unordered_set<cIonLabel, hash_cIonLabel> labels;
-	labels.clear();
+		// get T-permutations of branch-cyclic rotations
+		vector<vector<TRotationInfo> > trotationsoflassorotations;
+		trotationsoflassorotations.resize(lassorotations.size());
+		for (int i = 0; i < (int)lassorotations.size(); i++) {
+			lassorotations[i].getPermutationsOfBranches(trotationsoflassorotations[i]);
+		}
 
-	int rotationid;
-	int half = (int)theoreticalspectrum->getVisualCoverage().size()/(int)parameters->fragmentionsfortheoreticalspectra.size()/2;
-	for (int i = 0; i < half; i++) {
+		int rotationid;
+		int half = (int)theoreticalspectrum->getVisualCoverage().size()/(int)parameters->fragmentionsfortheoreticalspectra.size()/2;
+		for (int i = 0; i < half; i++) {
 		
-		if ((visibletrotationid != -1) && (visibletrotationid != i % 6)) {
-			continue;
-		}
+			if ((visibletrotationid != -1) && (visibletrotationid != i % 6)) {
+				continue;
+			}
 		
-		if (i/6 == 0) {
-			rotationid = half/6;
-		}
-		else {
-			rotationid = 2*half/6 - i/6;
-		}
+			if (i/6 == 0) {
+				rotationid = half/6;
+			}
+			else {
+				rotationid = 2*half/6 - i/6;
+			}
 		
-		switch (i % 6)
-		{
-		case 0:
-			generateCyclicLabelsToRight(true, i, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][0].middlebranchstart, trotationsoflassorotations[i/6][0].middlebranchend);
-			break;
-		case 1:
-			generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
-			generateCyclicLabelsToRight(true, i, -1, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
-			break;
-		case 2:
-			generateCyclicLabelsToRight(true, rotationid*6 + 2, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][2].middlebranchstart, trotationsoflassorotations[rotationid][2].middlebranchend);
-			break;
-		case 3:
-			generateCyclicLabelsToRight(true, i, i/6, 0, trotationsoflassorotations[i/6][3].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchstart, trotationsoflassorotations[i/6][3].middlebranchend);
-			generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchend);
-			generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
-			generateCyclicLabelsToLeft(false, i, 0, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
-			break;
-		case 4:
-			generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
-			generateCyclicLabelsToLeft(true, i, 0, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
-			break;
-		case 5:
-			generateCyclicLabelsToRight(true, rotationid*6 + 5, i/6, 0, trotationsoflassorotations[rotationid][5].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][5].middlebranchstart, trotationsoflassorotations[rotationid][5].middlebranchend);
-			generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][5].middlebranchend);
-			generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
-			generateCyclicLabelsToRight(false, i, -1, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
-			break;
-		default:
-			break;
+			switch (i % 6)
+			{
+			case 0:
+				generateCyclicLabelsToRight(true, i, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][0].middlebranchstart, trotationsoflassorotations[i/6][0].middlebranchend);
+				break;
+			case 1:
+				generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
+				generateCyclicLabelsToRight(true, i, -1, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
+				break;
+			case 2:
+				generateCyclicLabelsToRight(true, rotationid*6 + 2, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][2].middlebranchstart, trotationsoflassorotations[rotationid][2].middlebranchend);
+				break;
+			case 3:
+				generateCyclicLabelsToRight(true, i, i/6, 0, trotationsoflassorotations[i/6][3].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchstart, trotationsoflassorotations[i/6][3].middlebranchend);
+				generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchend);
+				generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
+				generateCyclicLabelsToLeft(false, i, 0, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
+				break;
+			case 4:
+				generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
+				generateCyclicLabelsToLeft(true, i, 0, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
+				break;
+			case 5:
+				generateCyclicLabelsToRight(true, rotationid*6 + 5, i/6, 0, trotationsoflassorotations[rotationid][5].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][5].middlebranchstart, trotationsoflassorotations[rotationid][5].middlebranchend);
+				generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][5].middlebranchend);
+				generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
+				generateCyclicLabelsToRight(false, i, -1, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
+				break;
+			default:
+				break;
+			}
+
 		}
 
-	}
+		for (int i = half; i < 2*half; i++) {
 
-	for (int i = half; i < 2*half; i++) {
+			if ((visibletrotationid != -1) && (visibletrotationid != i % 6)) {
+				continue;
+			}
 
-		if ((visibletrotationid != -1) && (visibletrotationid != i % 6)) {
-			continue;
-		}
+			if (i/6 == half/6) {
+				rotationid = 0;
+			}
+			else {
+				rotationid = 2*half/6 - i/6;
+			}
 
-		if (i/6 == half/6) {
-			rotationid = 0;
-		}
-		else {
-			rotationid = 2*half/6 - i/6;
-		}
+			switch (i % 6)
+			{
+			case 0:
+				generateCyclicLabelsToLeft(true, i, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][0].middlebranchstart, trotationsoflassorotations[i/6][0].middlebranchend);
+				break;
+			case 1:
+				generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
+				generateCyclicLabelsToLeft(true, i, 0, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
+				break;
+			case 2:
+				generateCyclicLabelsToLeft(true, rotationid*6 + 2, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][2].middlebranchstart, trotationsoflassorotations[rotationid][2].middlebranchend);
+				break;
+			case 3:
+				generateCyclicLabelsToLeft(true, i, i/6, 0, trotationsoflassorotations[i/6][3].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchstart, trotationsoflassorotations[i/6][3].middlebranchend);
+				generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchend);
+				generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
+				generateCyclicLabelsToRight(false, i, -1, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
+				break;
+			case 4:
+				generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
+				generateCyclicLabelsToRight(true, i, -1, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
+				break;
+			case 5:
+				generateCyclicLabelsToLeft(true, rotationid*6 + 5, i/6, 0, trotationsoflassorotations[rotationid][5].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][5].middlebranchstart, trotationsoflassorotations[rotationid][5].middlebranchend);
+				generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][5].middlebranchend);
+				generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
+				generateCyclicLabelsToLeft(false, i, 0, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
+				break;
+			default:
+				break;
+			}
 
-		switch (i % 6)
-		{
-		case 0:
-			generateCyclicLabelsToLeft(true, i, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][0].middlebranchstart, trotationsoflassorotations[i/6][0].middlebranchend);
-			break;
-		case 1:
-			generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
-			generateCyclicLabelsToLeft(true, i, 0, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
-			break;
-		case 2:
-			generateCyclicLabelsToLeft(true, rotationid*6 + 2, i/6, 0, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][2].middlebranchstart, trotationsoflassorotations[rotationid][2].middlebranchend);
-			break;
-		case 3:
-			generateCyclicLabelsToLeft(true, i, i/6, 0, trotationsoflassorotations[i/6][3].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchstart, trotationsoflassorotations[i/6][3].middlebranchend);
-			generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][3].middlebranchend);
-			generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
-			generateCyclicLabelsToRight(false, i, -1, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
-			break;
-		case 4:
-			generateBranchLabelsDown(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart);
-			generateCyclicLabelsToRight(true, i, -1, trotationsoflassorotations[i/6][4].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][4].middlebranchstart, trotationsoflassorotations[i/6][4].middlebranchend);
-			break;
-		case 5:
-			generateCyclicLabelsToLeft(true, rotationid*6 + 5, i/6, 0, trotationsoflassorotations[rotationid][5].middlebranchstart, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[rotationid][5].middlebranchstart, trotationsoflassorotations[rotationid][5].middlebranchend);
-			generateBranchLabelsUp(true, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][5].middlebranchend);
-			generateBranchLabelsDown(false, i, labels, parameters, theoreticalspectrum, centerx, topmargin, horizontalstep, verticalstep, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart);
-			generateCyclicLabelsToLeft(false, i, 0, trotationsoflassorotations[i/6][1].middlebranchend, backbonesize + branchsize - 1, backbonesize, labels, parameters, theoreticalspectrum, centerx, centery, radius, angle, linesize, cornerlinesize, visiblerotationid, trotationsoflassorotations[i/6][1].middlebranchstart, trotationsoflassorotations[i/6][1].middlebranchend);
-			break;
-		default:
-			break;
 		}
 
-	}
-
-	painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
-	for (auto it = labels.begin(); it != labels.end(); ++it) {
-		if (it->alignright) {
-			painter.drawText(it->x - (int)it->label.size()*7, it->y, (int)it->label.size()*7, 20, Qt::AlignLeft, it->label.c_str());
-		}
-		else {
-			painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+		painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
+		for (auto it = labels.begin(); it != labels.end(); ++it) {
+			if (it->alignright) {
+				painter.drawText(it->x - fm.width(it->label.c_str()), it->y, fm.width(it->label.c_str()), 20, Qt::AlignLeft, it->label.c_str());
+			}
+			else {
+				painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+			}
 		}
+
 	}
 
 }
diff --git a/CycloBranch/gui/cLassoWidget.h b/CycloBranch/gui/cLassoWidget.h
index ee21684..5417ce6 100644
--- a/CycloBranch/gui/cLassoWidget.h
+++ b/CycloBranch/gui/cLassoWidget.h
@@ -1,6 +1,6 @@
 /**
 	\file cLassoWidget.h
-	\brief Visualization of a lasso peptide.
+	\brief Visualization of a branch-cyclic peptide.
 */
 
 
@@ -21,7 +21,7 @@ class QPaintEvent;
 
 
 /**
-	\brief Generate labels of fragment ions on a branch of a lasso peptide (direction down).
+	\brief Generate labels of fragment ions on a branch of a branch-cyclic peptide (direction down).
 	\param nterminal if true only nterminal fragment ions are drawn, if false only cterminal fragment ions are drawn
 	\param rotationid id of a sequence rotation
 	\param labels labels of fragment ions
@@ -38,7 +38,7 @@ void generateBranchLabelsDown(bool nterminal, int rotationid, unordered_set<cIon
 
 
 /**
-	\brief Generate labels of fragment ions on a branch of a lasso peptide (direction up).
+	\brief Generate labels of fragment ions on a branch of a branch-cyclic peptide (direction up).
 	\param nterminal if true only nterminal fragment ions are drawn, if false only cterminal fragment ions are drawn
 	\param rotationid id of a sequence rotation
 	\param labels labels of fragment ions
@@ -55,7 +55,7 @@ void generateBranchLabelsUp(bool nterminal, int rotationid, unordered_set<cIonLa
 
 
 /**
-	\brief Visualization of a lasso peptide.
+	\brief Visualization of a branch-cyclic peptide.
 */
 class cLassoWidget : public QWidget
 {
@@ -78,6 +78,28 @@ class cLassoWidget : public QWidget
 	void initialize(cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum);
 
 
+	/**
+		\brief Export peptide into a PDF or a PS file.
+		\param filename filename
+		\param postscript if true then PS file is generated instead of PDF
+	*/ 
+	void exportToPDF(QString filename, bool postscript);
+
+
+	/**
+		\brief Export peptide scene into a PNG file.
+		\param filename filename
+	*/ 
+	void exportToPNG(QString filename);
+
+
+	/**
+		\brief Export peptide scene into a SVG file.
+		\param filename filename
+	*/ 
+	void exportToSVG(QString filename);
+
+
 protected:
 
 
@@ -90,6 +112,8 @@ class cLassoWidget : public QWidget
 
 private:
 
+	void paint(QPainter& painter);
+
 	cParameters* parameters;
 	cTheoreticalSpectrum* theoreticalspectrum;
 	int visiblerotationid;
diff --git a/CycloBranch/gui/cLinearWidget.cpp b/CycloBranch/gui/cLinearWidget.cpp
index 33ceddd..cdda0a9 100644
--- a/CycloBranch/gui/cLinearWidget.cpp
+++ b/CycloBranch/gui/cLinearWidget.cpp
@@ -4,6 +4,9 @@
 #include <QVBoxLayout>
 #include <QPainter>
 #include <QPaintEvent>
+#include <QMessageBox>
+#include <QPrinter>
+#include <QSvgGenerator>
 
 
 bool operator == (cIonLabel const& a, cIonLabel const& b) {
@@ -40,28 +43,113 @@ void cLinearWidget::initialize(cParameters* parameters, cTheoreticalSpectrum* th
 }
 
 
+void cLinearWidget::exportToPDF(QString filename, bool postscript) {
+	QPrinter printer;
+	if (postscript) {
+		printer.setPaperSize(QSizeF(width() + 100, height() + 100), QPrinter::DevicePixel);
+		printer.setPageMargins (50, 50, 50, 50, QPrinter::DevicePixel);
+	}
+	else {
+		printer.setPaperSize(QSizeF(width(), height()), QPrinter::DevicePixel);
+		printer.setPageMargins (0, 0, 0, 0, QPrinter::DevicePixel);
+	}
+	printer.setOutputFormat(QPrinter::NativeFormat);
+	printer.setOutputFileName(filename);
+
+	QPainter painter;
+	if (!painter.begin(&printer)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		#if OS_TYPE == UNX
+			errstr += "\nDo you have a properly configured print server (sudo apt-get install cups-pdf) ?";
+			errstr += "\nIf you cannot create a ps file, you can create a pdf file and then use pdf2ps tool.";
+		#endif
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+}
+
+
+void cLinearWidget::exportToPNG(QString filename) {
+	QImage image(width(), height(), QImage::Format_ARGB32);
+	image.fill(Qt::white);
+
+	QPainter painter;
+	if (!painter.begin(&image)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	paint(painter);
+	painter.end();
+	image.save(filename);
+}
+
+
+void cLinearWidget::exportToSVG(QString filename) {
+	QSvgGenerator generator;
+	generator.setFileName(filename);
+	generator.setSize(QSize(width(), height()));
+	generator.setViewBox(QRect(0, 0, width(), height()));
+
+	QPainter painter;
+	if (!painter.begin(&generator)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	paint(painter);
+	painter.end();
+}
+
+
 void cLinearWidget::paintEvent(QPaintEvent *event) {
+	QPainter painter;
+	painter.begin(this);
+	paint(painter);
+	painter.end();
+}
 
-	if (theoreticalspectrum->getVisualCoverage().size() == 0) {
+
+void cLinearWidget::paint(QPainter& painter) {
+
+	if (!theoreticalspectrum) {
 		return;
 	}
 
-	QPainter painter(this);
 	const int topmargin = max(20,(height() - 80)/2);
 	const int leftmargin = 20;
 	const int bottommargin = 80;
 	const int rightmargin = 20;
 
-	int size = (int)theoreticalspectrum->getAcronyms().size();
+	int size = (int)theoreticalspectrum->getCandidate().getAcronyms().size();
 
 	const int horizontalstep = (width() - leftmargin - rightmargin)/std::max(size, 1);
 
 	QFont myFont("Courier", 9);
+	QFontMetrics fm(myFont);
 	painter.setFont(myFont);
 
 	for (int i = 0; i < size; i++) {
 		painter.setPen(QPen(Qt::blue, 2, Qt::SolidLine));
-		painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*i, topmargin, horizontalstep/2, 20, Qt::AlignCenter, theoreticalspectrum->getAcronyms()[i].c_str());
+		if (fm.width(theoreticalspectrum->getCandidate().getAcronyms()[i].c_str()) > horizontalstep/2) {
+			painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*i + 2, topmargin, horizontalstep/2 - 2, 20, Qt::AlignLeft|Qt::AlignVCenter, theoreticalspectrum->getCandidate().getAcronyms()[i].c_str());
+		}
+		else {
+			painter.drawText(leftmargin + horizontalstep/4 + horizontalstep*i, topmargin, horizontalstep/2, 20, Qt::AlignCenter, theoreticalspectrum->getCandidate().getAcronyms()[i].c_str());
+		}
 
 		painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 		painter.drawRect(leftmargin + horizontalstep/4 + horizontalstep*i, topmargin, horizontalstep/2, 20);
@@ -69,41 +157,48 @@ void cLinearWidget::paintEvent(QPaintEvent *event) {
 		if (i < size - 1) {
 			painter.setPen(QPen(Qt::black, 2, Qt::SolidLine));
 			painter.drawLine(leftmargin + horizontalstep/4 + horizontalstep*i + horizontalstep/2, topmargin + 11, leftmargin + horizontalstep/4 + horizontalstep*(i + 1), topmargin + 11);
-			painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
-			painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin - 10, leftmargin + horizontalstep*(i + 1), topmargin + 30);	
-			painter.drawLine(leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*i + horizontalstep/2, topmargin - 10, leftmargin + horizontalstep*(i + 1), topmargin + - 10);
-			painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin + 30, leftmargin + horizontalstep*(i + 1) + horizontalstep/8, topmargin + 30);
+
+			if (theoreticalspectrum->getVisualCoverage().size() > 0) {
+				painter.setPen(QPen(Qt::black, 2, Qt::DashLine));
+				painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin - 10, leftmargin + horizontalstep*(i + 1), topmargin + 30);	
+				painter.drawLine(leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*i + horizontalstep/2, topmargin - 10, leftmargin + horizontalstep*(i + 1), topmargin + - 10);
+				painter.drawLine(leftmargin + horizontalstep*(i + 1), topmargin + 30, leftmargin + horizontalstep*(i + 1) + horizontalstep/8, topmargin + 30);
+			}
 		}
 	}
 	
-	unordered_set<cIonLabel, hash_cIonLabel> labels;
-	labels.clear();
-
-	string name;
-	int len = (int)theoreticalspectrum->getVisualCoverage()[0].series.size();
-
-	for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
-		if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) {
-			for (int j = 0; j < len; j++) {
-				if (theoreticalspectrum->getVisualCoverage()[i].series[j] > 0) {
-					name = parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name[0] + to_string(j + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name.substr(1);
-					insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*j + horizontalstep/2, topmargin - 35, name, false);
+	if (parameters && (theoreticalspectrum->getVisualCoverage().size() > 0)) {
+
+		unordered_set<cIonLabel, hash_cIonLabel> labels;
+		labels.clear();
+
+		string name;
+		int len = (int)theoreticalspectrum->getVisualCoverage()[0].series.size();
+
+		for (int i = 0; i < (int)parameters->fragmentionsfortheoreticalspectra.size(); i++) {
+			if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].nterminal) {
+				for (int j = 0; j < len; j++) {
+					if (theoreticalspectrum->getVisualCoverage()[i].series[j] > 0) {
+						name = parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name[0] + to_string(j + 1) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name.substr(1);
+						insertLabel(labels, leftmargin + horizontalstep/4 + horizontalstep/8 + horizontalstep*j + horizontalstep/2, topmargin - 35, name, false);
+					}
 				}
 			}
-		}
-		if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal) {
-			for (int j = len - 1; j >= 0; j--) {
-				if (theoreticalspectrum->getVisualCoverage()[i].series[len - j - 1] > 0) {
-					name = parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name[0] + to_string(len - j) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name.substr(1);
-					insertLabel(labels, leftmargin + horizontalstep*(j + 1), topmargin + 35, name, false);
+			if (parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].cterminal) {
+				for (int j = len - 1; j >= 0; j--) {
+					if (theoreticalspectrum->getVisualCoverage()[i].series[len - j - 1] > 0) {
+						name = parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name[0] + to_string(len - j) + parameters->fragmentdefinitions[parameters->fragmentionsfortheoreticalspectra[i]].name.substr(1);
+						insertLabel(labels, leftmargin + horizontalstep*(j + 1), topmargin + 35, name, false);
+					}
 				}
 			}
 		}
-	}
 
-	painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
-	for (auto it = labels.begin(); it != labels.end(); ++it) {
-		painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+		painter.setPen(QPen(Qt::red, 2, Qt::SolidLine));
+		for (auto it = labels.begin(); it != labels.end(); ++it) {
+			painter.drawText(it->x, it->y, width(), 20, Qt::AlignLeft, it->label.c_str());
+		}
+	
 	}
 	
 }
diff --git a/CycloBranch/gui/cLinearWidget.h b/CycloBranch/gui/cLinearWidget.h
index 092d3cc..e14d1a6 100644
--- a/CycloBranch/gui/cLinearWidget.h
+++ b/CycloBranch/gui/cLinearWidget.h
@@ -77,7 +77,7 @@ struct hash_cIonLabel {
 		\retval size_t hashed ion label
 	*/
 	size_t operator()(const cIonLabel& label) const {
-		return hash<string>()(to_string(label.x) + to_string(label.y));
+		return std::hash<string>()(to_string(label.x) + to_string(label.y));
 	}
 
 };
@@ -127,6 +127,28 @@ class cLinearWidget : public QWidget
 	void initialize(cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum);
 
 
+	/**
+		\brief Export peptide into a PDF or a PS file.
+		\param filename filename
+		\param postscript if true then PS file is generated instead of PDF
+	*/ 
+	void exportToPDF(QString filename, bool postscript);
+
+
+	/**
+		\brief Export peptide scene into a PNG file.
+		\param filename filename
+	*/ 
+	void exportToPNG(QString filename);
+
+
+	/**
+		\brief Export peptide scene into a SVG file.
+		\param filename filename
+	*/ 
+	void exportToSVG(QString filename);
+
+
 protected:
 
 
@@ -139,6 +161,8 @@ class cLinearWidget : public QWidget
 
 private:
 
+	void paint(QPainter& painter);
+
 	cParameters* parameters;
 	cTheoreticalSpectrum* theoreticalspectrum;
 
diff --git a/CycloBranch/gui/cMainThread.cpp b/CycloBranch/gui/cMainThread.cpp
index e7464a0..d5da33b 100644
--- a/CycloBranch/gui/cMainThread.cpp
+++ b/CycloBranch/gui/cMainThread.cpp
@@ -1,30 +1,26 @@
 #include "gui/cMainThread.h"
 
 
-QString appname = "CycloBranch";
-QString appversion = "v. 1.0.850 (64-bit)";
-
-
 bool cMainThread::checkModifications(cParameters& parameters, cSequence& sequence, int& startmodifid, int& endmodifid, int& middlemodifid, string& errormessage) {
 	startmodifid = 0;
 	endmodifid = 0;
 	middlemodifid = 0;
 	errormessage = "";
 
-	if ((parameters.peptidetype == linear) || (parameters.peptidetype == branched) || (parameters.peptidetype == lasso) || (parameters.peptidetype == linearpolysaccharide)) {
+	if ((sequence.getPeptideType() == linear) || (sequence.getPeptideType() == branched) || (sequence.getPeptideType() == lasso) || (sequence.getPeptideType() == linearpolysaccharide)) {
 
-		if ((parameters.peptidetype == linear) || (parameters.peptidetype == branched) || (parameters.peptidetype == linearpolysaccharide)) {
+		if ((sequence.getPeptideType() == linear) || (sequence.getPeptideType() == branched) || (sequence.getPeptideType() == linearpolysaccharide)) {
 			startmodifid = -1;
 			endmodifid = -1;
 		}
 
-		if ((parameters.peptidetype == branched) || (parameters.peptidetype == lasso)) {
+		if ((sequence.getPeptideType() == branched) || (sequence.getPeptideType() == lasso)) {
 			middlemodifid = -1;
 		}
 
 		for (int i = 0; i < (int)parameters.searchedmodifications.size(); i++) {
 
-			if ((parameters.peptidetype == linear) || (parameters.peptidetype == branched) || (parameters.peptidetype == linearpolysaccharide)) {
+			if ((sequence.getPeptideType() == linear) || (sequence.getPeptideType() == branched) || (sequence.getPeptideType() == linearpolysaccharide)) {
 				if (parameters.searchedmodifications[i].name.compare(sequence.getNTterminalModification()) == 0) {
 					startmodifid = i;
 				}
@@ -34,7 +30,7 @@ bool cMainThread::checkModifications(cParameters& parameters, cSequence& sequenc
 				}
 			}
 
-			if ((parameters.peptidetype == branched) || (parameters.peptidetype == lasso)) {
+			if ((sequence.getPeptideType() == branched) || (sequence.getPeptideType() == lasso)) {
 				if (parameters.searchedmodifications[i].name.compare(sequence.getBranchModification()) == 0) {
 					middlemodifid = i;
 				}
@@ -43,18 +39,17 @@ bool cMainThread::checkModifications(cParameters& parameters, cSequence& sequenc
 		}
 
 		if (startmodifid == -1) {
-			errormessage = "The N-terminal modification in the sequence " + sequence.getSequence() + " is not listed in the field 'N-terminal and C-terminal modifications': " + sequence.getNTterminalModification();
-
+			errormessage = "The N-terminal modification in the sequence " + sequence.getSequence() + " is not defined: " + sequence.getNTterminalModification();
 			return false;
 		}
 
 		if (endmodifid == -1) {
-			errormessage = "The C-terminal modification in the sequence " + sequence.getSequence() + " is not listed in the field 'N-terminal and C-terminal modifications': " + sequence.getCTterminalModification();
+			errormessage = "The C-terminal modification in the sequence " + sequence.getSequence() + " is not defined: " + sequence.getCTterminalModification();
 			return false;
 		}
 
 		if (middlemodifid == -1) {
-			errormessage = "The branch modification in the sequence " + sequence.getSequence() + " is not listed in the field 'N-terminal and C-terminal modifications': " + sequence.getBranchModification();
+			errormessage = "The branch modification in the sequence " + sequence.getSequence() + " is not defined: " + sequence.getBranchModification();
 			return false;
 		}
 		
@@ -64,112 +59,9 @@ bool cMainThread::checkModifications(cParameters& parameters, cSequence& sequenc
 }
 
 
-void cMainThread::parseBranch(peptideType peptidetype, string& composition, vector<string>& vectorcomposition, int& branchstart, int& branchend) {
-	string s = composition;
-	cBrick b;
-	branchstart = -1;
-	branchend = -1;
-
-	if ((peptidetype == branched) || (peptidetype == lasso)) {
-		int i = 0;
-		while (i < (int)s.size()) {
-			if (s[i] == '\\') {
-				s.erase(s.begin() + i);
-			}
-			else {
-				i++;
-			}
-		}
-
-		for (int i = 0; i < (int)s.size(); i++) {
-			if (s[i] == '(') {
-				if (i > 0) {
-					b.clear();
-					b.setComposition(s.substr(0, i - 1), false);
-					branchstart = getNumberOfBricks(b.getComposition());
-					s[i] = '-';
-				}
-				else {
-					s.erase(s.begin());
-					branchstart = 0;
-				}
-				break;
-			}
-		}
-
-		for (int i = 0; i < (int)s.size(); i++) {
-			if (s[i] == ')') {
-				b.clear();
-				b.setComposition(s.substr(0, i - 1), false);
-				branchend = getNumberOfBricks(b.getComposition()) - 1;
-				if (i < (int)s.size() - 1) {
-					s[i] = '-';
-				}
-				else {
-					s.erase(s.begin() + i);
-				}
-				break;
-			}
-		}
-
-		if (branchend <= branchstart) {
-			branchstart = -1;
-			branchend = -1;
-		}
-	}
-
-	b.clear();
-	b.setComposition(s, false);
-	b.explodeToStringComposition(vectorcomposition);
-}
-
-
-bool cMainThread::checkRegex(cParameters& parameters, string& sequence, string& errormessage) {
-	errormessage = "";
-
-	if (sequence.compare("") == 0) {
-		errormessage = "The sequence is empty.";
-		return false;
-	}
-
-	regex rx;
-	// [^\\[\\]]+ is used instead of .+ to prevent from a too complex regex error
-	switch (parameters.peptidetype)
-	{
-	case linear:
-	case cyclic:
-	case linearpolysaccharide:
-		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
-		break;
-	case branched:
-		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
-		break;
-	case lasso:
-		rx = "(^(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$|^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?$)";
-		break;
-	case other:
-	default:
-		rx = ".*";
-		break;
-	}
-
-	try {
-		if (!(regex_search(sequence, rx))) {
-			errormessage = "The format of sequence is invalid: " + sequence + ".";
-			return false;
-		}
-	}
-	catch (std::regex_error& e) {
-		errormessage = "cMainThread::checkRegex: regex_search failed, error no. " + to_string(e.code());
-		return false;
-	}
-
-	return true;
-}
-
-
-cMainThread::cMainThread(cParameters& parameters, bool enablelogwindow, bool enablestdout) {
+cMainThread::cMainThread(cParameters& parameters, cTheoreticalSpectrumList& theoreticalspectrumlist, bool enablelogwindow, bool enablestdout) {
 	this->parameters = parameters;
+	this->theoreticalspectrumlist = &theoreticalspectrumlist;
 	this->enablelogwindow = enablelogwindow;
 	this->enablestdout = enablestdout;
 
@@ -234,7 +126,9 @@ cMainThread& cMainThread::operator<<(StandardEndLine manip) {
 
 void cMainThread::run() {
 
-	emitStartSignals();
+	if (parameters.mode != denovoengine) {
+		emit setGraph("");
+	}
 
 	cMainThread* os = this;
 	string errormessage;
@@ -242,6 +136,8 @@ void cMainThread::run() {
 	cCandidateSet candidates;
 	candidates.getSet().clear();
 
+	theoreticalspectrumlist->clear();
+
 	QTime time;
 	time.start();
 
@@ -251,24 +147,15 @@ void cMainThread::run() {
 
 	parameters.setOutputStream(*os);
 	if (parameters.checkAndPrepare() == -1) {
-		emit safeExit();
+		emitEndSignals();
 		return;
 	}
 	*os << parameters.printToString();
 
-	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
-		if (!parameters.bricksdatabase.replaceAcronymsByIDs(parameters.sequencetag, errormessage)) {
-			*os << "Error: " << errormessage << endl;
-			emit safeExit();
-			return;	
-		}
-	}
-
 	if (parameters.mode == singlecomparison) {
-		errormessage = "";
-		if (!checkRegex(parameters, parameters.searchedsequence, errormessage)) {
+		if (!checkRegex(parameters.peptidetype, parameters.searchedsequence, errormessage)) {
 			*os << "Error: " << errormessage << endl;
-			emit safeExit();
+			emitEndSignals();
 			return;	
 		}
 	}
@@ -276,41 +163,27 @@ void cMainThread::run() {
 	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
 		if (!parameters.bricksdatabase.replaceAcronymsByIDs(parameters.searchedsequence, errormessage)) {
 			*os << "Error: " << errormessage << endl;
-			emit safeExit();
+			emitEndSignals();
 			return;	
 		}
-	}
 
-	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
-		if (parameters.peptidetype != cyclic) {
-			// check summary formulas of modifications
-			errormessage = "";
-			cSummaryFormula formula;
-			for (int i = 0; i < (int)parameters.searchedmodifications.size(); i++) {
-				formula.clear();
-				formula.setFormula(parameters.searchedmodifications[i].summary);
-				if (formula.isValid(errormessage)) {
-					parameters.searchedmodifications[i].massdifference = formula.getMass();
-				}
-				else {
-					*os << errormessage << endl;
-					emit safeExit();
-					return;	
-				}
-			}
+		if (!parameters.bricksdatabase.replaceAcronymsByIDs(parameters.sequencetag, errormessage)) {
+			*os << "Error: " << errormessage << endl;
+			emitEndSignals();
+			return;	
 		}
 	}
 
 	parameters.peaklist.sortbyMass();
-	parameters.peaklist.cropMinimumMZRatio(parameters.minimummz);
+	parameters.peaklist.cropMinimumMZRatio(parameters.minimummz, parameters.fragmentmasserrortolerance);
 
 	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
-		parameters.peaklist.cropMaximumMZRatio(uncharge(parameters.precursormass, parameters.precursorcharge));
+		parameters.peaklist.cropMaximumMZRatio(charge(uncharge(parameters.precursormass, parameters.precursorcharge), (parameters.precursorcharge > 0)?1:-1), parameters.precursormasserrortolerance);
 	}
 
 	if (parameters.peaklist.normalizeIntenzity() == -1) {
-		*os << "Error: the spectrum cannot be normalized; the maximum intensity is <= 0." << endl;
-		emit safeExit();
+		*os << "Error: the spectrum cannot be normalized because the maximum intensity is <= 0. The format of peaklist is likely incorrect." << endl;
+		emitEndSignals();
 		return;
 	}
 	parameters.peaklist.cropIntenzity(parameters.minimumrelativeintensitythreshold);
@@ -323,13 +196,47 @@ void cMainThread::run() {
 	}
 
 
+	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
+		int startmodifid, endmodifid, middlemodifid;
+		
+		cSequence sequence;
+		sequence.setNTterminalModification(parameters.searchedsequenceNtermmodif);
+		sequence.setCTterminalModification(parameters.searchedsequenceCtermmodif);
+		sequence.setBranchModification(parameters.searchedsequenceTmodif);
+		sequence.setPeptideType(parameters.peptidetype);
+
+		// check for names of modifications which are used with the searched sequence
+		errormessage = "";
+		if (!checkModifications(parameters, sequence, startmodifid, endmodifid, middlemodifid, errormessage)) {
+			*os << endl << "Error: " << errormessage << endl;
+			emitEndSignals();
+			return;
+		}
+
+		// single comparison of a peaklist with a theoretical spectrum
+		if (parameters.mode == singlecomparison) {
+			int branchstart, branchend;
+			vector<string> v;
+			cCandidate c;
+			vector<nodeEdge> netmp;
+
+			parseBranch(parameters.peptidetype, parameters.searchedsequence, v, branchstart, branchend);
+			// startmodifid, endmodifid and middlemodifid were filled up by checkModifications
+			c.setCandidate(v, netmp, startmodifid, endmodifid, middlemodifid, branchstart, branchend);
+			candidates.getSet().insert(c);
+		
+			graphreaderisworking = false;
+		}
+	}
+
+
 	// de novo search engine
 	if (parameters.mode == denovoengine) {
 
 		// create the de novo graph
 		graph.initialize(*os, parameters);
 		if (graph.createGraph(terminatecomputation) == -1) {
-			endNow();
+			emitEndSignals();
 			return;
 		}
 
@@ -339,12 +246,12 @@ void cMainThread::run() {
 		// note: paths finishing in precursor minus X are removed, however, precursor peak is always present thus any candidate should not be lost
 		if (parameters.blindedges == 1) {
 			if (graph.removeEdgesFormingPathsNotStartingFromFirstNode(terminatecomputation) == -1) {
-				endNow();
+				emitEndSignals();
 				return;
 			}
 
 			if (graph.removeEdgesFormingPathsNotFinishingInPrecursor(terminatecomputation) == -1) {
-				endNow();
+				emitEndSignals();
 				return;
 			}
 		}
@@ -352,12 +259,12 @@ void cMainThread::run() {
 		// blind paths are connected
 		if (parameters.blindedges == 2) {
 			if (graph.connectEdgesFormingPathsNotStartingFromFirstNode(terminatecomputation) == -1) {
-				endNow();
+				emitEndSignals();
 				return;
 			}
 
 			if (graph.connectEdgesFormingPathsNotFinishingInPrecursor(terminatecomputation) == -1) {
-				endNow();
+				emitEndSignals();
 				return;
 			}
 		}
@@ -366,7 +273,7 @@ void cMainThread::run() {
 		emit setGraph(graph.printGraph());
 
 		if (graph.removePathsWhichCanBeSubstitutedByLongerPath(terminatecomputation) == -1) {
-			endNow();
+			emitEndSignals();
 			return;
 		}
 
@@ -395,7 +302,6 @@ void cMainThread::run() {
 			*os << "The number of sequence candidates is too high. The identification would be very time-consuming. Please, change the settings and search again." << endl << endl;
 			*os << "Aborted." << endl;
 			emitEndSignals();
-			endNow();
 			return;
 		}
 
@@ -405,35 +311,6 @@ void cMainThread::run() {
 	}
 
 
-	// single comparison of a peaklist with a theoretical spectrum
-	if (parameters.mode == singlecomparison) {
-		vector<string> v;
-		cCandidate c;
-		int startmodifid, endmodifid, middlemodifid, branchstart, branchend;
-
-		cSequence sequence;
-		sequence.setNTterminalModification(parameters.searchedsequenceNtermmodif);
-		sequence.setCTterminalModification(parameters.searchedsequenceCtermmodif);
-		sequence.setBranchModification(parameters.searchedsequenceTmodif);
-
-		errormessage = "";
-		if (!checkModifications(parameters, sequence, startmodifid, endmodifid, middlemodifid, errormessage)) {
-			*os << endl << "Error: " << errormessage << endl;
-			emitEndSignals();
-			endNow();
-			return;
-		}
-
-		parseBranch(parameters.peptidetype, parameters.searchedsequence, v, branchstart, branchend);
-
-		vector<nodeEdge> netmp;
-		c.setCandidate(v, netmp, startmodifid, endmodifid, middlemodifid, branchstart, branchend);
-		candidates.getSet().insert(c);
-		
-		graphreaderisworking = false;
-	}
-
-
 	// database search - MS/MS mode
 	if (parameters.mode == databasesearch) {
 		string composition;
@@ -457,7 +334,7 @@ void cMainThread::run() {
 			}
 
 			// check format of sequence
-			if (!calculatesummaries && !checkRegex(parameters, parameters.sequencedatabase[i].getSequence(), errormessage)) {
+			if (!calculatesummaries && !checkRegex(parameters.sequencedatabase[i].getPeptideType(), parameters.sequencedatabase[i].getSequence(), errormessage)) {
 				*os << "Ignored sequence: " << errormessage << endl;
 				continue;
 			}
@@ -475,12 +352,12 @@ void cMainThread::run() {
 				continue;
 			}
 
-			// parse branch of a branched or a lasso peptide
+			// parse branch of a branched or a branch-cyclic peptide
 			parseBranch(parameters.sequencedatabase[i].getPeptideType(), composition, v, branchstart, branchend);
 
 			// set candidate and check precursor mass error
 			c.setCandidate(v, netmp, startmodifid, endmodifid, middlemodifid, branchstart, branchend);
-			if (!calculatesummaries && !isInPpmMassErrorTolerance(uncharge(parameters.precursormass, parameters.precursorcharge), c.getPrecursorMass(parameters.bricksdatabase, &parameters), parameters.precursormasserrortolerance)) {
+			if (!calculatesummaries && !isInPpmMassErrorTolerance(charge(uncharge(parameters.precursormass, parameters.precursorcharge), (parameters.precursorcharge > 0)?1:-1), c.getPrecursorMass(parameters.bricksdatabase, &parameters), parameters.precursormasserrortolerance)) {
 				continue;
 			}
 
@@ -494,7 +371,7 @@ void cMainThread::run() {
 		
 		if (calculatesummaries) {
 			*os << endl << "done." << endl;
-			emit safeExit();
+			emitEndSignals();
 			return;
 		}
 
@@ -510,18 +387,17 @@ void cMainThread::run() {
 		*os << "Comparing theoretical peaks with the peak list... " << endl;
 		cTheoreticalSpectrum ts;
 		ts.compareMSSpectrum(&parameters);
-		theoreticalspectra.initialize(*os, parameters, &graph);
-		theoreticalspectra.add(ts);
+		theoreticalspectrumlist->initialize(*os, parameters, &graph);
+		theoreticalspectrumlist->add(ts);
 		*os << " ok" << endl;
 	}
 	
 
 	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
 		*os << "Comparing theoretical spectra of candidates with the peak list... " << endl;
-		theoreticalspectra.initialize(*os, parameters, &graph);
-		if (theoreticalspectra.parallelCompareAndStore(candidates, terminatecomputation) == -1) {
+		theoreticalspectrumlist->initialize(*os, parameters, &graph);
+		if (theoreticalspectrumlist->parallelCompareAndStore(candidates, terminatecomputation) == -1) {
 			emitEndSignals();
-			endNow();
 			return;
 		}
 		*os << " ok" << endl;
@@ -561,8 +437,6 @@ void cMainThread::run() {
 	}
 	*/
 	
-	emitEndSignals();
-
 	int secs = time.elapsed() / 1000;
 	int mins = (secs / 60) % 60;
 	int hrs =  (secs / 3600);
@@ -573,49 +447,31 @@ void cMainThread::run() {
 
 	*os << "====================================================================================================" << endl;
 
-}
-
-
-void cMainThread::emitStartSignals() {
-	emit enableRunButtonAndSettings(false);
-	emit enableStopButton(true);
-	emit enableButtonsHandlingResults(false);
+	emitEndSignals();
 
-	if (parameters.mode != denovoengine) {
-		emit setGraph("");
-	}
 }
 
 
 void cMainThread::emitEndSignals() {
-	emit sendParameters(parameters);
+	emit setGraph(graph.printGraph());
 
-	emit prepareColumns();
+	emit sendParameters(parameters);
+	emit reportSpectra();
 
-	for (int i = 0; i < theoreticalspectra.size(); i++) {
-		emit sendTheoreticalSpectrum(theoreticalspectra[i]);
-		theoreticalspectra[i].clear();
+	if (terminatecomputation) {
+		*this << endl << "Aborted by user. Partial results have been reported if they are available." << endl;
 	}
 
-	emit fitColumns();
-
 	emit enableRunButtonAndSettings(true);
 	emit enableStopButton(false);
 	emit enableButtonsHandlingResults(true);
 }
 
 
-void cMainThread::endNow() {
-	emit setGraph(graph.printGraph());
-	emit safeExit();
-	if (terminatecomputation) {
-		*this << endl << "Aborted by user." << endl;
-	}
-}
-
-
 void cMainThread::stopComputation() {
-	*this << endl << endl << "Please wait while stopping threads and generating partial results..." << endl;
+	if (!terminatecomputation) {
+		*this << endl << endl << "Stopping..." << endl;
+	}
 	terminatecomputation = true;
 }
 
diff --git a/CycloBranch/gui/cMainThread.h b/CycloBranch/gui/cMainThread.h
index 3d7c680..a52e15d 100644
--- a/CycloBranch/gui/cMainThread.h
+++ b/CycloBranch/gui/cMainThread.h
@@ -12,6 +12,7 @@
 #include <QThreadPool>
 #include <QTime>
 
+#include "core/utilities.h"
 #include "core/cParameters.h"
 #include "core/cDeNovoGraph.h"
 #include "core/cTheoreticalSpectrum.h"
@@ -19,18 +20,6 @@
 using namespace std;
 
 
-/**
-	\brief The name of the application.
-*/
-extern QString appname;
-
-
-/**
-	\brief The version of the application.
-*/
-extern QString appversion;
-
-
 /**
 	\brief The class representing a thread launched by the command 'Search->Run'.
 */
@@ -46,25 +35,22 @@ class cMainThread : public QThread {
 	bool graphreaderisworking;
 
 	cDeNovoGraph graph;
-	cTheoreticalSpectrumList theoreticalspectra;
+	cTheoreticalSpectrumList* theoreticalspectrumlist;
 	cParameters parameters;
 
 	bool checkModifications(cParameters& parameters, cSequence& sequence, int& startmodifid, int& endmodifid, int& middlemodifid, string& errormessage);
 
-	void parseBranch(peptideType peptidetype, string& composition, vector<string>& vectorcomposition, int& branchstart, int& branchend);
-
-	bool checkRegex(cParameters& parameters, string& sequence, string& errormessage);
-
 public:
 
 
 	/**
 		\brief The constructor.
 		\param parameters reference to input paramaters
+		\param theoreticalspectrumlist a list of theoretical spectra
 		\param enablelogwindow if true then messages are logged into the log window
 		\param enablestdout if true then messages are logged into the standard output
 	*/ 
-	cMainThread(cParameters& parameters, bool enablelogwindow = true, bool enablestdout = true);
+	cMainThread(cParameters& parameters, cTheoreticalSpectrumList& theoreticalspectrumlist, bool enablelogwindow = true, bool enablestdout = true);
 
 
 	/**
@@ -136,24 +122,12 @@ class cMainThread : public QThread {
 	void run();
 
 
-	/**
-		\brief The signals emitted when the thread has launched.
-	*/ 
-	void emitStartSignals();
-
-
 	/**
 		\brief The signals emitted when the thread has successfully finished.
 	*/ 
 	void emitEndSignals();
 
 
-	/**
-		\brief The signals emitted when the thread was forced to stop.
-	*/ 
-	void endNow();
-
-
 signals:
 
 
@@ -185,13 +159,6 @@ class cMainThread : public QThread {
 	void enableButtonsHandlingResults(bool enable);
 
 
-	/**
-		\brief Send a theoretical spectrum to cMainWindow when the thread has finished.
-		\param theoreticalspectrum a theoretical spectrum
-	*/ 
-	void sendTheoreticalSpectrum(cTheoreticalSpectrum theoreticalspectrum);
-
-
 	/**
 		\brief Send parameters to cMainWindow when the thread has finished.
 		\param parameters parameters
@@ -200,15 +167,9 @@ class cMainThread : public QThread {
 
 
 	/**
-		\brief Prepare columns in cMainWindow when the thread has finished.
+		\brief Report results.
 	*/ 
-	void prepareColumns();
-
-
-	/**
-		\brief Fit the width of columns in cMainWindow.
-	*/ 
-	void fitColumns();
+	void reportSpectra();
 
 
 	/**
@@ -218,12 +179,6 @@ class cMainThread : public QThread {
 	void setGraph(string s);
 
 
-	/**
-		\brief Safely exit when the thread was forced to stop.
-	*/ 
-	void safeExit();
-
-
 private slots:
 
 	void stopComputation();
diff --git a/CycloBranch/gui/cMainWindow.cpp b/CycloBranch/gui/cMainWindow.cpp
index d4c954f..c8bd9e3 100644
--- a/CycloBranch/gui/cMainWindow.cpp
+++ b/CycloBranch/gui/cMainWindow.cpp
@@ -1,4 +1,5 @@
 #include "gui/cMainWindow.h"
+#include "gui/cEventFilter.h"
 
 #include <QApplication>
 #include <QMenuBar>
@@ -13,38 +14,113 @@
 #include <QAbstractItemView>
 #include <QScrollBar>
 #include <QMessageBox>
+#include <QProgressDialog>
+#include <QCloseEvent>
 
 
 cMainWindow::cMainWindow() {
+	setWindowTitle(appname);
+	setWindowIcon(QIcon(":/images/cb.png"));
+
 
 	// main menu
 	menuBar = new QMenuBar(this);
+	menuBar->setNativeMenuBar(false);
 	
+
 	// items in the menu
 	menuFile = new QMenu(tr("&File"), this);
 	menuSearch = new QMenu(tr("&Search"), this);
 	menuTools = new QMenu(tr("&Tools"), this);
 	menuView = new QMenu(tr("&View"), this);
 	menuHelp = new QMenu(tr("&Help"), this);
-	
+
+
 	// subitems in the menu
-	// actionOpen = new QAction(tr("&Open"), this);
-	actionOpenResults = new QAction(tr("&Open Results..."), this);
-	actionSaveResults = new QAction(tr("&Save Results..."), this);
-	actionExportToCsv = new QAction(tr("&Export to CSV"), this);
-	actionExportToHTML = new QAction(tr("&Export to HTML"), this);
-	actionQuit = new QAction(tr("&Quit"), this);
-	actionRun = new QAction(tr("&Run"), this);
-	actionStop = new QAction(tr("&Stop"), this);
+	actionOpenResults = new QAction(QIcon(":/images/icons/52.png"), tr("&Open Results..."), this);
+	actionOpenResults->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_O));
+
+	actionSaveResults = new QAction(QIcon(":/images/icons/22.png"), tr("&Save Results..."), this);
+	actionSaveResults->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_S));
+
+	actionExportToCsv = new QAction(QIcon(":/images/icons/62.png"), tr("&Export to CSV"), this);
+	actionExportToCsv->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_E));
+	
+	actionExportToHTML = new QAction(QIcon(":/images/icons/77.png"), tr("Export to &HTML"), this);
+	actionExportToHTML->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_H));
+
+	actionQuit = new QAction(QIcon(":/images/icons/33.png"), tr("&Quit"), this);
+	actionQuit->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_Q));
+
+
+	actionRun = new QAction(QIcon(":/images/icons/93.png"), tr("&Run"), this);
+	actionRun->setShortcut(QKeySequence(Qt::Key_F5));
+
+	actionStop = new QAction(QIcon(":/images/icons/89.png"), tr("S&top"), this);
+	actionStop->setShortcut(QKeySequence(Qt::Key_F6));
 	actionStop->setEnabled(false);
-	actionProperties = new QAction(tr("&Settings..."), this);
-	actionBricksDatabase = new QAction(tr("&Building Blocks Editor"), this);
-	actionSequenceDatabase = new QAction(tr("&Sequence Database Editor"), this);
-	actionGraph = new QAction(tr("&Graph"), this);
-	actionLog = new QAction(tr("&Log Window"), this);
-	actionHTMLDocumentation = new QAction(tr("&HTML Documentation"), this);
-	actionPDFManual = new QAction(tr("&PDF Manual"), this);
-	actionAbout = new QAction(tr("&About"), this);
+
+	actionProperties = new QAction(QIcon(":/images/icons/73.png"), tr("&Settings..."), this);
+	actionProperties->setShortcut(QKeySequence(Qt::Key_F7));
+
+
+	actionBricksDatabase = new QAction(QIcon(":/images/icons/68.png"), tr("&Building Blocks Editor"), this);
+	actionBricksDatabase->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_B));
+
+	actionSequenceDatabase = new QAction(QIcon(":/images/icons/26.png"), tr("Sequence &Database Editor"), this);
+	actionSequenceDatabase->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_D));
+
+	actionModifications = new QAction(QIcon(":/images/icons/61.png"), tr("&Modifications Editor"), this);
+	actionModifications->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_M));
+
+	actionDrawPeptide = new QAction(QIcon(":/images/icons/96.png"), tr("Draw &Peptide"), this);
+	actionDrawPeptide->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_P));
+
+
+	actionGraph = new QAction(QIcon(":/images/icons/32.png"), tr("De Novo &Graph"), this);
+	actionGraph->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_G));
+
+	actionLog = new QAction(QIcon(":/images/icons/2.png"), tr("&Log Window"), this);
+	actionLog->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_L));
+
+
+	actionHTMLDocumentation = new QAction(QIcon(":/images/icons/3.png"), tr("&HTML Documentation"), this);
+	actionHTMLDocumentation->setShortcut(QKeySequence(Qt::Key_F1));
+
+	actionPDFManual = new QAction(QIcon(":/images/icons/4.png"), tr("&PDF Manual"), this);
+	actionPDFManual->setShortcut(QKeySequence(Qt::Key_F2));
+
+	actionAbout = new QAction(QIcon(":/images/icons/48.png"), tr("&About"), this);
+	actionAbout->setShortcut(QKeySequence(Qt::Key_F3));
+
+
+	toolbarFile = addToolBar(tr("File"));
+	toolbarFile->addAction(actionOpenResults);
+	toolbarFile->addAction(actionSaveResults);
+	toolbarFile->addAction(actionExportToCsv);
+	toolbarFile->addAction(actionExportToHTML);
+	toolbarFile->addAction(actionQuit);
+
+	toolbarSearch = addToolBar(tr("Search"));
+	toolbarSearch->addAction(actionRun);
+	toolbarSearch->addAction(actionStop);
+	toolbarSearch->addAction(actionProperties);
+
+	toolbarTools = addToolBar(tr("Tools"));
+	toolbarTools->addAction(actionBricksDatabase);
+	toolbarTools->addAction(actionSequenceDatabase);
+	toolbarTools->addAction(actionModifications);
+	toolbarTools->addAction(actionDrawPeptide);
+
+	toolbarView = addToolBar(tr("View"));
+	toolbarView->addAction(actionGraph);
+	toolbarView->addAction(actionLog);
+
+	toolbarHelp = addToolBar(tr("Help"));
+	toolbarHelp->addAction(actionHTMLDocumentation);
+	toolbarHelp->addAction(actionPDFManual);
+	toolbarHelp->addAction(actionAbout);
+
 
 	// widgets
 	results = new QTableWidget(0, 0, this);
@@ -55,8 +131,10 @@ cMainWindow::cMainWindow() {
 
 	graph = new cGraphWidget();
 	bricksdatabasewidget = new cBricksDatabaseWidget();
-	sequencedatabasewidget = new cSequenceDatabaseWidget();
-	parameterswidget = new cParametersWidget();
+	sequencedatabasewidget = new cSequenceDatabaseWidget(this);
+	modificationswidget = new cModificationsWidget();
+	drawpeptidewidget = new cDrawPeptideWidget(this);
+	parameterswidget = new cParametersWidget(this);
 	
 	// additional key shortcuts
 	// actionOpen->setShortcut(QKeySequence("Ctrl+O"));
@@ -67,13 +145,14 @@ cMainWindow::cMainWindow() {
 	connect(actionSaveResults, SIGNAL(triggered()), this, SLOT(saveResultsFile()));
 	connect(actionExportToCsv, SIGNAL(triggered()), this, SLOT(exportToCsv()));
 	connect(actionExportToHTML, SIGNAL(triggered()), this, SLOT(exportToHTML()));
-	connect(actionQuit, SIGNAL(triggered()), this, SLOT(stop()));
-	connect(actionQuit, SIGNAL(triggered()), qApp, SLOT(quit()));
+	connect(actionQuit, SIGNAL(triggered()), this, SLOT(quitApplication()));
 	connect(actionRun, SIGNAL(triggered()), this, SLOT(run()));
 	connect(actionStop, SIGNAL(triggered()), this, SLOT(stop()));
 	connect(actionProperties, SIGNAL(triggered()), this, SLOT(showProperties()));
 	connect(actionBricksDatabase, SIGNAL(triggered()), this, SLOT(showBricksDatabase()));
 	connect(actionSequenceDatabase, SIGNAL(triggered()), this, SLOT(showSequenceDatabase()));
+	connect(actionModifications, SIGNAL(triggered()), this, SLOT(showModifications()));
+	connect(actionDrawPeptide, SIGNAL(triggered()), this, SLOT(showDrawPeptideWidget()));
 	connect(actionGraph, SIGNAL(triggered()), this, SLOT(showGraph()));
 	connect(actionLog, SIGNAL(triggered()), this, SLOT(showHideLog()));
 	connect(actionHTMLDocumentation, SIGNAL(triggered()), this, SLOT(showHTMLDocumentation()));
@@ -95,6 +174,9 @@ cMainWindow::cMainWindow() {
 	menuSearch->addAction(actionProperties);
 	menuTools->addAction(actionBricksDatabase);
 	menuTools->addAction(actionSequenceDatabase);
+	menuTools->addAction(actionModifications);
+	menuTools->addSeparator();
+	menuTools->addAction(actionDrawPeptide);
 	menuView->addAction(actionGraph);
 	menuView->addSeparator();
 	menuView->addAction(actionLog);
@@ -125,6 +207,8 @@ cMainWindow::cMainWindow() {
 	graph->hide();
 	bricksdatabasewidget->hide();
 	sequencedatabasewidget->hide();
+	modificationswidget->hide();
+	drawpeptidewidget->hide();
 	parameterswidget->hide();
 
 	splitter->setOrientation(Qt::Vertical);
@@ -138,24 +222,131 @@ cMainWindow::cMainWindow() {
 	// set the size of main window
 	resize(1280, 700);
 
-	setWindowTitle(appname);
-
 	resultsbasecolumncount = 8;
 	resultsspecificcolumncount = 0;
 	dbsearchspecificcolumncount = 0;
 
-	resultsDetails.clear();
+	theoreticalspectrumlist.clear();
+	spectradetails.clear();
 
 	lastdirexporttocsv = "./";
 	lastdirexporttohtml = "./";
 	lastdirsaveresults = "./";
 	lastdiropenresults = "./";
+
+	quitapp = false;
 }
 
 
 void cMainWindow::closeEvent(QCloseEvent *event) {
-	emit stopComputation();
-	qApp->quit();
+	quitApplication();
+	event->ignore();
+}
+
+
+void cMainWindow::reportSpectrum(int id, cTheoreticalSpectrum& theoreticalspectrum) {
+	int row = results->rowCount();
+    results->insertRow(row);
+	
+	results->setItem(row, 0, widgetitemallocator.getNewItem());
+	
+	results->setItem(row, 1, widgetitemallocator.getNewItem());
+	results->item(row, 1)->setData(Qt::DisplayRole, results->rowCount());
+
+	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
+
+		if (parameters.mode == databasesearch) {
+			results->setItem(row, 2, widgetitemallocator.getNewItem());
+			results->item(row, 2)->setText(theoreticalspectrum.getCandidate().getName().c_str());
+		}
+
+		results->setItem(row, 2 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+		results->item(row, 2 + dbsearchspecificcolumncount)->setText(stripHTML(theoreticalspectrum.getCandidate().getAcronymPeptideNameWithHTMLReferences()).c_str());
+
+		results->setItem(row, 3 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+		results->item(row, 3 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getCandidate().getSummaryFormula(parameters, parameters.peptidetype).c_str());
+
+		results->setItem(row, 4 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+		results->item(row, 4 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, getNumberOfBricks(theoreticalspectrum.getCandidate().getComposition()));
+
+		switch (parameters.peptidetype)
+		{
+		case linear:
+			results->setItem(row, 5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 5 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str());
+			results->setItem(row, 6 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 6 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str());
+			break;
+		case branched:
+			results->setItem(row, 5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 5 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str());
+			results->setItem(row, 6 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 6 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str());
+			results->setItem(row, 7 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 7 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str());
+			break;
+		case cyclic:
+			results->setItem(row, 5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 5 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedBricks());	
+			break;
+		case lasso:
+			results->setItem(row, 5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 5 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str());
+			break;
+		case linearpolysaccharide:
+			results->setItem(row, 5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 5 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str());
+			results->setItem(row, 6 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->item(row, 6 + dbsearchspecificcolumncount)->setText(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str());
+			break;
+		case other:
+		default:
+			break;
+		}
+
+		results->setItem(row, 5 + dbsearchspecificcolumncount + resultsspecificcolumncount, widgetitemallocator.getNewItem());
+		results->item(row, 5 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
+
+		results->setItem(row, 6 + dbsearchspecificcolumncount + resultsspecificcolumncount, widgetitemallocator.getNewItem());
+		results->item(row, 6 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
+
+		results->setItem(row, 7 + dbsearchspecificcolumncount + resultsspecificcolumncount, widgetitemallocator.getNewItem());
+		results->item(row, 7 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
+
+		for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
+			results->setItem(row, resultsbasecolumncount  + dbsearchspecificcolumncount + resultsspecificcolumncount + i, widgetitemallocator.getNewItem());
+			results->item(row, resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks(parameters.fragmentionsfortheoreticalspectra[i]));
+		}
+
+		if ((parameters.peptidetype == cyclic) && parameters.enablescrambling) {
+			results->setItem(row, results->columnCount() - 1, widgetitemallocator.getNewItem());
+			results->item(row, results->columnCount() - 1)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfScrambledPeaks());
+		}
+
+		if (theoreticalspectrum.isValid()) {
+			results->item(row, 0)->setData(Qt::DisplayRole, "*");
+			for (int i = 0; i < results->columnCount(); i++) {
+				results->item(row, i)->setBackground(Qt::yellow);
+			}
+		}
+
+	}
+
+
+	if (parameters.mode == dereplication) {
+		results->setItem(row, 2, widgetitemallocator.getNewItem());
+		results->item(row, 2)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
+
+		results->setItem(row, 3, widgetitemallocator.getNewItem());
+		results->item(row, 3)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
+
+		results->setItem(row, 4, widgetitemallocator.getNewItem());
+		results->item(row, 4)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
+	}
+
+
+	spectradetails[id].initialize(&parameters, theoreticalspectrum);
+	spectradetails[id].setWindowTitle(("Theoretical Spectrum No. " + to_string(row+1)).c_str());
 }
 
 
@@ -189,6 +380,24 @@ void cMainWindow::showSequenceDatabase() {
 }
 
 
+void cMainWindow::showModifications() {
+	modificationswidget->show();
+	modificationswidget->activateWindow();
+}
+
+
+void cMainWindow::showDrawPeptideWidget() {
+	drawpeptidewidget->show();
+	drawpeptidewidget->activateWindow();
+}
+
+
+void cMainWindow::setAndShowDrawPeptideWidget(int peptidetypeindex, QString sequence) {
+	drawpeptidewidget->setSequence(peptidetypeindex, sequence);
+	showDrawPeptideWidget();
+}
+
+
 void cMainWindow::showGraph() {
 	graph->show();
 	graph->activateWindow();
@@ -202,22 +411,26 @@ void cMainWindow::showProperties() {
 
 
 void cMainWindow::run() {
+	enableRunButtonAndSettings(false);
+	enableStopButton(true);
+	enableButtonsHandlingResults(false);
+
 	logWindow->clear();
+	
 	deleteResults();
-	resultsDetails.clear();
+	
+	theoreticalspectrumlist.clear();
+	spectradetails.clear();
 
-	cMainThread* thread = new cMainThread(parameterswidget->getParameters(), true, false);
+	cMainThread* thread = new cMainThread(parameterswidget->getParameters(), theoreticalspectrumlist, true, false);
 	connect(thread, SIGNAL(message(QString)), this, SLOT(updateLog(QString)));
 	connect(thread, SIGNAL(enableRunButtonAndSettings(bool)), this, SLOT(enableRunButtonAndSettings(bool)));
 	connect(thread, SIGNAL(enableStopButton(bool)), this, SLOT(enableStopButton(bool)));
 	connect(thread, SIGNAL(enableButtonsHandlingResults(bool)), this, SLOT(enableButtonsHandlingResults(bool)));
-	connect(thread, SIGNAL(sendTheoreticalSpectrum(cTheoreticalSpectrum)), this, SLOT(sendTheoreticalSpectrum(cTheoreticalSpectrum)));
 	connect(thread, SIGNAL(sendParameters(cParameters)), this, SLOT(sendParameters(cParameters)));
-	connect(thread, SIGNAL(prepareColumns()), this, SLOT(prepareColumns()));
-	connect(thread, SIGNAL(fitColumns()), this, SLOT(fitColumns()));
+	connect(thread, SIGNAL(reportSpectra()), this, SLOT(reportSpectra()));
 	connect(thread, SIGNAL(setGraph(string)), this, SLOT(setGraph(string)));
 	connect(this, SIGNAL(stopComputation()), thread, SLOT(stopComputation()));
-	connect(thread, SIGNAL(safeExit()), this, SLOT(safeExit()));
 
 	thread->start();
 }
@@ -239,6 +452,11 @@ void cMainWindow::updateLog(QString qstr) {
 
 
 void cMainWindow::enableRunButtonAndSettings(bool enable) {
+
+	if (enable && quitapp) {
+		qApp->quit();
+	}
+
 	actionRun->setEnabled(enable);
 
 	actionProperties->setEnabled(enable);
@@ -259,111 +477,16 @@ void cMainWindow::enableButtonsHandlingResults(bool enable) {
 }
 
 
-void cMainWindow::sendTheoreticalSpectrum(cTheoreticalSpectrum theoreticalspectrum) {
-	int row = results->rowCount();
-    results->insertRow(row);
-	
-	results->setItem(row, 0, new QTableWidgetItem(""));
-	
-	results->setItem(row, 1, new QTableWidgetItem());
-	results->item(row, 1)->setData(Qt::DisplayRole, results->rowCount());
-
-
-	if ((parameters.mode == denovoengine) || (parameters.mode == singlecomparison) || (parameters.mode == databasesearch)) {
-
-		if (parameters.mode == databasesearch) {
-			results->setItem(row, 2, new QTableWidgetItem(theoreticalspectrum.getCandidate().getName().c_str()));
-		}
-
-		results->setItem(row, 2 + dbsearchspecificcolumncount, new QTableWidgetItem(stripHTML(theoreticalspectrum.getAcronymPeptideNameWithHTMLReferences()).c_str()));
-
-		results->setItem(row, 3 + dbsearchspecificcolumncount, new QTableWidgetItem());
-		results->item(row, 3 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getCandidate().getSummaryFormula(parameters, parameters.peptidetype).c_str());
-
-		results->setItem(row, 4 + dbsearchspecificcolumncount, new QTableWidgetItem());
-		results->item(row, 4 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, getNumberOfBricks(theoreticalspectrum.getCandidate().getComposition()));
-
-		switch (parameters.peptidetype)
-		{
-		case linear:
-			results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
-			results->setItem(row, 6 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
-			break;
-		case branched:
-			results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
-			results->setItem(row, 6 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str()));
-			results->setItem(row, 7 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
-			break;
-		case cyclic:
-			results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem());
-			results->item(row, 5 + dbsearchspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedBricks());	
-			break;
-		case lasso:
-			results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getMiddleModifID()].name.c_str()));
-			break;
-		case linearpolysaccharide:
-			results->setItem(row, 5 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getStartModifID()].name.c_str()));
-			results->setItem(row, 6 + dbsearchspecificcolumncount, new QTableWidgetItem(parameters.searchedmodifications[theoreticalspectrum.getCandidate().getEndModifID()].name.c_str()));
-			break;
-		case other:
-		default:
-			break;
-		}
-
-		results->setItem(row, 5 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem());
-		results->item(row, 5 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
-
-		results->setItem(row, 6 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem());
-		results->item(row, 6 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
-
-		results->setItem(row, 7 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem());
-		results->item(row, 7 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
-
-		for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
-			results->setItem(row, resultsbasecolumncount  + dbsearchspecificcolumncount + resultsspecificcolumncount + i, new QTableWidgetItem());
-			results->item(row, resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks(parameters.fragmentionsfortheoreticalspectra[i]));
-		}
-
-		if ((parameters.peptidetype == cyclic) && parameters.enablescrambling) {
-			results->setItem(row, results->columnCount() - 1, new QTableWidgetItem());
-			results->item(row, results->columnCount() - 1)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfScrambledPeaks());
-		}
-
-		if (theoreticalspectrum.isValid()) {
-			results->item(row, 0)->setData(Qt::DisplayRole, "*");
-			for (int i = 0; i < results->columnCount(); i++) {
-				results->item(row, i)->setBackground(Qt::yellow);
-			}
-		}
-
-	}
-
-
-	if (parameters.mode == dereplication) {
-		results->setItem(row, 2, new QTableWidgetItem());
-		results->item(row, 2)->setData(Qt::DisplayRole, theoreticalspectrum.getNumberOfMatchedPeaks());
-
-		results->setItem(row, 3, new QTableWidgetItem());
-		results->item(row, 3)->setData(Qt::DisplayRole, theoreticalspectrum.getRatioOfMatchedPeaks()*100);
-
-		results->setItem(row, 4, new QTableWidgetItem());
-		results->item(row, 4)->setData(Qt::DisplayRole, theoreticalspectrum.getWeightedIntensityScore());
-	}
-
-
-	cSpectrumDetailWidget sd;
-	sd.initialize(&parameters, theoreticalspectrum);
-	sd.setWindowTitle(("Theoretical Spectrum No. " + to_string(row+1)).c_str());
-	resultsDetails.push_back(sd);
-}
-
-
 void cMainWindow::sendParameters(cParameters parameters) {
 	this->parameters = parameters;
 }
 
 
-void cMainWindow::prepareColumns() {
+void cMainWindow::reportSpectra() {
+
+	if (quitapp) {
+		return;
+	}
 
 	switch (parameters.peptidetype)
 	{
@@ -404,51 +527,75 @@ void cMainWindow::prepareColumns() {
 			results->setColumnCount(results->columnCount() + 1);
 		}
 
-		results->setHorizontalHeaderItem(0, new QTableWidgetItem("*"));
-		results->setHorizontalHeaderItem(1, new QTableWidgetItem("Result ID"));
+		results->setHorizontalHeaderItem(0, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(0)->setText("*");
+
+		results->setHorizontalHeaderItem(1, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(1)->setText("Result ID");
+
 		if (parameters.mode == databasesearch) {
-			results->setHorizontalHeaderItem(2, new QTableWidgetItem("Name"));
+			results->setHorizontalHeaderItem(2, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(2)->setText("Name");
 		}
-		results->setHorizontalHeaderItem(2 + dbsearchspecificcolumncount, new QTableWidgetItem("Peptide Sequence"));
-		results->setHorizontalHeaderItem(3 + dbsearchspecificcolumncount, new QTableWidgetItem("Summary Formula"));
-		results->setHorizontalHeaderItem(4 + dbsearchspecificcolumncount, new QTableWidgetItem("Number of Bricks"));
+		results->setHorizontalHeaderItem(2 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(2 + dbsearchspecificcolumncount)->setText("Peptide Sequence");
+		results->setHorizontalHeaderItem(3 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(3 + dbsearchspecificcolumncount)->setText("Summary Formula");
+		results->setHorizontalHeaderItem(4 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(4 + dbsearchspecificcolumncount)->setText("Number of Bricks");
 
 		switch (parameters.peptidetype)
 		{
 		case linear:
-			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("N-terminal Modification"));
-			results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, new QTableWidgetItem("C-terminal Modification"));
+			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(5 + dbsearchspecificcolumncount)->setText("N-terminal Modification");
+			results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(6 + dbsearchspecificcolumncount)->setText("C-terminal Modification");
 			break;
 		case branched:
-			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("N-terminal Modification"));
-			results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, new QTableWidgetItem("Branch Modification"));
-			results->setHorizontalHeaderItem(7 + dbsearchspecificcolumncount, new QTableWidgetItem("C-terminal Modification"));
+			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(5 + dbsearchspecificcolumncount)->setText("N-terminal Modification");
+			results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(6 + dbsearchspecificcolumncount)->setText("Branch Modification");
+			results->setHorizontalHeaderItem(7 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(7 + dbsearchspecificcolumncount)->setText("C-terminal Modification");
 			break;
 		case cyclic:
-			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("Matched Bricks"));
+			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(5 + dbsearchspecificcolumncount)->setText("Matched Bricks");
 			break;
 		case lasso:
-			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("Branch Modification"));
+			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(5 + dbsearchspecificcolumncount)->setText("Branch Modification");
 			break;
 		case linearpolysaccharide:
-			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, new QTableWidgetItem("N-terminal Modification"));
-			results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, new QTableWidgetItem("C-terminal Modification"));
+			results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(5 + dbsearchspecificcolumncount)->setText("N-terminal Modification");
+			results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(6 + dbsearchspecificcolumncount)->setText("C-terminal Modification");
 			break;
 		case other:
 		default:
 			break;
 		}
 		
-		results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem("Matched Peaks"));
-		results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem("Ratio of Matched Peaks [%]"));
-		results->setHorizontalHeaderItem(7 + dbsearchspecificcolumncount + resultsspecificcolumncount, new QTableWidgetItem("Sum of Relative Intensities"));
+		results->setHorizontalHeaderItem(5 + dbsearchspecificcolumncount + resultsspecificcolumncount, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(5 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setText("Matched Peaks");
+
+		results->setHorizontalHeaderItem(6 + dbsearchspecificcolumncount + resultsspecificcolumncount, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(6 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setText("Ratio of Matched Peaks [%]");
+				
+		results->setHorizontalHeaderItem(7 + dbsearchspecificcolumncount + resultsspecificcolumncount, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(7 + dbsearchspecificcolumncount + resultsspecificcolumncount)->setText("Sum of Relative Intensities");
 
 		for (int i = 0; i < (int)parameters.fragmentionsfortheoreticalspectra.size(); i++) {
-			results->setHorizontalHeaderItem(resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i, new QTableWidgetItem(parameters.fragmentdefinitions[(fragmentIonType)parameters.fragmentionsfortheoreticalspectra[i]].name.c_str()));
+			results->setHorizontalHeaderItem(resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(resultsbasecolumncount + dbsearchspecificcolumncount + resultsspecificcolumncount + i)->setText(parameters.fragmentdefinitions[(fragmentIonType)parameters.fragmentionsfortheoreticalspectra[i]].name.c_str());
 		}
 
 		if ((parameters.peptidetype == cyclic) && parameters.enablescrambling) {
-			results->setHorizontalHeaderItem(results->columnCount() - 1, new QTableWidgetItem("Scrambled Peaks"));
+			results->setHorizontalHeaderItem(results->columnCount() - 1, widgetitemallocator.getNewItem());
+			results->horizontalHeaderItem(results->columnCount() - 1)->setText("Scrambled Peaks");
 		}
 
 	}
@@ -456,11 +603,16 @@ void cMainWindow::prepareColumns() {
 
 	if (parameters.mode == dereplication) {
 		results->setColumnCount(5);
-		results->setHorizontalHeaderItem(0, new QTableWidgetItem("*"));
-		results->setHorizontalHeaderItem(1, new QTableWidgetItem("Result ID"));
-		results->setHorizontalHeaderItem(2, new QTableWidgetItem("Matched Peaks"));
-		results->setHorizontalHeaderItem(3, new QTableWidgetItem("Ratio of Matched Peaks [%]"));
-		results->setHorizontalHeaderItem(4, new QTableWidgetItem("Sum of Relative Intensities"));
+		results->setHorizontalHeaderItem(0, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(0)->setText("*");
+		results->setHorizontalHeaderItem(1, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(1)->setText("Result ID");
+		results->setHorizontalHeaderItem(2, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(2)->setText("Matched Peaks");
+		results->setHorizontalHeaderItem(3, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(3)->setText("Ratio of Matched Peaks [%]");
+		results->setHorizontalHeaderItem(4, widgetitemallocator.getNewItem());
+		results->horizontalHeaderItem(4)->setText("Sum of Relative Intensities");
 	}
 
 
@@ -471,35 +623,43 @@ void cMainWindow::prepareColumns() {
 		resultsheadersort[i] = -1;
 	}
 
-}
 
+	QProgressDialog progress("Preparing the report...", /*"Cancel"*/0, 0, theoreticalspectrumlist.size(), this);
+	cEventFilter filter;
+	progress.installEventFilter(&filter);
+	progress.setMinimumDuration(0);
+	progress.setWindowModality(Qt::WindowModal);
+
+	spectradetails.clear();
+	spectradetails.resize(theoreticalspectrumlist.size());
+	for (int i = 0; i < theoreticalspectrumlist.size(); i++) {
+		reportSpectrum(i, theoreticalspectrumlist[i]);
+		progress.setValue(i);
+		//if (progress.wasCanceled()) {
+		//	break;
+		//}
+	}
 
-void cMainWindow::fitColumns() {
 	for (int i = 0; i < results->columnCount(); i++) {
 		results->resizeColumnToContents(i);
 	}
+
+	progress.setValue(theoreticalspectrumlist.size());
+
 }
 
 
 void cMainWindow::deleteResults() {
-	while (results->rowCount() > 0) {
-		for (int i = 0; i < results->columnCount(); i++) {
-			delete results->item(results->rowCount() - 1, i);
-		}
-		results->removeRow(results->rowCount() - 1);
-	}
-
-	for (int i = 0; i < results->columnCount(); i++) {
-		delete results->horizontalHeaderItem(i);
-	}
+	widgetitemallocator.reset();
 	results->setColumnCount(0);
+	results->setRowCount(0);
 }
 
 
 void cMainWindow::resultsCellClicked(int row, int column) {
-	resultsDetails[results->item(row, 1)->data(Qt::DisplayRole).toInt() - 1].prepareToShow(parameters.peptidetype);
-	resultsDetails[results->item(row, 1)->data(Qt::DisplayRole).toInt() - 1].show();
-	resultsDetails[results->item(row, 1)->data(Qt::DisplayRole).toInt() - 1].activateWindow();
+	spectradetails[results->item(row, 1)->data(Qt::DisplayRole).toInt() - 1].prepareToShow(parameters.peptidetype);
+	spectradetails[results->item(row, 1)->data(Qt::DisplayRole).toInt() - 1].show();
+	spectradetails[results->item(row, 1)->data(Qt::DisplayRole).toInt() - 1].activateWindow();
 }
 
 
@@ -526,18 +686,17 @@ void cMainWindow::headerItemDoubleClicked(int index) {
 }
 
 
-void cMainWindow::safeExit() {
-	enableRunButtonAndSettings(true);
-	enableStopButton(false);
-	enableButtonsHandlingResults(true);
-}
-
-
 void cMainWindow::exportToCsv() {
 	QString filename = QFileDialog::getSaveFileName(this, tr("Export to CSV"), lastdirexporttocsv, tr("Files (*.csv)"));
-	lastdirexporttocsv = filename;
 	
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdirexporttocsv = filename;
+
+		QProgressDialog progress("Exporting the CSV file...", /*"Cancel"*/0, 0, results->rowCount(), this);
+		cEventFilter filter;
+		progress.installEventFilter(&filter);
+		progress.setMinimumDuration(0);
+		progress.setWindowModality(Qt::WindowModal);
 		
 		QFile file(filename);
 		if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
@@ -562,19 +721,34 @@ void cMainWindow::exportToCsv() {
 				}
 			}
 			out << endl;
+
+			progress.setValue(i);
+			//if (progress.wasCanceled()) {
+			//	break;
+			//}
 		}
 
 		file.close();
+
+		progress.setValue(results->rowCount());
 	}
+
 }
 
 
 void cMainWindow::exportToHTML() {
+
 	QString filename = QFileDialog::getSaveFileName(this, tr("Export to HTML"), lastdirexporttohtml, tr("HTML Files (*.htm *.html)"));
-	lastdirexporttohtml = filename;
 	
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdirexporttohtml = filename;
 		
+		QProgressDialog progress("Exporting the HTML report...", /*"Cancel"*/0, 0, results->rowCount(), this);
+		cEventFilter filter;
+		progress.installEventFilter(&filter);
+		progress.setMinimumDuration(0);
+		progress.setWindowModality(Qt::WindowModal);
+
 		QFile file(filename);
 		if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
 			return;
@@ -637,10 +811,15 @@ void cMainWindow::exportToHTML() {
 				out << results->columnCount();
 				out << "\">\n";
 
-				out << "<p style=\"margin: 20px\">" << resultsDetails[i].getTheoreticalSpectrum().getCoverageBySeries().c_str();
-				out << "<br/>" << resultsDetails[i].getDetailsAsHTMLString().c_str() << "</p>\n";
+				out << "<p style=\"margin: 20px\">" << spectradetails[i].getTheoreticalSpectrum().getCoverageBySeries().c_str();
+				out << "<br/>" << spectradetails[i].getDetailsAsHTMLString().c_str() << "</p>\n";
 
 				out << "</td></tr>\n";
+
+				progress.setValue(i);
+				//if (progress.wasCanceled()) {
+				//	break;
+				//}
 			}
 			out << "</table></font></p>\n";
 
@@ -663,28 +842,49 @@ void cMainWindow::exportToHTML() {
 		
 		file.close();
 
+		progress.setValue(results->rowCount());
+
 	}
 
 }
 
 
 void cMainWindow::showHTMLDocumentation() {
-	QDesktopServices::openUrl(QUrl::fromLocalFile(QFileInfo("docs/html/userguide.html").absoluteFilePath()));
+	#if OS_TYPE == WIN
+		QDesktopServices::openUrl(QUrl::fromLocalFile(QFileInfo("docs/html/userguide.html").absoluteFilePath()));
+	#else
+		QDesktopServices::openUrl(QUrl::fromLocalFile(QFileInfo(linuxinstalldir + "docs/html/userguide.html").absoluteFilePath()));
+	#endif
 }
 
 
 void cMainWindow::showPDFManual() {
-	QDesktopServices::openUrl(QUrl::fromLocalFile(QFileInfo("docs/refman.pdf").absoluteFilePath()));
+	#if OS_TYPE == WIN
+		QDesktopServices::openUrl(QUrl::fromLocalFile(QFileInfo("docs/refman.pdf").absoluteFilePath()));
+	#else
+		QDesktopServices::openUrl(QUrl::fromLocalFile(QFileInfo(linuxinstalldir + "docs/refman.pdf").absoluteFilePath()));
+	#endif	
 }
 
 
 void cMainWindow::saveResultsFile() {
+
+	#if OS_TYPE == WIN
+		string filetypes = appname.toStdString() + " " + appversion.toStdString() + " Results Files (*.res)";
+	#else
+		string filetypes = "Results Files (*.res)";
+	#endif
 	
-	string filetypes = appname.toStdString() + " " + appversion.toStdString() + " Results Files (*.res)";
 	QString filename = QFileDialog::getSaveFileName(this, tr("Save Results..."), lastdirsaveresults, tr(filetypes.c_str()));
-	lastdirsaveresults = filename;
 	
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdirsaveresults = filename;
+
+		QProgressDialog progress("Saving the report...", /*"Cancel"*/0, 0, theoreticalspectrumlist.size(), this);
+		cEventFilter filter;
+		progress.installEventFilter(&filter);
+		progress.setMinimumDuration(0);
+		progress.setWindowModality(Qt::WindowModal);
 		
 		ofstream outfile;
 		outfile.open(filename.toStdString().c_str(), ios::out | ios::binary | ios::trunc);
@@ -710,28 +910,39 @@ void cMainWindow::saveResultsFile() {
 			parameters.store(outfile);
 
 			// store theoretical spectra
-			size = (int)resultsDetails.size();
+			size = theoreticalspectrumlist.size();
 			outfile.write((char *)&size, sizeof(int));
-			for (int i = 0; i < (int)resultsDetails.size(); i++) {
-				resultsDetails[i].getTheoreticalSpectrum().store(outfile);
+			for (int i = 0; i < theoreticalspectrumlist.size(); i++) {
+				theoreticalspectrumlist[i].store(outfile);
+				progress.setValue(i);
+				//if (progress.wasCanceled()) {
+				//	break;
+				//}
 			}
 
 			// close file
 			outfile.close();
 		}
 	
+		progress.setValue(theoreticalspectrumlist.size());
+
 	}
 
 }
 
 
 void cMainWindow::openResultsFile() {
-
-	string filetypes = appname.toStdString() + " " + appversion.toStdString() + " Results Files (*.res)";
+	
+	#if OS_TYPE == WIN
+		string filetypes = appname.toStdString() + " " + appversion.toStdString() + " Results Files (*.res)";
+	#else
+		string filetypes = "Results Files (*.res)";
+	#endif
+	
 	QString filename = QFileDialog::getOpenFileName(this, tr("Open Results..."), lastdiropenresults, tr(filetypes.c_str()));
-	lastdiropenresults = filename;
 	
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdiropenresults = filename;
 
 		ifstream infile;
 		infile.open(filename.toStdString().c_str(), ios::in | ios::binary);
@@ -759,7 +970,9 @@ void cMainWindow::openResultsFile() {
 			}
 
 			deleteResults();
-			resultsDetails.clear();
+			
+			theoreticalspectrumlist.clear();
+			spectradetails.clear();
 			
 			// load graph window
 			graph->load(infile);
@@ -777,13 +990,26 @@ void cMainWindow::openResultsFile() {
 			parameterswidget->setAndRestoreParameters(parameters);
 
 			// load theoretical spectra
-			prepareColumns();
 			infile.read((char *)&size, sizeof(int));
+
+			QProgressDialog progress("Loading the report...", /*"Cancel"*/0, 0, size, this);
+			cEventFilter filter;
+			progress.installEventFilter(&filter);
+			progress.setMinimumDuration(0);
+			progress.setWindowModality(Qt::WindowModal);
+
 			for (int i = 0; i < size; i++) {
 				theoreticalspectrum.load(infile);
-				sendTheoreticalSpectrum(theoreticalspectrum);
+				theoreticalspectrumlist.add(theoreticalspectrum);
+				progress.setValue(i);
+				//if (progress.wasCanceled()) {
+				//	break;
+				//}
 			}
-			fitColumns();
+
+			progress.setValue(size);
+
+			reportSpectra();
 
 			// close file
 			infile.close();
@@ -794,6 +1020,34 @@ void cMainWindow::openResultsFile() {
 }
 
 
+void cMainWindow::setSequence(int peptidetypeindex, QString sequence) {
+	showProperties();
+	parameterswidget->setSequence(peptidetypeindex, sequence);
+}
+
+
+void cMainWindow::setTag(int peptidetypeindex, QString tag) {
+	showProperties();
+	parameterswidget->setTag(peptidetypeindex, tag);
+}
+
+
+void cMainWindow::insertSequence(int peptidetypeindex, QString sequence) {
+	showSequenceDatabase();
+	sequencedatabasewidget->insertRow(peptidetypeindex, sequence);
+}
+
+
+void cMainWindow::quitApplication() {
+	emit stopComputation();
+	quitapp = true;
+
+	if (actionRun->isEnabled()) {
+		qApp->quit();
+	}
+}
+
+
 /*
 void cMainWindow::showContextMenu(const QPoint &pt) {
     QMenu *menu = logWindow->createStandardContextMenu();
@@ -824,6 +1078,8 @@ cMainWindow::~cMainWindow() {
 	delete actionRun;
 	delete actionBricksDatabase;
 	delete actionSequenceDatabase;
+	delete actionModifications;
+	delete actionDrawPeptide;
 	delete actionGraph;
 	delete actionLog;
 	delete actionHTMLDocumentation;
@@ -838,6 +1094,8 @@ cMainWindow::~cMainWindow() {
 	delete graph;
 	delete bricksdatabasewidget;
 	delete sequencedatabasewidget;
+	delete modificationswidget;
+	delete drawpeptidewidget;
 	delete parameterswidget;
 }
 
diff --git a/CycloBranch/gui/cMainWindow.h b/CycloBranch/gui/cMainWindow.h
index 6a780ee..d95dcd3 100644
--- a/CycloBranch/gui/cMainWindow.h
+++ b/CycloBranch/gui/cMainWindow.h
@@ -11,6 +11,7 @@
 #include <QDesktopServices>
 #include <QUrl>
 #include <QFileInfo>
+#include "core/utilities.h"
 #include "core/cTheoreticalSpectrum.h"
 #include "gui/cAboutWidget.h"
 #include "gui/cGraphWidget.h"
@@ -18,7 +19,11 @@
 #include "gui/cSpectrumDetailWidget.h"
 #include "gui/cBricksDatabaseWidget.h"
 #include "gui/cSequenceDatabaseWidget.h"
+#include "gui/cModificationsWidget.h"
+#include "gui/cDrawPeptideWidget.h"
 #include "gui/cMainThread.h"
+#include "core/cAllocator.h"
+
 
 // forward declaration
 class QTextEdit;
@@ -60,6 +65,13 @@ class cMainWindow : public QMainWindow
 	QMenu* menuView;
 	QMenu* menuHelp;
 	
+	// toolbars
+	QToolBar* toolbarFile;
+	QToolBar* toolbarSearch;
+	QToolBar* toolbarTools;
+	QToolBar* toolbarView;
+	QToolBar* toolbarHelp;
+
 	// subitems in the menu
 	QAction* actionOpenResults;
 	QAction* actionSaveResults;
@@ -71,6 +83,8 @@ class cMainWindow : public QMainWindow
 	QAction* actionProperties;
 	QAction* actionBricksDatabase;
 	QAction* actionSequenceDatabase;
+	QAction* actionModifications;
+	QAction *actionDrawPeptide;
 	QAction* actionGraph;
 	QAction* actionLog;
 	QAction* actionHTMLDocumentation;
@@ -78,8 +92,9 @@ class cMainWindow : public QMainWindow
 	QAction* actionAbout;
 
 	QTableWidget* results;
+	cTheoreticalSpectrumList theoreticalspectrumlist;
+	vector<cSpectrumDetailWidget> spectradetails;
 
-	vector<cSpectrumDetailWidget> resultsDetails;
 	cParameters parameters;
 
 	QTextEdit* logWindow;
@@ -89,6 +104,8 @@ class cMainWindow : public QMainWindow
 	cGraphWidget* graph;
 	cBricksDatabaseWidget* bricksdatabasewidget;
 	cSequenceDatabaseWidget* sequencedatabasewidget;
+	cModificationsWidget* modificationswidget;
+	cDrawPeptideWidget* drawpeptidewidget;
 	cParametersWidget* parameterswidget;
 
 	int resultsbasecolumncount;
@@ -102,9 +119,17 @@ class cMainWindow : public QMainWindow
 	QString lastdirsaveresults;
 	QString lastdiropenresults;
 
+	cAllocator<QTableWidgetItem> widgetitemallocator;
+
+	bool quitapp;
+
 	void closeEvent(QCloseEvent *event);
 
+	void reportSpectrum(int id, cTheoreticalSpectrum& theoreticalspectrum);
+
+	void deleteResults();
 
+	
 private slots:
 
 	void showHideLog();
@@ -115,6 +140,12 @@ private slots:
 
 	void showSequenceDatabase();
 
+	void showModifications();
+
+	void showDrawPeptideWidget();
+
+	void setAndShowDrawPeptideWidget(int peptidetypeindex, QString sequence);
+	
 	void showGraph();
 
 	void showProperties();
@@ -131,15 +162,9 @@ private slots:
 
 	void enableButtonsHandlingResults(bool enable);
 
-	void sendTheoreticalSpectrum(cTheoreticalSpectrum theoreticalspectrum);
-
 	void sendParameters(cParameters parameters);
 
-	void prepareColumns();
-
-	void fitColumns();
-
-	void deleteResults();
+	void reportSpectra();
 
 	void resultsCellClicked(int row, int column);
 
@@ -147,8 +172,6 @@ private slots:
 
 	void headerItemDoubleClicked(int);
 
-	void safeExit();
-
 	void exportToCsv();
 
 	void exportToHTML();
@@ -161,6 +184,14 @@ private slots:
 
 	void openResultsFile();
 
+	void setSequence(int peptidetypeindex, QString sequence);
+
+	void setTag(int peptidetypeindex, QString tag);
+
+	void insertSequence(int peptidetypeindex, QString tag);
+
+	void quitApplication();
+
 	//void showContextMenu(const QPoint &pt);
 
 signals:
diff --git a/CycloBranch/gui/cModificationsWidget.cpp b/CycloBranch/gui/cModificationsWidget.cpp
new file mode 100644
index 0000000..cc175be
--- /dev/null
+++ b/CycloBranch/gui/cModificationsWidget.cpp
@@ -0,0 +1,434 @@
+#include "gui/cModificationsWidget.h"
+#include "gui/cEventFilter.h"
+
+#include <QTableWidget>
+#include <QTableWidgetItem>
+#include <QVBoxLayout>
+#include <QDialogButtonBox>
+#include <QPushButton>
+#include <QFileDialog>
+#include <QHeaderView>
+#include <QMessageBox>
+#include <QLabel>
+#include <QProgressDialog>
+#include <QCheckBox>
+#include <QKeyEvent>
+#include <QIcon>
+
+
+cModificationsWidget::cModificationsWidget(QWidget* parent) {
+	this->parent = parent;
+
+	setWindowTitle("Modifications Editor");
+	setWindowIcon(QIcon(":/images/icons/61.png"));
+
+	insertrow = new QPushButton(tr("Add Row"));
+	insertrow->setToolTip("Add a new row.");
+	removechecked = new QPushButton(tr(" Remove Rows "));
+	removechecked->setToolTip("Remove selected rows.");
+
+	close = new QPushButton(tr("Close"));
+	close->setToolTip("Close the window.");
+	load = new QPushButton(tr("Load"));
+	load->setToolTip("Load modifications.");
+	save = new QPushButton(QString("Save"));
+	save->setToolTip("Save modifications in the current file. When a file has not been loaded yet, the \"Save As ...\" file dialog is opened.");
+	saveas = new QPushButton(tr("Save As..."));
+	saveas->setToolTip("Save modifications into a file.");
+
+	buttons = new QHBoxLayout();
+	buttons->addWidget(close);
+	buttons->addStretch(1);
+	buttons->addWidget(insertrow);
+	buttons->addWidget(removechecked);
+	buttons->addStretch(10);
+	buttons->addWidget(load);
+	buttons->addWidget(save);
+	buttons->addWidget(saveas);
+
+	database = new QTableWidget(0, 0, this);
+	database->setColumnCount(6);
+	database->setHorizontalHeaderItem(0, new QTableWidgetItem(""));
+	database->setHorizontalHeaderItem(1, new QTableWidgetItem("Name"));
+	database->setHorizontalHeaderItem(2, new QTableWidgetItem("Summary Formula"));
+	database->setHorizontalHeaderItem(3, new QTableWidgetItem("Monoisotopic Mass"));
+	database->setHorizontalHeaderItem(4, new QTableWidgetItem("N-terminal"));
+	database->setHorizontalHeaderItem(5, new QTableWidgetItem("C-terminal"));
+	database->horizontalHeader()->setStretchLastSection(true);
+	for (int i = 0; i < database->columnCount(); i++) {
+		database->resizeColumnToContents(i);
+	}
+
+	headersort.resize(database->columnCount());
+	for (int i = 0; i < database->columnCount(); i++) {
+		headersort[i] = -1;
+	}
+
+	mainlayout = new QVBoxLayout();
+	mainlayout->addWidget(database);
+	mainlayout->addLayout(buttons);
+
+	connect(database->horizontalHeader(), SIGNAL(sectionDoubleClicked(int)), this, SLOT(headerItemDoubleClicked(int)));
+	connect(database, SIGNAL(itemChanged(QTableWidgetItem *)), this, SLOT(itemChanged(QTableWidgetItem *)));
+	connect(insertrow, SIGNAL(released()), this, SLOT(addRow()));
+	connect(removechecked, SIGNAL(released()), this, SLOT(removeEmptyRows()));
+	connect(close, SIGNAL(released()), this, SLOT(closeWindow()));
+	connect(load, SIGNAL(released()), this, SLOT(loadDatabase()));
+	connect(save, SIGNAL(released()), this, SLOT(saveDatabase()));
+	connect(saveas, SIGNAL(released()), this, SLOT(saveDatabaseAs()));
+
+	setLayout(mainlayout);
+
+	resize(1280, 700);
+
+	databasefile = "";
+
+	#if OS_TYPE == WIN
+		lastdir = "./Modifications/";
+	#else
+		lastdir = linuxinstalldir + "Modifications/";
+	#endif
+	
+	modifications.clear();
+}
+
+
+cModificationsWidget::~cModificationsWidget() {
+	deleteTable(false);
+
+	for (int i = 0; i < database->columnCount(); i++) {
+		delete database->horizontalHeaderItem(i);
+	}
+
+	database->setColumnCount(0);
+
+	delete insertrow;
+	delete removechecked;
+	delete close;
+	delete load;
+	delete save;
+	delete saveas;
+	delete database;
+	delete buttons;
+	delete mainlayout;
+}
+
+
+void cModificationsWidget::closeEvent(QCloseEvent *event) {
+	closeWindow();
+}
+
+
+void cModificationsWidget::deleteTable(bool enableprogress) {
+	QProgressDialog* progress;
+	cEventFilter filter;
+	int rowcount = database->rowCount();
+
+	if (enableprogress) {
+		progress = new QProgressDialog("Clearing the table...", /*"Cancel"*/0, 0, rowcount, this);
+		progress->installEventFilter(&filter);
+		progress->setMinimumDuration(0);
+		progress->setWindowModality(Qt::WindowModal);
+		progress->setValue(0);
+	}
+
+	widgetitemallocator.reset();
+
+	for (int i = 0; i < rowcount; i++) {
+		delete database->cellWidget(rowcount - i - 1, 4);
+		delete database->cellWidget(rowcount - i - 1, 5);
+
+		if (enableprogress) {
+			progress->setValue(i);
+			//if (progress->wasCanceled()) {
+			//	break;
+			//}
+		}
+	}
+	
+	database->setRowCount(0);
+
+	if (enableprogress) {
+		progress->setValue(rowcount);
+		delete progress;
+	}
+}
+
+
+void cModificationsWidget::removeRow(int row) {
+	for (int i = 0; i < database->columnCount(); i++) {
+		if ((i == 4) || (i == 5)) {
+			delete database->cellWidget(row, i);
+		}
+		else {
+			database->takeItem(row, i);
+		}
+	}
+	database->removeRow(row);
+}
+
+
+bool cModificationsWidget::checkTable() {
+	// check summary formulas
+	for (int i = 0; i < database->rowCount(); i++) {
+		if (!checkFormula(i, database->item(i, 2)->text().toStdString())) {
+			return false;
+		}
+	}
+
+	return true;
+}
+
+
+bool cModificationsWidget::checkFormula(int row, const string& summary) {
+	cSummaryFormula formula;
+	string errmsg;
+	formula.setFormula(summary);
+	if (!formula.isValid(errmsg)) {
+		QMessageBox msgBox;
+		QString errstr = "Syntax error in the row no. ";
+		errstr += to_string(row + 1).c_str();
+		errstr += ": ";
+		errstr += errmsg.c_str();
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return false;
+	}
+	if (database->item(row, 3)) {
+		database->item(row, 3)->setData(Qt::DisplayRole, formula.getMass());
+	}
+	return true;
+}
+
+
+void cModificationsWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+}
+
+
+void cModificationsWidget::closeWindow() {
+	hide();
+}
+
+
+void cModificationsWidget::loadDatabase() {
+	QString filename = QFileDialog::getOpenFileName(this, tr("Load Modifications"), lastdir, tr("Modifications (*.txt)"));
+
+	if (!filename.isEmpty()) {
+		lastdir = filename;
+		string errormessage;
+		
+		databasefile = filename;
+		save->setText(QString("  Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("'  "));
+		
+		inputstream.open(filename.toStdString().c_str());
+
+		if (!inputstream.good()) {
+			QMessageBox msgBox;
+			msgBox.setText("Cannot open the file '" + databasefile + "'.");
+			msgBox.exec();
+		}
+		else {
+
+			modifications.clear();
+			loadModificationsFromPlainTextStream(inputstream, modifications, errormessage, true);
+
+			deleteTable(true);
+
+			QProgressDialog progress("Loading Modifications...", /*"Cancel"*/0, 0, (int)modifications.size(), this);
+			cEventFilter filter;
+			progress.installEventFilter(&filter);
+			progress.setMinimumDuration(0);
+			progress.setWindowModality(Qt::WindowModal);
+
+			database->setRowCount((int)modifications.size());
+			for (int i = 0; i < (int)modifications.size(); i++) {
+				QCheckBox* checkbox = new QCheckBox();
+				database->setCellWidget(i, 0, checkbox);
+
+				database->setItem(i, 1, widgetitemallocator.getNewItem());
+				database->item(i, 1)->setText(modifications[i].name.c_str());
+
+				database->setItem(i, 2, widgetitemallocator.getNewItem());
+				database->item(i, 2)->setText(modifications[i].summary.c_str());
+
+				database->setItem(i, 3, widgetitemallocator.getNewItem());
+				database->item(i, 3)->setData(Qt::DisplayRole, modifications[i].massdifference);
+
+				checkbox = new QCheckBox();
+				if (modifications[i].nterminal) {
+					checkbox->setChecked(true);
+				}
+				database->setCellWidget(i, 4, checkbox);
+
+				checkbox = new QCheckBox();
+				if (modifications[i].cterminal) {
+					checkbox->setChecked(true);
+				}
+				database->setCellWidget(i, 5, checkbox);
+
+				progress.setValue(i);
+				//if (progress.wasCanceled()) {
+				//	break;
+				//}
+			}
+
+			for (int i = 0; i < database->columnCount(); i++) {
+				database->resizeColumnToContents(i);
+			}
+
+			progress.setValue((int)modifications.size());
+
+		}
+
+		inputstream.close();
+
+	}
+}
+
+
+void cModificationsWidget::saveDatabase() {
+
+	if (!checkTable()) {
+		return;
+	}
+
+	if (databasefile.compare("") == 0) {
+		saveDatabaseAs();
+		return;
+	}
+
+	outputstream.open(databasefile.toStdString().c_str());
+	if (!outputstream.good()) {
+		QMessageBox msgBox;
+		msgBox.setText("Cannot open the file '" + databasefile + "'.");
+		msgBox.exec();
+	}
+	else {
+
+		QProgressDialog progress("Saving Modifications...", /*"Cancel"*/0, 0, database->rowCount(), this);
+		cEventFilter filter;
+		progress.installEventFilter(&filter);
+		progress.setMinimumDuration(0);
+		progress.setWindowModality(Qt::WindowModal);
+
+		fragmentDescription modification;
+		modifications.clear();
+
+		removeEmptyRows();
+
+		for (int i = 0; i < database->rowCount(); i++) {
+			modification.clear();
+			for (int j = 0; j < database->columnCount(); j++) {
+				switch (j)
+				{
+				case 0:
+					// nothing to do
+					break;
+				case 1:
+					modification.name = database->item(i,j)->text().toStdString();
+					break;
+				case 2:
+					modification.summary = database->item(i,j)->text().toStdString();
+					break;
+				case 3:
+					modification.massdifference = database->item(i,j)->data(Qt::DisplayRole).toDouble();
+					break;
+				case 4:
+					modification.nterminal = ((QCheckBox *)database->cellWidget(i, j))->isChecked();
+					break;
+				case 5:
+					modification.cterminal = ((QCheckBox *)database->cellWidget(i, j))->isChecked();
+					break;
+				default:
+					break;
+				}
+			}
+			modifications.push_back(modification);
+
+			progress.setValue(i);
+			//if (progress.wasCanceled()) {
+			//	break;
+			//}
+		}
+
+		storeModificationsToPlainTextStream(outputstream, modifications);
+
+		progress.setValue(progress.maximum());
+
+	}
+	outputstream.close();
+}
+
+
+void cModificationsWidget::saveDatabaseAs() {
+
+	if (!checkTable()) {
+		return;
+	}
+
+	QString filename = QFileDialog::getSaveFileName(this, tr("Save Modifications As..."), lastdir, tr("Modifications (*.txt)"));
+
+	if (!filename.isEmpty()) {
+		lastdir = filename;
+	
+		databasefile = filename;
+		save->setText(QString("  Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("'  "));
+		saveDatabase();
+	}
+}
+
+
+void cModificationsWidget::addRow() {
+	int row = database->rowCount();
+	database->insertRow(row);
+
+	database->setCellWidget(row, 0, new QCheckBox());
+	database->setItem(row, 1, widgetitemallocator.getNewItem());
+	database->setItem(row, 2, widgetitemallocator.getNewItem());
+	database->setItem(row, 3, widgetitemallocator.getNewItem());
+	database->setCellWidget(row, 4, new QCheckBox());
+	database->setCellWidget(row, 5, new QCheckBox());
+}
+
+
+void cModificationsWidget::removeEmptyRows() {
+	int i = 0;
+	while (i < database->rowCount()) {
+		if (((QCheckBox *)(database->cellWidget(i, 0)))->isChecked()) {
+			removeRow(i);
+		}
+		else {
+			i++;
+		}
+	}
+}
+
+
+void cModificationsWidget::itemChanged(QTableWidgetItem* item) {
+	// recalculate mass when formula is changed
+	if (item->column() == 2) {
+		checkFormula(item->row(), item->text().toStdString());
+	}
+}
+
+
+void cModificationsWidget::headerItemDoubleClicked(int index) {
+	if (headersort[index] == -1) {
+		database->sortByColumn(index, Qt::AscendingOrder);
+		headersort[index] = 1;
+		return;
+	}
+
+	if (headersort[index] == 0) {
+		database->sortByColumn(index, Qt::AscendingOrder);
+		headersort[index] = 1;
+	}
+	else {
+		database->sortByColumn(index, Qt::DescendingOrder);
+		headersort[index] = 0;
+	}
+}
+
diff --git a/CycloBranch/gui/cModificationsWidget.h b/CycloBranch/gui/cModificationsWidget.h
new file mode 100644
index 0000000..3deb65f
--- /dev/null
+++ b/CycloBranch/gui/cModificationsWidget.h
@@ -0,0 +1,119 @@
+/**
+	\file cModificationsWidget.h
+	\brief Editor of N-terminal and C-terminal modifications.
+*/
+
+
+#ifndef _CMODIFICATIONSWIDGET_H
+#define _CMODIFICATIONSWIDGET_H
+
+#include <QWidget>
+#include <fstream>
+#include "core/utilities.h"
+#include "core/cFragmentIons.h"
+#include "core/cSummaryFormula.h"
+#include "core/cAllocator.h"
+
+using namespace std;
+
+
+// forward declaration
+class QHBoxLayout;
+class QVBoxLayout;
+class QTableWidget;
+class QTableWidgetItem;
+class QPushButton;
+
+
+/**
+	\brief Editor of N-terminal and C-terminal modifications.
+*/
+class cModificationsWidget : public QWidget
+{
+	Q_OBJECT
+
+public:
+
+
+	/**
+		\brief The constructor.
+		\param parent pointer to a parent widget
+	*/ 
+	cModificationsWidget(QWidget* parent = (QWidget *)0);
+
+
+	/**
+		\brief The destructor.
+	*/ 
+	~cModificationsWidget();
+
+
+	/**
+		\brief Handle the window close event.
+		\param event pointer to QCloseEvent
+	*/ 
+	void closeEvent(QCloseEvent *event);
+
+
+private:
+	QWidget* parent;
+	QPushButton* insertrow;
+	QPushButton* removechecked;
+	QPushButton* close;
+	QPushButton* load;
+	QPushButton* save;
+	QPushButton* saveas;
+	QTableWidget* database;
+	QHBoxLayout* buttons;
+	QVBoxLayout* mainlayout;
+
+	QString databasefile;
+	QString lastdir;
+	ifstream inputstream;
+	ofstream outputstream;
+	vector<fragmentDescription> modifications;
+
+	vector<int> headersort;
+
+	cAllocator<QTableWidgetItem> widgetitemallocator;
+
+	void deleteTable(bool enableprogress);
+
+	void removeRow(int row);
+
+	bool checkTable();
+
+	bool checkFormula(int row, const string& summary);
+
+
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
+
+private slots:
+
+	void closeWindow();
+
+	void loadDatabase();
+
+	void saveDatabase();
+
+	void saveDatabaseAs();
+
+	void addRow();
+
+	void removeEmptyRows();
+
+	void itemChanged(QTableWidgetItem* item);
+
+	void headerItemDoubleClicked(int index);
+
+};
+
+#endif
diff --git a/CycloBranch/gui/cParametersWidget.cpp b/CycloBranch/gui/cParametersWidget.cpp
index 6848117..bd2a3f3 100644
--- a/CycloBranch/gui/cParametersWidget.cpp
+++ b/CycloBranch/gui/cParametersWidget.cpp
@@ -17,16 +17,18 @@
 #include <QTableWidget>
 #include <QHeaderView>
 #include <QMessageBox>
+#include <QKeyEvent>
+#include <QIcon>
 
 
-cParametersWidget::cParametersWidget() {
+cParametersWidget::cParametersWidget(QWidget* parent) {
+	this->parent = parent;
+
 	setWindowTitle("Settings...");
+	setWindowIcon(QIcon(":/images/icons/73.png"));
 
 	settingsfile = "";
 	oldsettingsfile = "";
-	peaklistfilename = "";
-	brickdatabasefilename = "";
-	sequencedatabasefilename = "";
 
 	stdbuttons = new QDialogButtonBox(QDialogButtonBox::Ok | QDialogButtonBox::Apply | QDialogButtonBox::Cancel);
 	stdbuttons->button(QDialogButtonBox::Ok)->setToolTip("Accept changes and hide window.");
@@ -54,15 +56,20 @@ cParametersWidget::cParametersWidget() {
 	peptidetype->addItem(tr("Linear"));
 	peptidetype->addItem(tr("Cyclic"));
 	peptidetype->addItem(tr("Branched"));
-	peptidetype->addItem(tr("Lasso"));
+	peptidetype->addItem(tr("Branch-cyclic"));
 	peptidetype->addItem(tr("Linear polysaccharide (beta version)"));
 	//peptidetype->addItem(tr("Other"));
 	peaklistformlayout->addRow(tr("Peptide Type: "), peptidetype);
 
 	peaklistline = new QLineEdit();
-	peaklistline->setToolTip("Select the peaklist. Following formats are supported: txt, mgf, mzML, mzXML, baf.");
 	peaklistbutton = new QPushButton("Select");
-	peaklistbutton->setToolTip("Select the peaklist. Following formats are supported: txt, mgf, mzML, mzXML, baf.");
+	#if OS_TYPE == UNX
+		peaklistline->setToolTip("Select the peaklist. Following formats are supported: txt, mgf, mzML, mzXML.");
+		peaklistbutton->setToolTip("Select the peaklist. Following formats are supported: txt, mgf, mzML, mzXML.");
+	#else
+		peaklistline->setToolTip("Select the peaklist. Following formats are supported: txt, mgf, mzML, mzXML, baf.");
+		peaklistbutton->setToolTip("Select the peaklist. Following formats are supported: txt, mgf, mzML, mzXML, baf.");
+	#endif
 	peaklistlayout = new QHBoxLayout();
 	peaklistlayout->addWidget(peaklistline);
 	peaklistlayout->addWidget(peaklistbutton);
@@ -75,11 +82,15 @@ cParametersWidget::cParametersWidget() {
 	precursormass->setSingleStep(1);
 	peaklistformlayout->addRow(tr("Precursor m/z Ratio: "), precursormass);
 
+	precursoradduct = new QLineEdit();
+	precursoradduct->setToolTip("Enter the formula of a precursor ion adduct (e.g., Na, K, Li). H is used by default when empty.");
+	peaklistformlayout->addRow(tr("Precursor Ion Adduct: "), precursoradduct);
+
 	precursorcharge = new QSpinBox();
-	precursorcharge->setToolTip("Enter the precursor charge (a precursor charge in the peaklist file is ignored).");
-	precursorcharge->setRange(1, 100);
+	precursorcharge->setToolTip("Enter the precursor charge (a precursor charge in the peaklist file is ignored). Negative values are allowed.\nWhen mode is set up to \"Compare Peaklist with Database - MS data\", the value determines the maximum charge of generated peaks.");
+	precursorcharge->setRange(-100, 100);
 	precursorcharge->setSingleStep(1);
-	peaklistformlayout->addRow(tr("Precursor Charge: "), precursorcharge);
+	peaklistformlayout->addRow(tr("Charge: "), precursorcharge);
 
 	precursormasserrortolerance = new QDoubleSpinBox();
 	precursormasserrortolerance->setToolTip("Enter the precursor m/z error tolerance in ppm.");
@@ -163,54 +174,63 @@ cParametersWidget::cParametersWidget() {
 	generatebrickspermutations->setToolTip("Permutations of combined blocks are generated when checked (e.g., when an edge corresponds to a combination of blocks leucine, proline and valine, the order of blocks can be LPV, LVP, PVL, PLV, VLP or VPL).\nIt is recommended to enable this option by default.");
 	brickdatabaseformlayout->addRow(tr("Generate Permutations of Combined Blocks: "), generatebrickspermutations);
 
+	modificationsline = new QLineEdit();
+	modificationsline->setToolTip("Select the txt file containing a list of modifications.");
+	modificationsbutton = new QPushButton("Select");
+	modificationsbutton->setToolTip("Select the txt file containing a list of modifications.");
+	modificationslayout = new QHBoxLayout();
+	modificationslayout->addWidget(modificationsline);
+	modificationslayout->addWidget(modificationsbutton);
+	brickdatabaseformlayout->addRow(tr("N-/C-terminal Modifications File: "), modificationslayout);
+
 	brickdatabasegroupbox = new QGroupBox("Database of Building Blocks");
 	brickdatabasegroupbox->setLayout(brickdatabaseformlayout);
 
 
-	modificationslayout = new QVBoxLayout();
-
-	modificationstable = new QTableWidget();
-	modificationstable->setColumnCount(4);
-	modificationstable->setHorizontalHeaderItem(0, new QTableWidgetItem("Name"));
-	modificationstable->horizontalHeaderItem(0)->setToolTip("A name of a modification.");
-	modificationstable->setHorizontalHeaderItem(1, new QTableWidgetItem("Summary"));
-	modificationstable->horizontalHeaderItem(1)->setToolTip("A residue summary formula of a modification (e.g., H2C2O for acetylation or HNO-1 for amidation). Negative numbers of atoms are supported (e.g., H-2O3N-5 means remove two hydrogens, add three oxygens and remove five nitrogens).");
-	modificationstable->setHorizontalHeaderItem(2, new QTableWidgetItem("N-terminal"));
-	modificationstable->horizontalHeaderItem(2)->setToolTip("When checked, the modification is considered to be N-terminal.");
-	modificationstable->setHorizontalHeaderItem(3, new QTableWidgetItem("C-terminal"));
-	modificationstable->horizontalHeaderItem(3)->setToolTip("When checked, the modification is considered to be C-terminal.");
-	modificationstable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
-	//modificationstable->horizontalHeader()->setSectionResizeMode(0, QHeaderView::Interactive);
-	
-	modificationsbuttoninsert = new QPushButton("Insert Modification");
-	modificationsbuttoninsert->setToolTip("Insert a new row for a modification.");
-	modificationsbuttoninsert->setMinimumWidth(120);
-	modificationsbuttoninsert->setMaximumWidth(120);
-	modificationsbuttonremove = new QPushButton("Remove Empty Rows");
-	modificationsbuttonremove->setToolTip("Remove rows having empty column \"Name\".");
-	modificationsbuttonremove->setMinimumWidth(120);
-	modificationsbuttonremove->setMaximumWidth(120);
-	modificationsbuttonslayout = new QHBoxLayout();
-	modificationsbuttonslayout->addWidget(modificationsbuttoninsert);
-	modificationsbuttonslayout->addWidget(modificationsbuttonremove);
-	modificationsbuttonslayout->addStretch(1);
-	modificationslayout->addWidget(modificationstable);
-	modificationslayout->addLayout(modificationsbuttonslayout);
-
-	modificationsgroupbox = new QGroupBox("N-terminal and C-terminal Modifications");
-	modificationsgroupbox->setLayout(modificationslayout);
+	miscformlayout = new QFormLayout();
+
+	blindedges = new QComboBox();
+	blindedges->setToolTip("An operation which is performed with edges in the de novo graph forming exclusively blind paths:\nnone (edges are kept - useful when you would like to see the whole de novo graph in 'View -> Graph');\nremove (edges are removed - speeds up the search);\nconnect (edges are connected - useful when you are looking for sequence tags).");
+	blindedges->addItem(tr("none (you can see a complete de novo graph)"));
+	blindedges->addItem(tr("remove (speed up the search)"));
+	blindedges->addItem(tr("connect (allow detection of sequence tags)"));
+	miscformlayout->addRow(tr("Action with Blind Paths in De Novo Graph: "), blindedges);
+
+	cyclicnterminus = new QCheckBox();
+	cyclicnterminus->setToolTip("N-terminal cyclization of a linear peptide is assumed when checked. H<sub>2</sub>O is subtracted from all theoretical N-terminal fragment ions and the theoretical precursor mass.");
+	miscformlayout->addRow(tr("Cyclic N-terminus: "), cyclicnterminus);
+
+	cycliccterminus = new QCheckBox();
+	cycliccterminus->setToolTip("C-terminal cyclization of a linear peptide is assumed when checked. H<sub>2</sub>O is subtracted from all theoretical C-terminal fragment ions and the theoretical precursor mass.");
+	miscformlayout->addRow(tr("Cyclic C-terminus: "), cycliccterminus);
+
+	enablescrambling = new QCheckBox();
+	enablescrambling->setToolTip("When checked, scrambled fragment ions of cyclic peptides are generated in theoretical spectra.");
+	miscformlayout->addRow(tr("Enable Scrambling: "), enablescrambling);
+
+	miscgroupbox = new QGroupBox("Miscellaneous");
+	miscgroupbox->setLayout(miscformlayout);
 
 
 	applicationformlayout = new QFormLayout();
 	
 	mode = new QComboBox();
-	mode->setToolTip("De Novo Search Engine (identification mode) - the default mode of the application.\nCompare Peaklist with Spectrum of Searched Sequence (annotation mode) - a theoretical spectrum is generated for an input \"Searched Peptide Sequence\" and it is compared with the peaklist.\nCompare Peaklist with Database - MS/MS data (identification mode) - the peaklist is compared with theoretical spectra generated from a database of sequences.\nCompare Peaklist with Database - MS data (identification mode) - the peaklist is compared with theoretical peaks generated from a database of sequences.");
+	mode->setToolTip("De Novo Search Engine (identification mode) - the default mode of the application.\nCompare Peaklist with Spectrum of Searched Sequence (annotation mode) - a theoretical spectrum is generated for an input \"Searched Peptide Sequence\" and it is compared with the peaklist.\nCompare Peaklist with Database - MS/MS data (identification mode) - a peaklist is compared with theoretical spectra generated from a database of sequences.\nCompare Peaklist with Database - MS data (identification mode) - a peaklist is compared with theoretical peaks generated from a database of compounds/sequences.");
 	mode->addItem(tr("De Novo Search Engine"));
 	mode->addItem(tr("Compare Peaklist with Spectrum of Searched Sequence"));
 	mode->addItem(tr("Compare Peaklist with Database - MS/MS data"));
 	mode->addItem(tr("Compare Peaklist with Database - MS data"));
 	applicationformlayout->addRow(tr("Mode: "), mode);
 
+	sequencedatabaseline = new QLineEdit();
+	sequencedatabaseline->setToolTip("Select the txt file containing a database of sequences.");
+	sequencedatabasebutton = new QPushButton("Select");
+	sequencedatabasebutton->setToolTip("Select the txt file containing a database of sequences.");
+	sequencedatabaselayout = new QHBoxLayout();
+	sequencedatabaselayout->addWidget(sequencedatabaseline);
+	sequencedatabaselayout->addWidget(sequencedatabasebutton);
+	applicationformlayout->addRow(tr("Sequence Database File: "), sequencedatabaselayout);
+
 	maximumnumberofthreads = new QSpinBox();
 	maximumnumberofthreads->setToolTip("A maximum number of threads used when the peaklist is compared with theoretical spectra of peptide sequence candidates.");
 	maximumnumberofthreads->setRange(1, 1024);
@@ -237,7 +257,7 @@ cParametersWidget::cParametersWidget() {
 
 	sequencetag = new QLineEdit();
 	sequencetag->setToolTip("Each peptide sequence candidate generated from a de novo graph must fulfil the peptide sequence tag. Otherwise, its theoretical spectrum is not generated and the peptide sequence candidate is excluded from the search.\nSee the syntax of tags in the documentation.");
-	sequencetag->setMaxLength(1024*1024);
+	sequencetag->setMaxLength(5000);
 	applicationformlayout->addRow(tr("Peptide Sequence Tag: "), sequencetag);
 
 	fragmentiontypes = new cFragmentIonsListWidget(this);
@@ -248,67 +268,33 @@ cParametersWidget::cParametersWidget() {
 	clearhitswithoutparent->setToolTip("When checked, a hit of a peak is not considered when corresponding parent peak is not hit (e.g., a hit of a dehydrated b-ion is not considered as a hit when corresponding b-ion has not been hit).");
 	applicationformlayout->addRow(tr("Remove Hits of Fragments without Hits of Parent Fragments: "), clearhitswithoutparent);
 
-	cyclicnterminus = new QCheckBox();
-	cyclicnterminus->setToolTip("N-terminal cyclization of a linear peptide is assumed when checked. H<sub>2</sub>O is subtracted from all theoretical N-terminal fragment ions and the theoretical precursor mass.");
-	applicationformlayout->addRow(tr("Cyclic N-terminus: "), cyclicnterminus);
-
-	cycliccterminus = new QCheckBox();
-	cycliccterminus->setToolTip("C-terminal cyclization of a linear peptide is assumed when checked. H<sub>2</sub>O is subtracted from all theoretical C-terminal fragment ions and the theoretical precursor mass.");
-	applicationformlayout->addRow(tr("Cyclic C-terminus: "), cycliccterminus);
-
-	enablescrambling = new QCheckBox();
-	enablescrambling->setToolTip("When checked, scrambled fragment ions of cyclic peptides are generated in theoretical spectra.");
-	applicationformlayout->addRow(tr("Enable Scrambling: "), enablescrambling);
-
 	applicationgroupbox = new QGroupBox("Application");
 	applicationgroupbox->setLayout(applicationformlayout);
 
 
-	denovographformlayout = new QFormLayout();
-
-	blindedges = new QComboBox();
-	blindedges->setToolTip("An operation with edges in the de novo graph forming exclusively blind paths:\nnone (edges are kept - useful when you would like to see the whole de novo graph in 'View -> Graph');\nremove (edges are removed - speeds up the search);\nconnect (edges are connected - useful when you are looking for sequence tags).");
-	blindedges->addItem(tr("none (you can see a complete de novo graph)"));
-	blindedges->addItem(tr("remove (speed up the search)"));
-	blindedges->addItem(tr("connect (allow detection of sequence tags)"));
-	denovographformlayout->addRow(tr("Action with Edges Forming Blind Paths: "), blindedges);
-
-	denovographgroupbox = new QGroupBox("De Novo Graph");
-	denovographgroupbox->setLayout(denovographformlayout);
-
-
-	databasesearchformlayout = new QFormLayout();
-
-	sequencedatabaseline = new QLineEdit();
-	sequencedatabaseline->setToolTip("Select the txt file containing a database of sequences.");
-	sequencedatabasebutton = new QPushButton("Select");
-	sequencedatabasebutton->setToolTip("Select the txt file containing a database of sequences.");
-	sequencedatabaselayout = new QHBoxLayout();
-	sequencedatabaselayout->addWidget(sequencedatabaseline);
-	sequencedatabaselayout->addWidget(sequencedatabasebutton);
-	databasesearchformlayout->addRow(tr("Sequence Database File: "), sequencedatabaselayout);
-
-	databasesearchgroupbox = new QGroupBox("Database Search");
-	databasesearchgroupbox->setLayout(databasesearchformlayout);
-
-
 	searchedsequenceformlayout = new QFormLayout();
 
-	searchedsequence = new QLineEdit();
-	searchedsequence->setToolTip("A peptide sequence which you are searching for or a peptide sequence tag.\nA peptide sequence must be entered when \"Mode\" is set up to \"Compare Peaklist with Spectrum of Searched Sequence\".\nOtherwise, it is similar to the option \"Peptide Sequence Tag\" with a difference that a peptide sequence candidate is not removed from the search but it is just highlighted in an output report of peptide sequence candidates.");
-	searchedsequence->setMaxLength(1024*1024);
-	searchedsequenceformlayout->addRow(tr("Sequence: "), searchedsequence);
+	searchedsequenceline = new QLineEdit();
+	searchedsequenceline->setToolTip("A peptide sequence which you are searching for or a peptide sequence tag.\nA peptide sequence must be entered when \"Mode\" is set up to \"Compare Peaklist with Spectrum of Searched Sequence\".\nOtherwise, it is similar to the option \"Peptide Sequence Tag\" with a difference that a peptide sequence candidate is not removed from the search but it is just highlighted in an output report of peptide sequence candidates.");
+	searchedsequenceline->setMaxLength(5000);
+	searchedsequencebutton = new QPushButton("Edit");
+	searchedsequencebutton->setMinimumWidth(50);
+	searchedsequencebutton->setToolTip("Edit the sequence using the 'Draw Peptide' tool.");
+	searchedsequencelayout = new QHBoxLayout();
+	searchedsequencelayout->addWidget(searchedsequenceline);
+	searchedsequencelayout->addWidget(searchedsequencebutton);
+	searchedsequenceformlayout->addRow(tr("Sequence: "), searchedsequencelayout);
 
 	searchedsequenceNtermmodif = new QLineEdit();
-	searchedsequenceNtermmodif->setToolTip("A name of an N-terminal modification as defined in the window \"N-terminal and C-terminal Modifications\" which belongs to the searched peptide.");
+	searchedsequenceNtermmodif->setToolTip("A name of an N-terminal modification which belongs to the searched peptide. The name must be defined in \"N-/C-terminal Modifications File\".");
 	searchedsequenceformlayout->addRow(tr("N-terminal Modification: "), searchedsequenceNtermmodif);
 
 	searchedsequenceCtermmodif = new QLineEdit();
-	searchedsequenceCtermmodif->setToolTip("A name of a C-terminal modification as defined in the window \"N-terminal and C-terminal Modifications\" which belongs to the searched peptide.");
+	searchedsequenceCtermmodif->setToolTip("A name of a C-terminal modification which belongs to the searched peptide. The name must be defined in \"N-/C-terminal Modifications File\".");
 	searchedsequenceformlayout->addRow(tr("C-terminal Modification: "), searchedsequenceCtermmodif);
 
 	searchedsequenceTmodif = new QLineEdit();
-	searchedsequenceTmodif->setToolTip("A name of an N-terminal or C-terminal modification as defined in the window \"N-terminal and C-terminal Modifications\"  which belongs to a branch of a searched peptide (branched and lasso peptides only).");
+	searchedsequenceTmodif->setToolTip("A name of an N-terminal or C-terminal modification which belongs to a branch of a searched peptide (branched and branch-cyclic peptides only). The name must be defined in \"N-/C-terminal Modifications File\".");
 	searchedsequenceformlayout->addRow(tr("Branch Modification: "), searchedsequenceTmodif);
 
 	searchedsequencegroupbox = new QGroupBox("Searched Peptide Sequence");
@@ -318,14 +304,11 @@ cParametersWidget::cParametersWidget() {
 	vlayout1 = new QVBoxLayout();
 	vlayout1->addWidget(peaklistgroupbox);
 	vlayout1->addWidget(brickdatabasegroupbox);
-	vlayout1->addWidget(modificationsgroupbox);
+	vlayout1->addWidget(miscgroupbox);
 
 	vlayout2 = new QVBoxLayout();
 	vlayout2->addWidget(applicationgroupbox);
-	vlayout2->addWidget(denovographgroupbox);
-	vlayout2->addWidget(databasesearchgroupbox);
 	vlayout2->addWidget(searchedsequencegroupbox);
-	vlayout2->addStretch(1);
 		
 
 	hlayout = new QHBoxLayout();
@@ -350,12 +333,13 @@ cParametersWidget::cParametersWidget() {
 	connect(stdbuttons, SIGNAL(rejected()), this, SLOT(restoreParameters()));
 	connect(peaklistbutton, SIGNAL(released()), this, SLOT(peaklistButtonReleased()));
 	connect(brickdatabasebutton, SIGNAL(released()), this, SLOT(brickDatabaseButtonReleased()));
-	connect(modificationsbuttoninsert, SIGNAL(released()), this, SLOT(modificationsInsertButtonReleased()));
-	connect(modificationsbuttonremove, SIGNAL(released()), this, SLOT(modificationsRemoveButtonReleased()));
+	connect(modificationsbutton, SIGNAL(released()), this, SLOT(modificationsButtonReleased()));
 	connect(peptidetype, SIGNAL(currentIndexChanged(int)), this, SLOT(updateSettingsWhenPeptideTypeChanged(int)));
 	connect(mode, SIGNAL(currentIndexChanged(int)), this, SLOT(updateSettingsWhenModeChanged(int)));
 	connect(fragmentiontypes, SIGNAL(resetReleased()), this, SLOT(resetFragmentIonTypes()));
 	connect(sequencedatabasebutton, SIGNAL(released()), this, SLOT(sequenceDatabaseButtonReleased()));
+	connect(searchedsequencebutton, SIGNAL(released()), this, SLOT(drawPeptideButtonReleased()));
+	connect(this, SIGNAL(sendSequenceLine(int, QString)), parent, SLOT(setAndShowDrawPeptideWidget(int, QString)));
 
 
 	updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
@@ -363,12 +347,22 @@ cParametersWidget::cParametersWidget() {
 
 	restoreParameters();
 
-
-	lastdirloadsettings = "./Settings/";
-	lastdirsavesettings = "./Settings/";
-	lastdirselectpeaklist = "./PeakLists/";
-	lastdirselectbricksdatabase = "./BrickDatabases/";
-	lastdirselectsequencedatabase = "./SequenceDatabases/";
+	#if OS_TYPE == WIN
+		lastdirloadsettings = "./Settings/";
+		lastdirsavesettings = "./Settings/";
+		lastdirselectpeaklist = "./PeakLists/";
+		lastdirselectbricksdatabase = "./BrickDatabases/";
+		lastdirselectmodifications = "./Modifications/";
+		lastdirselectsequencedatabase = "./SequenceDatabases/";
+	#else
+		lastdirloadsettings = linuxinstalldir + "Settings/";
+		lastdirsavesettings = linuxinstalldir + "Settings/";
+		lastdirselectpeaklist = linuxinstalldir + "PeakLists/";
+		lastdirselectbricksdatabase = linuxinstalldir + "BrickDatabases/";
+		lastdirselectmodifications = linuxinstalldir + "Modifications/";
+		lastdirselectsequencedatabase = linuxinstalldir + "SequenceDatabases/";
+	#endif
+	
 }
 
 
@@ -385,6 +379,7 @@ cParametersWidget::~cParametersWidget() {
 	delete peaklistbutton;
 	delete peaklistlayout;
 	delete precursormass;
+	delete precursoradduct;
 	delete precursorcharge;
 	delete precursormasserrortolerance;
 	delete fragmentmasserrortolerance;
@@ -402,46 +397,35 @@ cParametersWidget::~cParametersWidget() {
 	delete maximumbricksincombinationend;
 	delete maximumcumulativemass;
 	delete generatebrickspermutations;
+	delete modificationsline;
+	delete modificationsbutton;
+	delete modificationslayout;
 	delete brickdatabaseformlayout;
 	delete brickdatabasegroupbox;
 	
-	deleteModificationsTableBody();
-
-	for (int i = 0; i < modificationstable->columnCount(); i++) {
-		delete modificationstable->horizontalHeaderItem(i);
-	}
-
-	delete modificationsbuttoninsert;
-	delete modificationsbuttonremove;
-	delete modificationsbuttonslayout;
-	delete modificationstable;
-	delete modificationslayout;
-	delete modificationsgroupbox;
+	delete blindedges;
+	delete cyclicnterminus;
+	delete cycliccterminus;
+	delete enablescrambling;
+	delete miscformlayout;
+	delete miscgroupbox;
 
 	delete mode;
+	delete sequencedatabaseline;
+	delete sequencedatabasebutton;
+	delete sequencedatabaselayout;
 	delete maximumnumberofthreads;
 	delete scoretype;
 	delete hitsreported;
 	delete sequencetag;
 	delete fragmentiontypes;
 	delete clearhitswithoutparent;
-	delete cyclicnterminus;
-	delete cycliccterminus;
-	delete enablescrambling;
 	delete applicationformlayout;
 	delete applicationgroupbox;
 
-	delete blindedges;
-	delete denovographformlayout;
-	delete denovographgroupbox;
-
-	delete sequencedatabaseline;
-	delete sequencedatabasebutton;
-	delete sequencedatabaselayout;
-	delete databasesearchformlayout;
-	delete databasesearchgroupbox;
-
-	delete searchedsequence;
+	delete searchedsequenceline;
+	delete searchedsequencebutton;
+	delete searchedsequencelayout;
 	delete searchedsequenceNtermmodif;
 	delete searchedsequenceCtermmodif;
 	delete searchedsequenceTmodif;
@@ -480,64 +464,32 @@ void cParametersWidget::closeEvent(QCloseEvent *event) {
 }
 
 
-void cParametersWidget::deleteRow(int number) {
-	for (int i = 0; i < modificationstable->columnCount(); i++) {
-		if ((i == 0) || (i == 1)) {
-			delete modificationstable->item(number, i);
-		}
-		else {
-			delete modificationstable->cellWidget(number, i);
-		}
-	}
-	modificationstable->removeRow(number);
+void cParametersWidget::setSequence(int peptidetypeindex, QString sequence) {
+	peptidetype->setCurrentIndex(peptidetypeindex);
+	searchedsequenceline->setText(sequence);
 }
 
 
-void cParametersWidget::deleteModificationsTableBody() {
-	while (modificationstable->rowCount() > 0) {
-		deleteRow(modificationstable->rowCount() - 1);
-	}
+void cParametersWidget::setTag(int peptidetypeindex, QString tag) {
+	peptidetype->setCurrentIndex(peptidetypeindex);
+	sequencetag->setText(tag);
 }
 
 
-void cParametersWidget::modificationsTableInsertRow() {
-	int row = modificationstable->rowCount();
-
-	modificationstable->insertRow(row);
-
-	modificationstable->setItem(row, 0, new QTableWidgetItem());
-	modificationstable->item(row, 0)->setData(Qt::DisplayRole, "");
-
-	modificationstable->setItem(row, 1, new QTableWidgetItem());
-	modificationstable->item(row, 1)->setData(Qt::DisplayRole, "");
-
-	modificationstable->setCellWidget(row, 2, new QCheckBox());
-
-	modificationstable->setCellWidget(row, 3, new QCheckBox());
-}
-
-
-void cParametersWidget::modificationsTableRemoveEmptyRows() {
-	int i = 0;
-	while (i < modificationstable->rowCount()) {
-		if (modificationstable->item(i, 0)->text().toStdString().compare("") == 0) {
-			deleteRow(i);
-		}
-		else {
-			i++;
-		}
-	}
+void cParametersWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		restoreParameters();
+    }
 }
 
 
 void cParametersWidget::loadSettings() {
 	QString filename = QFileDialog::getOpenFileName(this, tr("Load Settings"), lastdirloadsettings, tr("Settings Files (*.ini)"));
-	lastdirloadsettings = filename;
 
-	if (filename.toStdString().compare("") != 0) {
-		int loadedrows = 0;
+	if (!filename.isEmpty()) {
+		lastdirloadsettings = filename;
+
 		QString qloadstring;
-		QCheckBox* tmpcheckbox;
 
 		settingsfile = filename;
 		save->setText(QString("  Save '") + QString(settingsfile.toStdString().substr(settingsfile.toStdString().rfind('/') + 1, settingsfile.toStdString().size()).c_str()) + QString("'  "));
@@ -546,6 +498,7 @@ void cParametersWidget::loadSettings() {
 		peptidetype->setCurrentIndex(settings.value("peptidetype", 0).toInt());
 		peaklistline->setText(settings.value("peaklist", "").toString());
 		precursormass->setValue(settings.value("precursormass", 0.0).toDouble());
+		precursoradduct->setText(settings.value("precursoradduct", "").toString());
 		precursormasserrortolerance->setValue(settings.value("precursormasserrortolerance", 5.0).toDouble());
 		precursorcharge->setValue(settings.value("precursorcharge", 1).toInt());
 		fragmentmasserrortolerance->setValue(settings.value("fragmentmasserrortolerance", 5.0).toDouble());
@@ -559,31 +512,15 @@ void cParametersWidget::loadSettings() {
 		maximumbricksincombinationend->setValue(settings.value("maximumbricksincombinationend", 3).toInt());
 		maximumcumulativemass->setValue(settings.value("maximumcumulativemass", 0).toDouble());
 		settings.value("generatebrickspermutations", 1).toInt() == 0 ? generatebrickspermutations->setChecked(false) : generatebrickspermutations->setChecked(true);
+		modificationsline->setText(settings.value("modificationsfile", "").toString());
 
-		deleteModificationsTableBody();
-
-		qloadstring = ("modification_" + to_string(loadedrows) + "_0").c_str();
-		while (settings.value(qloadstring, "").toString().toStdString().compare("") != 0) {
-			modificationsTableInsertRow();
-
-			modificationstable->item(loadedrows, 0)->setText(settings.value(qloadstring, "").toString());
-
-			qloadstring = ("modification_" + to_string(loadedrows) + "_1").c_str();
-			modificationstable->item(loadedrows, 1)->setText(settings.value(qloadstring, "").toString());
-
-			tmpcheckbox = (QCheckBox *)(modificationstable->cellWidget(loadedrows, 2));
-			qloadstring = ("modification_" + to_string(loadedrows) + "_2").c_str();
-			settings.value(qloadstring, 0).toInt() == 0 ? tmpcheckbox->setChecked(false) : tmpcheckbox->setChecked(true);
-
-			tmpcheckbox = (QCheckBox *)(modificationstable->cellWidget(loadedrows, 3));
-			qloadstring = ("modification_" + to_string(loadedrows) + "_3").c_str();
-			settings.value(qloadstring, 0).toInt() == 0 ? tmpcheckbox->setChecked(false) : tmpcheckbox->setChecked(true);
-
-			loadedrows++;
-			qloadstring = ("modification_" + to_string(loadedrows) + "_0").c_str();
-		}
+		blindedges->setCurrentIndex(settings.value("blindedges", 2).toInt());
+		settings.value("cyclicnterminus", 0).toInt() == 0 ? cyclicnterminus->setChecked(false) : cyclicnterminus->setChecked(true);
+		settings.value("cycliccterminus", 0).toInt() == 0 ? cycliccterminus->setChecked(false) : cycliccterminus->setChecked(true);
+		settings.value("enablescrambling", 0).toInt() == 0 ? enablescrambling->setChecked(false) : enablescrambling->setChecked(true);
 
 		mode->setCurrentIndex(settings.value("mode", 0).toInt());
+		sequencedatabaseline->setText(settings.value("sequencedatabase", "").toString());
 		maximumnumberofthreads->setValue(settings.value("maximumnumberofthreads", 1).toInt());
 		scoretype->setCurrentIndex(settings.value("scoretype", 0).toInt());
 		hitsreported->setValue(settings.value("hitsreported", 1000).toInt());
@@ -595,15 +532,8 @@ void cParametersWidget::loadSettings() {
 		}
 
 		settings.value("clearhitswithoutparent", 0).toInt() == 0 ? clearhitswithoutparent->setChecked(false) : clearhitswithoutparent->setChecked(true);
-		settings.value("cyclicnterminus", 0).toInt() == 0 ? cyclicnterminus->setChecked(false) : cyclicnterminus->setChecked(true);
-		settings.value("cycliccterminus", 0).toInt() == 0 ? cycliccterminus->setChecked(false) : cycliccterminus->setChecked(true);
-		settings.value("enablescrambling", 0).toInt() == 0 ? enablescrambling->setChecked(false) : enablescrambling->setChecked(true);
-
-		blindedges->setCurrentIndex(settings.value("blindedges", 2).toInt());
-
-		sequencedatabaseline->setText(settings.value("sequencedatabase", "").toString());
 
-		searchedsequence->setText(settings.value("searchedsequence", "").toString());
+		searchedsequenceline->setText(settings.value("searchedsequence", "").toString());
 		searchedsequenceNtermmodif->setText(settings.value("searchedsequenceNtermmodif", "").toString());
 		searchedsequenceCtermmodif->setText(settings.value("searchedsequenceCtermmodif", "").toString());
 		searchedsequenceTmodif->setText(settings.value("searchedsequenceTmodif", "").toString());
@@ -620,9 +550,7 @@ void cParametersWidget::saveSettings() {
 		return;
 	}
 
-	int savedrows = 0;
 	QString qsavestring;
-	QCheckBox* tmpcheckbox;
 
 	QSettings settings(settingsfile, QSettings::IniFormat);
 	settings.clear();
@@ -630,6 +558,7 @@ void cParametersWidget::saveSettings() {
 	settings.setValue("peptidetype", peptidetype->currentIndex());
 	settings.setValue("peaklist", peaklistline->text());
 	settings.setValue("precursormass", precursormass->value());
+	settings.setValue("precursoradduct", precursoradduct->text());
 	settings.setValue("precursormasserrortolerance", precursormasserrortolerance->value());
 	settings.setValue("precursorcharge", precursorcharge->value());
 	settings.setValue("fragmentmasserrortolerance", fragmentmasserrortolerance->value());
@@ -643,28 +572,15 @@ void cParametersWidget::saveSettings() {
 	settings.setValue("maximumbricksincombinationend", maximumbricksincombinationend->value());
 	settings.setValue("maximumcumulativemass", maximumcumulativemass->value());
 	generatebrickspermutations->isChecked() ? settings.setValue("generatebrickspermutations", 1) : settings.setValue("generatebrickspermutations", 0);
+	settings.setValue("modificationsfile", modificationsline->text());
 
-	modificationsTableRemoveEmptyRows();
-
-	for (int i = 0; i < modificationstable->rowCount(); i++) {
-		qsavestring = ("modification_" + to_string(savedrows) + "_0").c_str();
-		settings.setValue(qsavestring, modificationstable->item(i, 0)->text());
-		
-		qsavestring = ("modification_" + to_string(savedrows) + "_1").c_str();
-		settings.setValue(qsavestring, modificationstable->item(i, 1)->text());
-
-		qsavestring = ("modification_" + to_string(savedrows) + "_2").c_str();
-		tmpcheckbox = (QCheckBox *)(modificationstable->cellWidget(i, 2));
-		tmpcheckbox->isChecked() ? settings.setValue(qsavestring, 1) : settings.setValue(qsavestring, 0);
-		
-		qsavestring = ("modification_" + to_string(savedrows) + "_3").c_str();
-		tmpcheckbox = (QCheckBox *)(modificationstable->cellWidget(i, 3));
-		tmpcheckbox->isChecked() ? settings.setValue(qsavestring, 1) : settings.setValue(qsavestring, 0);
-
-		savedrows++;
-	}
+	settings.setValue("blindedges", blindedges->currentIndex());
+	cyclicnterminus->isChecked() ? settings.setValue("cyclicnterminus", 1) : settings.setValue("cyclicnterminus", 0);
+	cycliccterminus->isChecked() ? settings.setValue("cycliccterminus", 1) : settings.setValue("cycliccterminus", 0);
+	enablescrambling->isChecked() ? settings.setValue("enablescrambling", 1) : settings.setValue("enablescrambling", 0);
 
 	settings.setValue("mode", mode->currentIndex());
+	settings.setValue("sequencedatabase", sequencedatabaseline->text());
 	settings.setValue("maximumnumberofthreads", maximumnumberofthreads->value());
 	settings.setValue("scoretype", scoretype->currentIndex());
 	settings.setValue("hitsreported", hitsreported->value());
@@ -676,15 +592,8 @@ void cParametersWidget::saveSettings() {
 	}
 
 	clearhitswithoutparent->isChecked() ? settings.setValue("clearhitswithoutparent", 1) : settings.setValue("clearhitswithoutparent", 0);
-	cyclicnterminus->isChecked() ? settings.setValue("cyclicnterminus", 1) : settings.setValue("cyclicnterminus", 0);
-	cycliccterminus->isChecked() ? settings.setValue("cycliccterminus", 1) : settings.setValue("cycliccterminus", 0);
-	enablescrambling->isChecked() ? settings.setValue("enablescrambling", 1) : settings.setValue("enablescrambling", 0);
-
-	settings.setValue("blindedges", blindedges->currentIndex());
-
-	settings.setValue("sequencedatabase", sequencedatabaseline->text());
 
-	settings.setValue("searchedsequence", searchedsequence->text());
+	settings.setValue("searchedsequence", searchedsequenceline->text());
 	settings.setValue("searchedsequenceNtermmodif", searchedsequenceNtermmodif->text());
 	settings.setValue("searchedsequenceCtermmodif", searchedsequenceCtermmodif->text());
 	settings.setValue("searchedsequenceTmodif", searchedsequenceTmodif->text());
@@ -694,9 +603,10 @@ void cParametersWidget::saveSettings() {
 
 void cParametersWidget::saveSettingsAs() {
 	QString filename = QFileDialog::getSaveFileName(this, tr("Save Settings As..."), lastdirsavesettings, tr("Files (*.ini)"));
-	lastdirsavesettings = filename;
 	
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdirsavesettings = filename;
+	
 		settingsfile = filename;
 		save->setText(QString("  Save '") + QString(settingsfile.toStdString().substr(settingsfile.toStdString().rfind('/') + 1, settingsfile.toStdString().size()).c_str()) + QString("'  "));
 		saveSettings();
@@ -705,11 +615,14 @@ void cParametersWidget::saveSettingsAs() {
 
 
 void cParametersWidget::peaklistButtonReleased() {
-	QString filename = QFileDialog::getOpenFileName(this, tr("Select Peaklist..."), lastdirselectpeaklist, tr("Peak Lists (*.txt *.mgf *.mzML *.mzXML *.baf)"));
-	lastdirselectpeaklist = filename;
-
-	if (filename.toStdString().compare("") != 0) {
-		peaklistfilename = filename.toStdString();
+	#if OS_TYPE == UNX
+		QString filename = QFileDialog::getOpenFileName(this, tr("Select Peaklist..."), lastdirselectpeaklist, tr("Peak Lists (*.txt *.mgf *.mzML *.mzXML)"));
+	#else
+		QString filename = QFileDialog::getOpenFileName(this, tr("Select Peaklist..."), lastdirselectpeaklist, tr("Peak Lists (*.txt *.mgf *.mzML *.mzXML *.baf)"));
+	#endif
+
+	if (!filename.isEmpty()) {
+		lastdirselectpeaklist = filename;
 		peaklistline->setText(filename);
 	}
 }
@@ -717,33 +630,31 @@ void cParametersWidget::peaklistButtonReleased() {
 
 void cParametersWidget::brickDatabaseButtonReleased() {
 	QString filename = QFileDialog::getOpenFileName(this, tr("Select Building Blocks Database..."), lastdirselectbricksdatabase, tr("Text Files (*.txt)"));
-	lastdirselectbricksdatabase = filename;
-
-	if (filename.toStdString().compare("") != 0) {
-		brickdatabasefilename = filename.toStdString();
+	
+	if (!filename.isEmpty()) {
+		lastdirselectbricksdatabase = filename;
 		brickdatabaseline->setText(filename);
 	}
 }
 
 
-void cParametersWidget::sequenceDatabaseButtonReleased() {
-	QString filename = QFileDialog::getOpenFileName(this, tr("Select Sequence Database..."), lastdirselectsequencedatabase, tr("Text Files (*.txt)"));
-	lastdirselectsequencedatabase = filename;
-
-	if (filename.toStdString().compare("") != 0) {
-		sequencedatabasefilename = filename.toStdString();
-		sequencedatabaseline->setText(filename);
+void cParametersWidget::modificationsButtonReleased() {
+	QString filename = QFileDialog::getOpenFileName(this, tr("Select Modifications File..."), lastdirselectmodifications, tr("Text Files (*.txt)"));
+	
+	if (!filename.isEmpty()) {
+		lastdirselectmodifications = filename;
+		modificationsline->setText(filename);
 	}
 }
 
 
-void cParametersWidget::modificationsInsertButtonReleased() {
-	modificationsTableInsertRow();
-}
-
+void cParametersWidget::sequenceDatabaseButtonReleased() {
+	QString filename = QFileDialog::getOpenFileName(this, tr("Select Sequence Database..."), lastdirselectsequencedatabase, tr("Text Files (*.txt)"));
 
-void cParametersWidget::modificationsRemoveButtonReleased() {
-	modificationsTableRemoveEmptyRows();
+	if (!filename.isEmpty()) {
+		lastdirselectsequencedatabase = filename;
+		sequencedatabaseline->setText(filename);
+	}
 }
 
 
@@ -752,29 +663,46 @@ bool cParametersWidget::updateParameters() {
 	QString errstr;
 
 	if (peaklistline->text().toStdString().compare("") == 0) {
-		errstr = "A peaklist must be specified.";
+		errstr = "A peaklist must be specified!";
 		msgBox.setText(errstr);
 		msgBox.exec();
 		return false;
 	}
 
 	if ((brickdatabaseline->text().toStdString().compare("") == 0) && (((modeType)mode->currentIndex() == denovoengine) || ((modeType)mode->currentIndex() == singlecomparison) || ((modeType)mode->currentIndex() == databasesearch))) {
-		errstr = "A database of building blocks must be specified.";
+		errstr = "A database of building blocks must be specified!";
 		msgBox.setText(errstr);
 		msgBox.exec();
 		return false;
 	}
 
 	if ((sequencedatabaseline->text().toStdString().compare("") == 0) && (((modeType)mode->currentIndex() == databasesearch) || ((modeType)mode->currentIndex() == dereplication))) {
-		errstr = "A sequence database must be specified.";
+		errstr = "A sequence database must be specified!";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return false;
+	}
+
+	if (precursorcharge->value() == 0) {
+		errstr = "The charge cannot be zero!";
 		msgBox.setText(errstr);
 		msgBox.exec();
 		return false;
 	}
 
+	/*
+	if ((maximumbricksincombinationmiddle->value() < 2) && ((modeType)mode->currentIndex() == denovoengine) && (((peptideType)peptidetype->currentIndex() == branched) || ((peptideType)peptidetype->currentIndex() == lasso))) {
+		errstr = "'Maximum Number of Combined Blocks (middle)' must be at least 2 when a branched or a branch-cyclic peptide is searched! (One block represents a branched residue, the other block(s) corresponds to a branch.)";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return false;
+	}
+	*/
+
 	parameters.peptidetype = (peptideType)peptidetype->currentIndex();
 	parameters.peaklistfilename = peaklistline->text().toStdString();
 	parameters.precursormass = precursormass->value();
+	parameters.precursoradduct = precursoradduct->text().toStdString();
 	parameters.precursormasserrortolerance = precursormasserrortolerance->value();
 	parameters.precursorcharge = precursorcharge->value();
 	parameters.fragmentmasserrortolerance = fragmentmasserrortolerance->value();
@@ -789,26 +717,15 @@ bool cParametersWidget::updateParameters() {
 	parameters.maximumcumulativemass = maximumcumulativemass->value();
 	parameters.maximumbricksincombination = max(max(parameters.maximumbricksincombinationbegin, parameters.maximumbricksincombinationmiddle), parameters.maximumbricksincombinationend);
 	parameters.generatebrickspermutations = generatebrickspermutations->isChecked();
+	parameters.modificationsfilename = modificationsline->text().toStdString();
 
-	QCheckBox* tmpcheckbox1;
-	QCheckBox* tmpcheckbox2;
-
-	parameters.searchedmodifications.clear();
-	parameters.searchedmodifications.push_back(fragmentDescription("", 0, "", true, true));
-
-	modificationsTableRemoveEmptyRows();
-	
-	int i = 0;
-	while (i < modificationstable->rowCount()) {
-		tmpcheckbox1 = (QCheckBox *)(modificationstable->cellWidget(i, 2));
-		tmpcheckbox2 = (QCheckBox *)(modificationstable->cellWidget(i, 3));
-
-		parameters.searchedmodifications.push_back(fragmentDescription(modificationstable->item(i, 0)->text().toStdString(), 0, modificationstable->item(i, 1)->text().toStdString(), tmpcheckbox1->isChecked(), tmpcheckbox2->isChecked()));
-
-		i++;
-	}
+	parameters.blindedges = blindedges->currentIndex();
+	parameters.cyclicnterminus = cyclicnterminus->isChecked();
+	parameters.cycliccterminus = cycliccterminus->isChecked();
+	parameters.enablescrambling = enablescrambling->isChecked();
 
 	parameters.mode = (modeType)mode->currentIndex();
+	parameters.sequencedatabasefilename = sequencedatabaseline->text().toStdString();
 	parameters.maximumnumberofthreads = maximumnumberofthreads->value();
 	parameters.scoretype = (scoreType)scoretype->currentIndex();
 	parameters.hitsreported = hitsreported->value();
@@ -826,13 +743,13 @@ bool cParametersWidget::updateParameters() {
 		{
 		case linear:
 		case branched:
-			start = b_ion;
+			start = a_ion;
 			break;
 		case cyclic:
-			start = b_ion;
+			start = a_ion;
 			break;
 		case lasso:
-			start = b_ion;
+			start = a_ion;
 			break;
 		case linearpolysaccharide:
 			start = ms_nterminal_ion_hplus;
@@ -850,22 +767,15 @@ bool cParametersWidget::updateParameters() {
 	}
 
 	parameters.clearhitswithoutparent = clearhitswithoutparent->isChecked();
-	parameters.cyclicnterminus = cyclicnterminus->isChecked();
-	parameters.cycliccterminus = cycliccterminus->isChecked();
-	parameters.updateFragmentDefinitions();
-
-	parameters.enablescrambling = enablescrambling->isChecked();
-
-	parameters.blindedges = blindedges->currentIndex();
 
-	parameters.sequencedatabasefilename = sequencedatabaseline->text().toStdString();
-
-	parameters.searchedsequence = searchedsequence->text().toStdString();
+	parameters.searchedsequence = searchedsequenceline->text().toStdString();
 	parameters.originalsearchedsequence = parameters.searchedsequence;
 	parameters.searchedsequenceNtermmodif = searchedsequenceNtermmodif->text().toStdString();
 	parameters.searchedsequenceCtermmodif = searchedsequenceCtermmodif->text().toStdString();
 	parameters.searchedsequenceTmodif = searchedsequenceTmodif->text().toStdString();
 
+	parameters.updateFragmentDefinitions();
+
 	oldsettingsfile = settingsfile;
 
 	return true;
@@ -883,6 +793,7 @@ void cParametersWidget::restoreParameters() {
 	peptidetype->setCurrentIndex(parameters.peptidetype);
 	peaklistline->setText(parameters.peaklistfilename.c_str());
 	precursormass->setValue(parameters.precursormass);
+	precursoradduct->setText(parameters.precursoradduct.c_str());
 	precursormasserrortolerance->setValue(parameters.precursormasserrortolerance);
 	precursorcharge->setValue(parameters.precursorcharge);
 	fragmentmasserrortolerance->setValue(parameters.fragmentmasserrortolerance);
@@ -896,29 +807,15 @@ void cParametersWidget::restoreParameters() {
 	maximumbricksincombinationend->setValue(parameters.maximumbricksincombinationend);
 	maximumcumulativemass->setValue(parameters.maximumcumulativemass);
 	generatebrickspermutations->setChecked(parameters.generatebrickspermutations);
+	modificationsline->setText(parameters.modificationsfilename.c_str());
 
-	QCheckBox* tmpcheckbox;
-
-	deleteModificationsTableBody();
-
-	int i = 1;
-	while (i < (int)parameters.searchedmodifications.size()) {
-		modificationsTableInsertRow();
-
-		modificationstable->item(i - 1, 0)->setText(parameters.searchedmodifications[i].name.c_str());
-
-		modificationstable->item(i - 1, 1)->setText(parameters.searchedmodifications[i].summary.c_str());
-
-		tmpcheckbox = (QCheckBox *)(modificationstable->cellWidget(i - 1, 2));
-		tmpcheckbox->setChecked(parameters.searchedmodifications[i].nterminal);
-
-		tmpcheckbox = (QCheckBox *)(modificationstable->cellWidget(i - 1, 3));
-		tmpcheckbox->setChecked(parameters.searchedmodifications[i].cterminal);
-
-		i++;
-	}
+	blindedges->setCurrentIndex(parameters.blindedges);
+	cyclicnterminus->setChecked(parameters.cyclicnterminus);
+	cycliccterminus->setChecked(parameters.cycliccterminus);
+	enablescrambling->setChecked(parameters.enablescrambling);
 
 	mode->setCurrentIndex(parameters.mode);
+	sequencedatabaseline->setText(parameters.sequencedatabasefilename.c_str());
 	maximumnumberofthreads->setValue(parameters.maximumnumberofthreads);
 	scoretype->setCurrentIndex(parameters.scoretype);
 	hitsreported->setValue(parameters.hitsreported);
@@ -933,13 +830,13 @@ void cParametersWidget::restoreParameters() {
 		{
 		case linear:
 		case branched:
-			start = b_ion;
+			start = a_ion;
 			break;
 		case cyclic:
-			start = b_ion;
+			start = a_ion;
 			break;
 		case lasso:
-			start = b_ion;
+			start = a_ion;
 			break;
 		case linearpolysaccharide:
 			start = ms_nterminal_ion_hplus;
@@ -955,15 +852,8 @@ void cParametersWidget::restoreParameters() {
 	}
 
 	clearhitswithoutparent->setChecked(parameters.clearhitswithoutparent);
-	cyclicnterminus->setChecked(parameters.cyclicnterminus);
-	cycliccterminus->setChecked(parameters.cycliccterminus);
-	enablescrambling->setChecked(parameters.enablescrambling);
 	
-	blindedges->setCurrentIndex(parameters.blindedges);
-
-	sequencedatabaseline->setText(parameters.sequencedatabasefilename.c_str());
-
-	searchedsequence->setText(parameters.searchedsequence.c_str());
+	searchedsequenceline->setText(parameters.searchedsequence.c_str());
 	searchedsequenceNtermmodif->setText(parameters.searchedsequenceNtermmodif.c_str());
 	searchedsequenceCtermmodif->setText(parameters.searchedsequenceCtermmodif.c_str());
 	searchedsequenceTmodif->setText(parameters.searchedsequenceTmodif.c_str());
@@ -987,49 +877,54 @@ void cParametersWidget::updateSettingsWhenPeptideTypeChanged(int index) {
 	switch ((peptideType)index)
 	{
 	case linear:
-		modificationsgroupbox->setDisabled(false);
-		searchedsequenceNtermmodif->setDisabled(false);
-		searchedsequenceCtermmodif->setDisabled(false);
-		searchedsequenceTmodif->setDisabled(true);
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
 		cyclicnterminus->setDisabled(false);
 		cycliccterminus->setDisabled(false);
 		enablescrambling->setDisabled(true);
+		searchedsequenceNtermmodif->setDisabled(false);
+		searchedsequenceCtermmodif->setDisabled(false);
+		searchedsequenceTmodif->setDisabled(true);
 		break;
 	case cyclic:
-		modificationsgroupbox->setDisabled(true);
-		searchedsequenceNtermmodif->setDisabled(true);
-		searchedsequenceCtermmodif->setDisabled(true);
-		searchedsequenceTmodif->setDisabled(true);
+		modificationsline->setDisabled(true);
+		modificationsbutton->setDisabled(true);
 		cyclicnterminus->setDisabled(true);
 		cycliccterminus->setDisabled(true);
 		enablescrambling->setDisabled(false);
+		searchedsequenceNtermmodif->setDisabled(true);
+		searchedsequenceCtermmodif->setDisabled(true);
+		searchedsequenceTmodif->setDisabled(true);
 		break;
 	case branched:
-		modificationsgroupbox->setDisabled(false);
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
+		cyclicnterminus->setDisabled(true);
+		cycliccterminus->setDisabled(true);
+		enablescrambling->setDisabled(true);
 		searchedsequenceNtermmodif->setDisabled(false);
 		searchedsequenceCtermmodif->setDisabled(false);
 		searchedsequenceTmodif->setDisabled(false);
+		break;
+	case lasso:
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
 		cyclicnterminus->setDisabled(true);
 		cycliccterminus->setDisabled(true);
 		enablescrambling->setDisabled(true);
-		break;
-	case lasso:
-		modificationsgroupbox->setDisabled(false);
 		searchedsequenceNtermmodif->setDisabled(true);
 		searchedsequenceCtermmodif->setDisabled(true);
 		searchedsequenceTmodif->setDisabled(false);
+		break;
+	case linearpolysaccharide:
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
 		cyclicnterminus->setDisabled(true);
 		cycliccterminus->setDisabled(true);
 		enablescrambling->setDisabled(true);
-		break;
-	case linearpolysaccharide:
-		modificationsgroupbox->setDisabled(false);
 		searchedsequenceNtermmodif->setDisabled(false);
 		searchedsequenceCtermmodif->setDisabled(false);
 		searchedsequenceTmodif->setDisabled(true);
-		cyclicnterminus->setDisabled(true);
-		cycliccterminus->setDisabled(true);
-		enablescrambling->setDisabled(true);
 		break;
 	case other:
 	default:
@@ -1045,6 +940,7 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
 	case denovoengine:
 		peptidetype->setDisabled(false);
 		precursormass->setDisabled(false);
+		precursoradduct->setDisabled(false);
 		precursorcharge->setDisabled(false);
 		precursormasserrortolerance->setDisabled(false);
 		brickdatabaseline->setDisabled(false);
@@ -1054,23 +950,28 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
 		maximumbricksincombinationend->setDisabled(false);
 		maximumcumulativemass->setDisabled(false);
 		generatebrickspermutations->setDisabled(false);
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
+		sequencedatabaseline->setDisabled(true);
+		sequencedatabasebutton->setDisabled(true);
+		blindedges->setDisabled(false);
 		maximumnumberofthreads->setDisabled(false);
 		scoretype->setDisabled(false);
 		hitsreported->setDisabled(false);
 		sequencetag->setDisabled(false);
 		fragmentiontypes->setDisabled(false);
 		clearhitswithoutparent->setDisabled(false);
-		denovographgroupbox->setDisabled(false);
-		databasesearchgroupbox->setDisabled(true);
-		searchedsequence->setDisabled(false);
+		searchedsequenceline->setDisabled(false);
+		searchedsequencebutton->setDisabled(false);
 
 		updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
 		break;
 	case singlecomparison:
 		peptidetype->setDisabled(false);
-		precursormass->setDisabled(true);
+		precursormass->setDisabled(false);
+		precursoradduct->setDisabled(false);
 		precursorcharge->setDisabled(false);
-		precursormasserrortolerance->setDisabled(true);
+		precursormasserrortolerance->setDisabled(false);
 		brickdatabaseline->setDisabled(false);
 		brickdatabasebutton->setDisabled(false);
 		maximumbricksincombinationbegin->setDisabled(true);
@@ -1078,21 +979,26 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
 		maximumbricksincombinationend->setDisabled(true);
 		maximumcumulativemass->setDisabled(true);
 		generatebrickspermutations->setDisabled(true);
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
+		sequencedatabaseline->setDisabled(true);
+		sequencedatabasebutton->setDisabled(true);
+		blindedges->setDisabled(true);
 		maximumnumberofthreads->setDisabled(true);
 		scoretype->setDisabled(true);
 		hitsreported->setDisabled(true);
 		sequencetag->setDisabled(true);
 		fragmentiontypes->setDisabled(false);
 		clearhitswithoutparent->setDisabled(false);
-		denovographgroupbox->setDisabled(true);
-		databasesearchgroupbox->setDisabled(true);
-		searchedsequence->setDisabled(false);
+		searchedsequenceline->setDisabled(false);
+		searchedsequencebutton->setDisabled(false);
 
 		updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
 		break;
 	case databasesearch:
 		peptidetype->setDisabled(false);
 		precursormass->setDisabled(false);
+		precursoradduct->setDisabled(false);
 		precursorcharge->setDisabled(false);
 		precursormasserrortolerance->setDisabled(false);
 		brickdatabaseline->setDisabled(false);
@@ -1102,21 +1008,26 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
 		maximumbricksincombinationend->setDisabled(true);
 		maximumcumulativemass->setDisabled(true);
 		generatebrickspermutations->setDisabled(true);
+		modificationsline->setDisabled(false);
+		modificationsbutton->setDisabled(false);
+		blindedges->setDisabled(true);
+		sequencedatabaseline->setDisabled(false);
+		sequencedatabasebutton->setDisabled(false);
 		maximumnumberofthreads->setDisabled(false);
 		scoretype->setDisabled(false);
 		hitsreported->setDisabled(false);
 		sequencetag->setDisabled(false);
 		fragmentiontypes->setDisabled(false);
 		clearhitswithoutparent->setDisabled(false);
-		denovographgroupbox->setDisabled(true);
-		databasesearchgroupbox->setDisabled(false);
-		searchedsequence->setDisabled(false);
+		searchedsequenceline->setDisabled(false);
+		searchedsequencebutton->setDisabled(false);
 
 		updateSettingsWhenPeptideTypeChanged(peptidetype->currentIndex());
 		break;
 	case dereplication:
 		peptidetype->setDisabled(true);
 		precursormass->setDisabled(true);
+		precursoradduct->setDisabled(true);
 		precursorcharge->setDisabled(false);
 		precursormasserrortolerance->setDisabled(true);
 		brickdatabaseline->setDisabled(true);
@@ -1126,25 +1037,30 @@ void cParametersWidget::updateSettingsWhenModeChanged(int index) {
 		maximumbricksincombinationend->setDisabled(true);
 		maximumcumulativemass->setDisabled(true);
 		generatebrickspermutations->setDisabled(true);
+		modificationsline->setDisabled(true);
+		modificationsbutton->setDisabled(true);
+		blindedges->setDisabled(true);
+		sequencedatabaseline->setDisabled(false);
+		sequencedatabasebutton->setDisabled(false);
 		maximumnumberofthreads->setDisabled(true);
 		scoretype->setDisabled(true);
 		hitsreported->setDisabled(true);
 		sequencetag->setDisabled(true);
 		fragmentiontypes->setDisabled(false);
 		clearhitswithoutparent->setDisabled(true);
-		denovographgroupbox->setDisabled(true);
-		databasesearchgroupbox->setDisabled(false);
-		searchedsequence->setDisabled(true);
+		searchedsequenceline->setDisabled(true);
+		searchedsequencebutton->setDisabled(true);
 
 		resetFragmentIonTypes();
 		
-		modificationsgroupbox->setDisabled(true);
-		searchedsequenceNtermmodif->setDisabled(true);
-		searchedsequenceCtermmodif->setDisabled(true);
-		searchedsequenceTmodif->setDisabled(true);
+		modificationsline->setDisabled(true);
+		modificationsbutton->setDisabled(true);
 		cyclicnterminus->setDisabled(true);
 		cycliccterminus->setDisabled(true);
 		enablescrambling->setDisabled(true);
+		searchedsequenceNtermmodif->setDisabled(true);
+		searchedsequenceCtermmodif->setDisabled(true);
+		searchedsequenceTmodif->setDisabled(true);
 		break;
 	default:
 		break;
@@ -1166,16 +1082,16 @@ void cParametersWidget::resetFragmentIonTypes() {
 		switch ((peptideType)peptidetype->currentIndex()) {
 		case linear:
 		case branched:
-			start = b_ion;
-			end = y_ion_water_and_ammonia_loss;
+			start = a_ion;
+			end = z_ion_dehydrated_and_deamidated;
 			break;
 		case cyclic:
-			start = b_ion;
-			end = a_ion_water_and_ammonia_loss;
+			start = a_ion;
+			end = c_ion_dehydrated_and_deamidated;
 			break;
 		case lasso:
-			start = b_ion;
-			end = y_ion_water_and_ammonia_loss;
+			start = a_ion;
+			end = z_ion_dehydrated_and_deamidated;
 			break;
 		case linearpolysaccharide:
 			start = ms_nterminal_ion_hplus;
@@ -1187,13 +1103,50 @@ void cParametersWidget::resetFragmentIonTypes() {
 		}
 	}
 
-	for (int i = start; i <= end; i++) {
+	for (int i = (int)start; i <= (int)end; i++) {
+
 		fragmentiontypes->getList()->addItem(tr(parameters.fragmentdefinitions[(fragmentIonType)i].name.c_str()));
 
-		if (parameters.fragmentdefinitions[(fragmentIonType)i].parent == (fragmentIonType)i) {
-			fragmentiontypes->getList()->item(i-start)->setSelected(true);
+		if ((modeType)mode->currentIndex() == dereplication) {
+			if ((fragmentIonType)i == ms_hplus) {
+				fragmentiontypes->getList()->item(i-start)->setSelected(true);
+			}
+		}
+		else {
+			switch ((peptideType)peptidetype->currentIndex()) {
+			case linear:
+			case branched:
+				if (((fragmentIonType)i == b_ion) || ((fragmentIonType)i == y_ion)) {
+					fragmentiontypes->getList()->item(i-start)->setSelected(true);
+				}
+				break;
+			case cyclic:
+				if ((fragmentIonType)i == b_ion) {
+					fragmentiontypes->getList()->item(i-start)->setSelected(true);
+				}
+				break;
+			case lasso:
+				if (((fragmentIonType)i == b_ion) || ((fragmentIonType)i == y_ion)) {
+					fragmentiontypes->getList()->item(i-start)->setSelected(true);
+				}
+				break;
+			case linearpolysaccharide:
+				if (((fragmentIonType)i == ms_nterminal_ion_hplus) || ((fragmentIonType)i == ms_cterminal_ion_hplus)) {
+					fragmentiontypes->getList()->item(i-start)->setSelected(true);
+				}
+				break;
+			case other:
+			default:
+				break;
+			}
 		}
+
 	}
 
 }
 
+
+void cParametersWidget::drawPeptideButtonReleased() {
+	emit sendSequenceLine(peptidetype->currentIndex(), searchedsequenceline->text());
+}
+
diff --git a/CycloBranch/gui/cParametersWidget.h b/CycloBranch/gui/cParametersWidget.h
index b5661da..a3bf011 100644
--- a/CycloBranch/gui/cParametersWidget.h
+++ b/CycloBranch/gui/cParametersWidget.h
@@ -14,6 +14,7 @@
 #include <QLineEdit>
 #include <QPushButton>
 
+#include "core/utilities.h"
 #include "core/cSummaryFormula.h"
 #include "core/cParameters.h"
 #include "gui/cFragmentIonsListWidget.h"
@@ -50,8 +51,9 @@ class cParametersWidget : public QWidget
 
 	/**
 		\brief The constructor.
+		\param parent pointer to a parent widget
 	*/ 
-	cParametersWidget();
+	cParametersWidget(QWidget* parent = (QWidget *)0);
 
 
 	/**
@@ -81,7 +83,26 @@ class cParametersWidget : public QWidget
 	void closeEvent(QCloseEvent *event);
 
 
+	/**
+		\brief Set peptide type and searched sequence.
+		\param peptidetypeindex an index of current peptide type
+		\param sequence searched sequence
+	*/ 
+	void setSequence(int peptidetypeindex, QString sequence);
+
+
+	/**
+		\brief Set peptide type and sequence tag.
+		\param peptidetypeindex an index of current peptide type
+		\param tag sequence tag
+	*/ 
+	void setTag(int peptidetypeindex, QString tag);
+
+
 private:
+
+	QWidget* parent;
+
 	cParameters parameters;
 
 	QVBoxLayout* vlayout1;
@@ -104,8 +125,8 @@ class cParametersWidget : public QWidget
 	QLineEdit* peaklistline;
 	QPushButton* peaklistbutton;
 	QHBoxLayout* peaklistlayout;
-	string peaklistfilename;
 	QDoubleSpinBox* precursormass;
+	QLineEdit* precursoradduct;
 	QSpinBox* precursorcharge;
 	QDoubleSpinBox* precursormasserrortolerance;
 	QDoubleSpinBox* fragmentmasserrortolerance;
@@ -118,47 +139,40 @@ class cParametersWidget : public QWidget
 	QLineEdit* brickdatabaseline;
 	QPushButton* brickdatabasebutton;
 	QHBoxLayout* brickdatabaselayout;
-	string brickdatabasefilename;
 	QSpinBox* maximumbricksincombinationbegin;
 	QSpinBox* maximumbricksincombinationmiddle;
 	QSpinBox* maximumbricksincombinationend;
 	QDoubleSpinBox* maximumcumulativemass;
 	QCheckBox* generatebrickspermutations;
+	QLineEdit* modificationsline;
+	QPushButton* modificationsbutton;
+	QHBoxLayout* modificationslayout;
 
-	QGroupBox* modificationsgroupbox;
-	QVBoxLayout* modificationslayout;
-	QTableWidget* modificationstable;
-	QHBoxLayout* modificationsbuttonslayout;
-	QPushButton* modificationsbuttoninsert;
-	QPushButton* modificationsbuttonremove;
+	QGroupBox* miscgroupbox;
+	QFormLayout* miscformlayout;
+	QComboBox* blindedges;
+	QCheckBox* cyclicnterminus;
+	QCheckBox* cycliccterminus;
+	QCheckBox* enablescrambling;
 
 	QFormLayout* applicationformlayout;
 	QGroupBox* applicationgroupbox;
 	QComboBox* mode;
+	QLineEdit* sequencedatabaseline;
+	QPushButton* sequencedatabasebutton;
+	QHBoxLayout* sequencedatabaselayout;
 	QSpinBox* maximumnumberofthreads;
 	QComboBox* scoretype;
 	QSpinBox* hitsreported;
 	QLineEdit* sequencetag;
 	cFragmentIonsListWidget* fragmentiontypes;
 	QCheckBox* clearhitswithoutparent;
-	QCheckBox* cyclicnterminus;
-	QCheckBox* cycliccterminus;
-	QCheckBox* enablescrambling;
-
-	QGroupBox* denovographgroupbox;
-	QFormLayout* denovographformlayout;
-	QComboBox* blindedges;
 
-	QGroupBox* databasesearchgroupbox;
-	QFormLayout* databasesearchformlayout;
-	QLineEdit* sequencedatabaseline;
-	QPushButton* sequencedatabasebutton;
-	QHBoxLayout* sequencedatabaselayout;
-	string sequencedatabasefilename;
-	
 	QGroupBox* searchedsequencegroupbox;
 	QFormLayout* searchedsequenceformlayout;
-	QLineEdit* searchedsequence;
+	QLineEdit* searchedsequenceline;
+	QPushButton* searchedsequencebutton;
+	QHBoxLayout* searchedsequencelayout;
 	QLineEdit* searchedsequenceNtermmodif;
 	QLineEdit* searchedsequenceCtermmodif;
 	QLineEdit* searchedsequenceTmodif;
@@ -167,15 +181,18 @@ class cParametersWidget : public QWidget
 	QString lastdirsavesettings;
 	QString lastdirselectpeaklist;
 	QString lastdirselectbricksdatabase;
+	QString lastdirselectmodifications;
 	QString lastdirselectsequencedatabase;
 
-	void deleteRow(int number);
 
-	void deleteModificationsTableBody();
+protected:
 
-	void modificationsTableInsertRow();
 
-	void modificationsTableRemoveEmptyRows();
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
 
 
 private slots:
@@ -190,11 +207,9 @@ private slots:
 
 	void brickDatabaseButtonReleased();
 
-	void sequenceDatabaseButtonReleased();
-
-	void modificationsInsertButtonReleased();
+	void modificationsButtonReleased();
 
-	void modificationsRemoveButtonReleased();
+	void sequenceDatabaseButtonReleased();
 
 	bool updateParameters();
 
@@ -208,6 +223,18 @@ private slots:
 
 	void resetFragmentIonTypes();
 
+	void drawPeptideButtonReleased();
+
+
+signals:
+
+	/**
+		\brief Send index of peptide type and searched sequence.
+		\param peptidetypeindex an index of current peptide type
+		\param sequence searched sequence
+	*/ 
+	void sendSequenceLine(int peptidetypeindex, QString sequence);
+
 };
 
 #endif
\ No newline at end of file
diff --git a/CycloBranch/gui/cSequenceDatabaseWidget.cpp b/CycloBranch/gui/cSequenceDatabaseWidget.cpp
index 819b1ea..7d70122 100644
--- a/CycloBranch/gui/cSequenceDatabaseWidget.cpp
+++ b/CycloBranch/gui/cSequenceDatabaseWidget.cpp
@@ -1,5 +1,6 @@
 #include "gui/cSequenceDatabaseWidget.h"
 #include "gui/cMainThread.h"
+#include "gui/cEventFilter.h"
 
 #include <QTableWidget>
 #include <QTableWidgetItem>
@@ -13,12 +14,15 @@
 #include <QComboBox>
 #include <QProgressDialog>
 #include <QCheckBox>
+#include <QKeyEvent>
+#include <QIcon>
 
 
 cSequenceDatabaseWidget::cSequenceDatabaseWidget(QWidget* parent) {
 	this->parent = parent;
 
 	setWindowTitle("Sequence Database Editor");
+	setWindowIcon(QIcon(":/images/icons/26.png"));
 
 	insertrow = new QPushButton(tr("Add Row"));
 	insertrow->setToolTip("Add a new row.");
@@ -71,11 +75,6 @@ cSequenceDatabaseWidget::cSequenceDatabaseWidget(QWidget* parent) {
 	mainlayout->addWidget(database);
 	mainlayout->addLayout(buttons);
 
-	progress = new QProgressDialog(this);
-	progress->setCancelButton(0);
-	progress->setMinimumDuration(1000);
-	progress->setWindowModality(Qt::WindowModal);
-
 	connect(database->horizontalHeader(), SIGNAL(sectionDoubleClicked(int)), this, SLOT(headerItemDoubleClicked(int)));
 	connect(database, SIGNAL(itemChanged(QTableWidgetItem *)), this, SLOT(itemChanged(QTableWidgetItem *)));
 	connect(insertrow, SIGNAL(released()), this, SLOT(addRow()));
@@ -90,7 +89,13 @@ cSequenceDatabaseWidget::cSequenceDatabaseWidget(QWidget* parent) {
 	resize(1280, 700);
 
 	databasefile = "";
-	lastdir = "./SequenceDatabases/";
+
+	#if OS_TYPE == WIN
+		lastdir = "./SequenceDatabases/";
+	#else
+		lastdir = linuxinstalldir + "SequenceDatabases/";
+	#endif
+
 	sequences.clear();
 }
 
@@ -113,7 +118,6 @@ cSequenceDatabaseWidget::~cSequenceDatabaseWidget() {
 	delete database;
 	delete buttons;
 	delete mainlayout;
-	delete progress;
 }
 
 
@@ -122,35 +126,51 @@ void cSequenceDatabaseWidget::closeEvent(QCloseEvent *event) {
 }
 
 
+void cSequenceDatabaseWidget::insertRow(int peptidetypeindex, QString sequence) {
+	addRow();
+	((QComboBox *)(database->cellWidget(database->rowCount() - 1, 1)))->setCurrentIndex(peptidetypeindex);
+	database->item(database->rowCount() - 1, 5)->setText(sequence);
+
+	for (int i = 0; i < database->columnCount(); i++) {
+		database->resizeColumnToContents(i);
+	}
+}
+
+
 void cSequenceDatabaseWidget::deleteTable(bool enableprogress) {
+	QProgressDialog* progress;
+	cEventFilter filter;
+	int rowcount = database->rowCount();
+
 	if (enableprogress) {
-		progress->setLabelText("Clearing the table...");
-		progress->setMinimum(0);
-		progress->setValue(1);
-		progress->setMaximum(database->rowCount());
-		progress->show();
+		progress = new QProgressDialog("Clearing the table...", /*"Cancel"*/0, 0, rowcount, this);
+		progress->installEventFilter(&filter);
+		progress->setMinimumDuration(0);
+		progress->setWindowModality(Qt::WindowModal);
+		progress->setValue(0);
 	}
 
-	for (int i = 0; i < database->rowCount(); i++) {
-		for (int j = 0; j < database->columnCount(); j++) {
-			if ((j == 0) || (j == 1) || (j == 10)) {
-				delete database->cellWidget(i, j);
-			}
-			else {
-				delete database->item(i, j);
-			}		
-		}
+	widgetitemallocator.reset();
+
+	for (int i = 0; i < rowcount; i++) {
+		delete database->cellWidget(rowcount - i - 1, 0);
+		delete database->cellWidget(rowcount - i - 1, 1);
+		delete database->cellWidget(rowcount - i - 1, 10);
 
-		if (enableprogress && ((i == 0) || ((i - 1)/100 != i/100))) {
+		if (enableprogress) {
 			progress->setValue(i);
+			//if (progress->wasCanceled()) {
+			//	break;
+			//}
 		}
 	}
 
+	database->setRowCount(0);
+
 	if (enableprogress) {
-		progress->setValue(database->rowCount());
-		progress->hide();
+		progress->setValue(rowcount);
+		delete progress;
 	}
-	database->setRowCount(0);
 }
 
 
@@ -160,7 +180,7 @@ void cSequenceDatabaseWidget::removeRow(int row) {
 			delete database->cellWidget(row, i);
 		}
 		else {
-			delete database->item(row, i);
+			database->takeItem(row, i);
 		}
 	}
 	database->removeRow(row);
@@ -187,7 +207,7 @@ bool cSequenceDatabaseWidget::checkTable() {
 }
 
 
-bool cSequenceDatabaseWidget::checkFormula(int row, string& summary) {
+bool cSequenceDatabaseWidget::checkFormula(int row, const string& summary) {
 	cSummaryFormula formula;
 	string errmsg;
 	formula.setFormula(summary);
@@ -209,20 +229,27 @@ bool cSequenceDatabaseWidget::checkFormula(int row, string& summary) {
 
 
 bool cSequenceDatabaseWidget::checkSequence(int row) {
+
+	if (database->item(row, 5)->text().toStdString().compare("") == 0) {
+		return true;
+	}
+
 	regex rx;
 	// [^\\[\\]]+ is used instead of .+ to prevent from a too complex regex error
 	switch ((peptideType)((QComboBox *)database->cellWidget(row, 1))->currentIndex())
 	{
 	case linear:
-	case cyclic:
 	case linearpolysaccharide:
 		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
 		break;
+	case cyclic:
+		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+$";
+		break;
 	case branched:
-		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
+		rx = "^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$";
 		break;
 	case lasso:
-		rx = "(^(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$|^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\)(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?$)";
+		rx = "(^(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+\\\\\\)\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*$|^\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*\\\\\\(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])+\\\\\\)(\\[[^\\[\\]]+\\](-\\[[^\\[\\]]+\\])*)?$)";
 		break;
 	case other:
 	default:
@@ -245,7 +272,7 @@ bool cSequenceDatabaseWidget::checkSequence(int row) {
 			return false;
 		}
 	}
-	catch (std::regex_error& e) {
+	catch (regex_error& e) {
 		QMessageBox msgBox;
 		QString errstr = "Row no. ";
 		errstr += to_string(row + 1).c_str();
@@ -263,6 +290,13 @@ bool cSequenceDatabaseWidget::checkSequence(int row) {
 }
 
 
+void cSequenceDatabaseWidget::keyPressEvent(QKeyEvent *event) {
+    if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+}
+
+
 void cSequenceDatabaseWidget::closeWindow() {
 	hide();
 }
@@ -270,9 +304,9 @@ void cSequenceDatabaseWidget::closeWindow() {
 
 void cSequenceDatabaseWidget::loadDatabase() {
 	QString filename = QFileDialog::getOpenFileName(this, tr("Load the Database of Sequences"), lastdir, tr("Database of Sequences (*.txt)"));
-	lastdir = filename;
 
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdir = filename;
 
 		databasefile = filename;
 		save->setText(QString("  Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("'  "));
@@ -291,11 +325,11 @@ void cSequenceDatabaseWidget::loadDatabase() {
 			sequences.clear();
 			sequences.loadFromPlainTextStream(inputstream);
 
-			progress->setLabelText("Loading the Sequence Databatase...");
-			progress->setMinimum(0);
-			progress->setValue(1);
-			progress->setMaximum(sequences.size());
-			progress->show();
+			QProgressDialog progress("Loading the Sequence Databatase...", /*"Cancel"*/0, 0, sequences.size(), this);
+			cEventFilter filter;
+			progress.installEventFilter(&filter);
+			progress.setMinimumDuration(0);
+			progress.setWindowModality(Qt::WindowModal);
 
             cSummaryFormula formula;
             database->setRowCount(sequences.size());
@@ -310,34 +344,48 @@ void cSequenceDatabaseWidget::loadDatabase() {
                 combo->setCurrentIndex((int)sequences[i].getPeptideType());
                 database->setCellWidget(i, 1, combo);
 
-                database->setItem(i, 2, new QTableWidgetItem(sequences[i].getName().c_str()));
-                database->setItem(i, 3, new QTableWidgetItem(sequences[i].getSummaryFormula().c_str()));
-                formula.setFormula(sequences[i].getSummaryFormula());
-                database->setItem(i, 4, new QTableWidgetItem());
+                database->setItem(i, 2, widgetitemallocator.getNewItem());
+				database->item(i, 2)->setText(sequences[i].getName().c_str());
+
+                database->setItem(i, 3, widgetitemallocator.getNewItem());
+				database->item(i, 3)->setText(sequences[i].getSummaryFormula().c_str());
+
+				formula.setFormula(sequences[i].getSummaryFormula());
+                database->setItem(i, 4, widgetitemallocator.getNewItem());
                 database->item(i, 4)->setData(Qt::DisplayRole, formula.getMass());
-                database->setItem(i, 5, new QTableWidgetItem(sequences[i].getSequence().c_str()));
-                database->setItem(i, 6, new QTableWidgetItem(sequences[i].getNTterminalModification().c_str()));
-                database->setItem(i, 7, new QTableWidgetItem(sequences[i].getCTterminalModification().c_str()));
-                database->setItem(i, 8, new QTableWidgetItem(sequences[i].getBranchModification().c_str()));
-                database->setItem(i, 9, new QTableWidgetItem(sequences[i].getReference().c_str()));
+
+				database->setItem(i, 5, widgetitemallocator.getNewItem());
+				database->item(i, 5)->setText(sequences[i].getSequence().c_str());
+
+				database->setItem(i, 6, widgetitemallocator.getNewItem());
+				database->item(i, 6)->setText(sequences[i].getNTterminalModification().c_str());
+
+				database->setItem(i, 7, widgetitemallocator.getNewItem());
+				database->item(i, 7)->setText(sequences[i].getCTterminalModification().c_str());
+
+				database->setItem(i, 8, widgetitemallocator.getNewItem());
+				database->item(i, 8)->setText(sequences[i].getBranchModification().c_str());
+
+				database->setItem(i, 9, widgetitemallocator.getNewItem());
+				database->item(i, 9)->setText(sequences[i].getReference().c_str());
 
                 database->setCellWidget(i, 10, new QLabel(sequences[i].getNameWithReferenceAsHTMLString().c_str()));
                 ((QLabel *)database->cellWidget(i, 10))->setTextFormat(Qt::RichText);
                 ((QLabel *)database->cellWidget(i, 10))->setTextInteractionFlags(Qt::TextBrowserInteraction);
                 ((QLabel *)database->cellWidget(i, 10))->setOpenExternalLinks(true);
 
-                if ((i == 0) || ((i - 1)/100 != i/100)) {
-                    progress->setValue(i);
-                }
-            }
+				progress.setValue(i);
+				//if (progress.wasCanceled()) {
+				//	break;
+				//}
+			}
 
 			for (int i = 0; i < database->columnCount(); i++) {
 				database->resizeColumnToContents(i);
 			}
 
-			progress->setValue(sequences.size());
-			progress->hide();
-			
+			progress.setValue(sequences.size());
+						
 		}
 
 		inputstream.close();
@@ -365,19 +413,18 @@ void cSequenceDatabaseWidget::saveDatabase() {
 	}
 	else {
 
-		progress->setLabelText("Saving the Sequence Databatase...");
-		progress->setMinimum(0);
-		progress->setMaximum(100);
-		progress->setValue(1);
-		progress->show();
+		QProgressDialog progress("Saving the Sequence Databatase...", /*"Cancel"*/0, 0, database->rowCount(), this);
+		cEventFilter filter;
+		progress.installEventFilter(&filter);
+		progress.setMinimumDuration(0);
+		progress.setWindowModality(Qt::WindowModal);
 
 		cSequence seq;
 		sequences.clear();
+		string s;
 
 		removeEmptyRows();
 
-		progress->setMaximum(database->rowCount());
-
 		for (int i = 0; i < database->rowCount(); i++) {
 			seq.clear();
 			for (int j = 0; j < database->columnCount(); j++) {
@@ -390,28 +437,35 @@ void cSequenceDatabaseWidget::saveDatabase() {
 					seq.setPeptideType((peptideType)(((QComboBox *)database->cellWidget(i,j))->currentIndex()));
 					break;
 				case 2:
-					seq.setName(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setName(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 3:
-					seq.setSummaryFormula(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setSummaryFormula(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 4:
 					// nothing to do
 					break;
 				case 5:
-					seq.setSequence(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setSequence(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 6:
-					seq.setNTterminalModification(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setNTterminalModification(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 7:
-					seq.setCTterminalModification(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setCTterminalModification(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 8:
-					seq.setBranchModification(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setBranchModification(removeWhiteSpacesExceptSpaces(s));
 					break;
 				case 9:
-					seq.setReference(database->item(i,j)->text().toStdString());
+					s = database->item(i,j)->text().toStdString();
+					seq.setReference(removeWhiteSpacesExceptSpaces(s));
 					break;
 				default:
 					break;
@@ -419,15 +473,15 @@ void cSequenceDatabaseWidget::saveDatabase() {
 			}
 			sequences.push_back(seq);
 			
-			if ((i == 0) || ((i - 1)/100 != i/100)) {
-				progress->setValue(i);
-			}
+			progress.setValue(i);
+			//if (progress.wasCanceled()) {
+			//	break;
+			//}
 		}
 
 		sequences.storeToPlainTextStream(outputstream);
 
-		progress->setValue(database->rowCount());
-		progress->hide();
+		progress.setValue(progress.maximum());
 		
 	}
 	outputstream.close();
@@ -440,10 +494,11 @@ void cSequenceDatabaseWidget::saveDatabaseAs() {
 		return;
 	}
 
-	QString filename = QFileDialog::getSaveFileName(this, tr("Save Settings As..."), lastdir, tr("Database of Sequences (*.txt)"));
-	lastdir = filename;
+	QString filename = QFileDialog::getSaveFileName(this, tr("Save the Database of Sequences As..."), lastdir, tr("Database of Sequences (*.txt)"));
 
-	if (filename.toStdString().compare("") != 0) {
+	if (!filename.isEmpty()) {
+		lastdir = filename;
+	
 		databasefile = filename;
 		save->setText(QString("  Save '") + QString(databasefile.toStdString().substr(databasefile.toStdString().rfind('/') + 1, databasefile.toStdString().size()).c_str()) + QString("'  "));
 		saveDatabase();
@@ -465,14 +520,14 @@ void cSequenceDatabaseWidget::addRow() {
 	combo->setCurrentIndex((int)other);
 	database->setCellWidget(row, 1, combo);
 
-	database->setItem(row, 2, new QTableWidgetItem());
-	database->setItem(row, 3, new QTableWidgetItem());
-	database->setItem(row, 4, new QTableWidgetItem());
-	database->setItem(row, 5, new QTableWidgetItem());
-	database->setItem(row, 6, new QTableWidgetItem());
-	database->setItem(row, 7, new QTableWidgetItem());
-	database->setItem(row, 8, new QTableWidgetItem());
-	database->setItem(row, 9, new QTableWidgetItem());
+	database->setItem(row, 2, widgetitemallocator.getNewItem());
+	database->setItem(row, 3, widgetitemallocator.getNewItem());
+	database->setItem(row, 4, widgetitemallocator.getNewItem());
+	database->setItem(row, 5, widgetitemallocator.getNewItem());
+	database->setItem(row, 6, widgetitemallocator.getNewItem());
+	database->setItem(row, 7, widgetitemallocator.getNewItem());
+	database->setItem(row, 8, widgetitemallocator.getNewItem());
+	database->setItem(row, 9, widgetitemallocator.getNewItem());
 
 	database->setCellWidget(row, 10, new QLabel());
 	((QLabel *)database->cellWidget(row, 10))->setTextFormat(Qt::RichText);
diff --git a/CycloBranch/gui/cSequenceDatabaseWidget.h b/CycloBranch/gui/cSequenceDatabaseWidget.h
index d568f39..204c984 100644
--- a/CycloBranch/gui/cSequenceDatabaseWidget.h
+++ b/CycloBranch/gui/cSequenceDatabaseWidget.h
@@ -9,9 +9,12 @@
 
 #include <QWidget>
 #include <fstream>
+#include "core/utilities.h"
 #include "core/cSequenceDatabase.h"
+#include "core/cAllocator.h"
 
 using namespace std;
+using namespace boost;
 
 
 // forward declaration
@@ -19,15 +22,11 @@ class QHBoxLayout;
 class QVBoxLayout;
 class QTableWidget;
 class QTableWidgetItem;
-class QDialogButtonBox;
 class QPushButton;
-class QLabel;
-class QComboBox;
-class QProgressDialog;
 
 
 /**
-	\brief The widget representing the dialog 'About'.
+	\brief Visualization of the database of sequences.
 */
 class cSequenceDatabaseWidget : public QWidget
 {
@@ -56,6 +55,14 @@ class cSequenceDatabaseWidget : public QWidget
 	void closeEvent(QCloseEvent *event);
 
 
+	/**
+		\brief Insert a new row, set its peptide type and sequence.
+		\param peptidetypeindex an index of current peptide type
+		\param sequence sequence
+	*/ 
+	void insertRow(int peptidetypeindex, QString sequence);
+
+
 private:
 	QWidget* parent;
 	QPushButton* insertrow;
@@ -67,7 +74,6 @@ class cSequenceDatabaseWidget : public QWidget
 	QTableWidget* database;
 	QHBoxLayout* buttons;
 	QVBoxLayout* mainlayout;
-	QProgressDialog* progress;
 
 	QString databasefile;
 	QString lastdir;
@@ -77,16 +83,29 @@ class cSequenceDatabaseWidget : public QWidget
 
 	vector<int> headersort;
 
+	cAllocator<QTableWidgetItem> widgetitemallocator;
+
 	void deleteTable(bool enableprogress);
 
 	void removeRow(int row);
 
 	bool checkTable();
 
-	bool checkFormula(int row, string& summary);
+	bool checkFormula(int row, const string& summary);
 
 	bool checkSequence(int row);
 
+
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
+
 private slots:
 
 	void closeWindow();
@@ -107,4 +126,4 @@ private slots:
 
 };
 
-#endif
\ No newline at end of file
+#endif
diff --git a/CycloBranch/gui/cSpectrumDetailWidget.cpp b/CycloBranch/gui/cSpectrumDetailWidget.cpp
index a3b82b3..6327cd4 100644
--- a/CycloBranch/gui/cSpectrumDetailWidget.cpp
+++ b/CycloBranch/gui/cSpectrumDetailWidget.cpp
@@ -5,28 +5,34 @@
 #include <QHBoxLayout>
 #include <QVBoxLayout>
 #include <QFormLayout>
-#include <QScrollArea>
 #include <QScrollBar>
 #include <QCheckBox>
 #include <QPushButton>
 #include <QSplitter>
 #include <QComboBox>
 #include <QDoubleSpinBox>
+#include <QKeyEvent>
+#include <QToolBar>
+#include <QAction>
+#include <QLabel>
+#include <QList>
+#include <QFileDialog>
+#include <QMessageBox>
 
 
 cSpectrumDetailWidget::cSpectrumDetailWidget() {
-	rotation = 0;
-	trotation = 0;
 	parameters = 0;
-
 	preparedToShow = false;
 	theoreticalspectrum = new cTheoreticalSpectrum();
 }
 
 
 cSpectrumDetailWidget::cSpectrumDetailWidget(const cSpectrumDetailWidget& sd) {
-	rotation = 0;
-	trotation = 0;
+	*this = sd;
+}
+
+
+cSpectrumDetailWidget& cSpectrumDetailWidget::operator=(const cSpectrumDetailWidget& sd) {
 	parameters = sd.parameters;
 
 	preparedToShow = false;
@@ -41,6 +47,8 @@ cSpectrumDetailWidget::cSpectrumDetailWidget(const cSpectrumDetailWidget& sd) {
 	}
 
 	setWindowTitle(sd.windowTitle());
+
+	return *this;
 }
 
 
@@ -63,15 +71,15 @@ string cSpectrumDetailWidget::getDetailsAsHTMLString() {
 		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
 
 			s += "Acronym Peptide Name:<br/>";
-			s += theoreticalspectrum->getAcronymPeptideNameWithHTMLReferences();
+			s += theoreticalspectrum->getCandidate().getAcronymPeptideNameWithHTMLReferences();
 			s += "<br/><br/>";
 			s += "Full Peptide Name:<br/>";
-			s += theoreticalspectrum->getRealPeptideName() + "<br/>";
+			s += theoreticalspectrum->getCandidate().getRealPeptideName() + "<br/>";
 
-			if ((int)theoreticalspectrum->getPath().size() > 0) {
+			if ((int)theoreticalspectrum->getCandidate().getPathAsString().size() > 0) {
 				s += "<br/>";
 				s += "Path in the De Novo Graph:<br/>";
-				s += theoreticalspectrum->getPath();
+				s += theoreticalspectrum->getCandidate().getPathAsString();
 			}
 			
 			s += "<br/>";
@@ -80,6 +88,7 @@ string cSpectrumDetailWidget::getDetailsAsHTMLString() {
 
 		s += "Unmatched Measured Peaks:<br/>" + theoreticalspectrum->getUnmatchedPeaks() + "<br/><br/>";
 		s += "Theoretical Peaks:<br/>" + theoreticalspectrum->getTheoreticalPeaks()->print(true);
+
 	}
 
 	return s;
@@ -92,39 +101,28 @@ cSpectrumDetailWidget::~cSpectrumDetailWidget() {
 
 	if (preparedToShow) {
 	
-		delete graphicalspectrum;
-		delete graphicalspectrumscroll;
-
-		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
-			delete textedit;
-		}
+		delete spectrumscene;
 
+		delete textedit;
 		delete textbrowser;
 
-		delete zoomin;
-		delete zoomout;
-		delete normalsize;
-		delete zoom;
-
+		delete labelmz;
 		delete minmz;
 		delete maxmz;
 		delete setmzinterval;
 		delete resetmzinterval;
-		delete mzinterval;
-
-		delete hideunmatched;
-		delete hidematched;
-
-		if (rotation) {
-			delete rotation;
-		}
+		delete hboxmz;
+		delete widgetmz;
 
-		if (trotation) {
-			delete trotation;
-		}
+		delete labelrotation;
+		delete rotation;
+		delete hboxrotation;
+		delete widgetrotation;
 
-		delete formlayout;
-		delete formwidget;
+		delete labeltrotation;
+		delete trotation;
+		delete hboxtrotation;
+		delete widgettrotation;
 
 		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
 
@@ -150,14 +148,24 @@ cSpectrumDetailWidget::~cSpectrumDetailWidget() {
 				break;
 			}
 
+			delete actionExportPeptide;
+
 		}
 		
-		delete vsplitter1;
-		delete vsplitter2;
+		delete hsplitter1;
+		delete hsplitter2;
+		
+		delete vsplitter;
 
-		delete hsplitter;
+		delete actionExportSpectrum;
+		delete actionZoomIn;
+		delete actionZoomOut;
+		delete actionZoomReset;
+		delete actionHideMatched;
+		delete actionHideUnmatched;
+		delete actionHideScrambled;
+		delete actionMouseMzSelection;
 
-		delete mainbox;
 	}
 }
 
@@ -171,14 +179,15 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 
 	if (!preparedToShow) {
 
-		hsplitter = new QSplitter();
-		hsplitter->setOrientation(Qt::Horizontal);
+		vsplitter = new QSplitter();
+		vsplitter->setOrientation(Qt::Vertical);
 
-		vsplitter1 = new QSplitter();
-		vsplitter1->setOrientation(Qt::Vertical);
+		hsplitter1 = new QSplitter();
+		hsplitter1->setOrientation(Qt::Horizontal);
+
+		hsplitter2 = new QSplitter();
+		hsplitter2->setOrientation(Qt::Horizontal);
 
-		vsplitter2 = new QSplitter();
-		vsplitter2->setOrientation(Qt::Vertical);
 
 		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
 			switch (peptidetype)
@@ -204,18 +213,89 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 			}
 		}
 
-		graphicalspectrumscroll = new QScrollArea();
-		graphicalspectrum = new cGraphicalSpectrumWidget(graphicalspectrumscroll);
-		graphicalspectrumscroll->setWidget(graphicalspectrum);
-		//graphicalspectrumscroll->setWidgetResizable(true);
+		spectrumscene = new cSpectrumSceneWidget(this);
+
+		toolbarExport = addToolBar(tr("Export"));
+		toolbarExport->setMovable(false);
+		toolbarExport->setFloatable(false);
+
+		actionExportSpectrum = new QAction(QIcon(":/images/icons/54.png"), tr("Export Spectrum"), this);
+		actionExportSpectrum->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_E));
+		actionExportSpectrum->setToolTip("Export Spectrum (Ctrl + E)");
+		toolbarExport->addAction(actionExportSpectrum);
+		connect(actionExportSpectrum, SIGNAL(triggered()), this, SLOT(exportSpectrum()));
 
 		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
-			textedit = new QTextEdit();
-			textedit->setReadOnly(true);
-			textedit->setFont(QFont("Courier", 9));
-			textedit->setLineWrapMode(QTextEdit::NoWrap);
+			actionExportPeptide = new QAction(QIcon(":/images/icons/57.png"), tr("Export Peptide"), this);
+			actionExportPeptide->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_P));
+			actionExportPeptide->setToolTip("Export Peptide (Ctrl + P)");
+			toolbarExport->addAction(actionExportPeptide);
+			connect(actionExportPeptide, SIGNAL(triggered()), this, SLOT(exportPeptide()));
 		}
 
+		toolbarZoom = addToolBar(tr("Zoom"));
+		toolbarZoom->setMovable(false);
+		toolbarZoom->setFloatable(false);
+				
+		actionZoomIn = new QAction(QIcon(":/images/icons/83.png"), tr("Zoom In"), this);
+		actionZoomIn->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_Plus));
+		actionZoomIn->setToolTip("Zoom In (Ctrl +)");
+		toolbarZoom->addAction(actionZoomIn);
+		connect(actionZoomIn, SIGNAL(triggered()), spectrumscene, SLOT(zoomIn()));
+
+		actionZoomOut = new QAction(QIcon(":/images/icons/82.png"), tr("Zoom Out"), this);
+		actionZoomOut->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_Minus));
+		actionZoomOut->setToolTip("Zoom Out (Ctrl -)");
+		toolbarZoom->addAction(actionZoomOut);
+		connect(actionZoomOut, SIGNAL(triggered()), spectrumscene, SLOT(zoomOut()));
+
+		actionZoomReset = new QAction(QIcon(":/images/icons/84.png"), tr("Reset Zoom"), this);
+		actionZoomReset->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_R));
+		actionZoomReset->setToolTip("Zoom Reset (Ctrl + R)");
+		toolbarZoom->addAction(actionZoomReset);
+		connect(actionZoomReset, SIGNAL(triggered()), spectrumscene, SLOT(normalSize()));
+
+
+		toolbarHide = addToolBar(tr("Show/Hide Peaks"));
+		toolbarHide->setMovable(false);
+		toolbarHide->setFloatable(false);
+
+		actionHideMatched = new QAction(QIcon(":/images/icons/20.png"), tr("Hide Matched Peaks"), this);
+		actionHideMatched->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_M));
+		actionHideMatched->setToolTip("Hide Matched Peaks (Ctrl + M)");
+		actionHideMatched->setCheckable(true);
+		toolbarHide->addAction(actionHideMatched);
+		connect(actionHideMatched, SIGNAL(toggled(bool)), spectrumscene, SLOT(hideMatchedPeaks(bool)));
+
+		actionHideUnmatched = new QAction(QIcon(":/images/icons/81.png"), tr("Hide Unmatched Peaks"), this);
+		actionHideUnmatched->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_U));
+		actionHideUnmatched->setToolTip("Hide Unmatched Peaks (Ctrl + U)");
+		actionHideUnmatched->setCheckable(true);
+		toolbarHide->addAction(actionHideUnmatched);
+		connect(actionHideUnmatched, SIGNAL(toggled(bool)), spectrumscene, SLOT(hideUnmatchedPeaks(bool)));
+
+		actionHideScrambled = new QAction(QIcon(":/images/icons/80.png"), tr("Hide Scrambled Peaks"), this);
+		actionHideScrambled->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_S));
+		actionHideScrambled->setToolTip("Hide Scrambled Peaks (Ctrl + S)");
+		actionHideScrambled->setCheckable(true);
+		actionHideScrambled->setEnabled(false);
+		toolbarHide->addAction(actionHideScrambled);
+
+
+		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+
+			if ((parameters->peptidetype == cyclic) && parameters->enablescrambling) {
+				actionHideScrambled->setEnabled(true);
+				connect(actionHideScrambled, SIGNAL(toggled(bool)), spectrumscene, SLOT(hideScrambledPeaks(bool)));
+			}
+
+		}
+
+		textedit = new QTextEdit();
+		textedit->setReadOnly(true);
+		textedit->setFont(QFont("Courier", 9));
+		textedit->setLineWrapMode(QTextEdit::NoWrap);
+		
 		textbrowser = new QTextBrowser();
 		textbrowser->setReadOnly(true);
 		textbrowser->setFont(QFont("Courier", 9));
@@ -223,22 +303,8 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 		textbrowser->setAcceptRichText(true);
 		textbrowser->setOpenExternalLinks(true);
 
-		zoomin = new QPushButton("In");
-		zoomin->setMaximumWidth(50);
-		connect(zoomin, SIGNAL(released()), graphicalspectrum, SLOT(zoomIn()));
 
-		zoomout = new QPushButton("Out");
-		zoomout->setMaximumWidth(50);
-		connect(zoomout, SIGNAL(released()), graphicalspectrum, SLOT(zoomOut()));
-
-		normalsize = new QPushButton("Reset");
-		normalsize->setMaximumWidth(50);
-		connect(normalsize, SIGNAL(released()), graphicalspectrum, SLOT(normalSize()));
-
-		zoom = new QHBoxLayout();
-		zoom->addWidget(zoomin);
-		zoom->addWidget(zoomout);
-		zoom->addWidget(normalsize);
+		labelmz = new QLabel(tr("View m/z (from - to): "));
 
 		minmz = new QDoubleSpinBox();
 		minmz->setDecimals(6);
@@ -253,39 +319,80 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 		setmzinterval = new QPushButton("Set");
 		setmzinterval->setMaximumWidth(50);
 		connect(setmzinterval, SIGNAL(released()), this, SLOT(setMZInterval()));
-		connect(this, SIGNAL(emitMZInterval(double, double)), graphicalspectrum, SLOT(setMZInterval(double, double)));
+		connect(this, SIGNAL(emitMZInterval(double, double)), spectrumscene, SLOT(setMZInterval(double, double)));
 
 		resetmzinterval = new QPushButton("Reset");
 		resetmzinterval->setMaximumWidth(50);
-		connect(resetmzinterval, SIGNAL(released()), graphicalspectrum, SLOT(resetMZInterval()));
+		connect(resetmzinterval, SIGNAL(released()), spectrumscene, SLOT(resetMZInterval()));
+		connect(spectrumscene, SIGNAL(updateMZInterval(double, double)), this, SLOT(updateMZInterval(double, double)));
+
+		hboxmz = new QHBoxLayout();
+		hboxmz->addSpacing(1);
+		hboxmz->addWidget(labelmz);
+		hboxmz->addSpacing(1);
+		hboxmz->addWidget(minmz);
+		hboxmz->addSpacing(1);
+		hboxmz->addWidget(maxmz);
+		hboxmz->addSpacing(1);
+		hboxmz->addWidget(setmzinterval);
+		hboxmz->addSpacing(1);
+		hboxmz->addWidget(resetmzinterval);
+		hboxmz->addSpacing(1);
 
-		mzinterval = new QHBoxLayout();
-		mzinterval->addWidget(minmz);
-		mzinterval->addWidget(maxmz);
-		mzinterval->addWidget(setmzinterval);
-		mzinterval->addWidget(resetmzinterval);
-		connect(graphicalspectrum, SIGNAL(updateMZInterval(double, double)), this, SLOT(updateMZInterval(double, double)));
+		widgetmz = new QWidget();
+		widgetmz->setLayout(hboxmz);
 
-		hideunmatched = new QCheckBox();
-		connect(hideunmatched, SIGNAL(stateChanged(int)), graphicalspectrum, SLOT(hideUnmatchedPeaks(int)));
+		toolbarMz = addToolBar(tr("Range of m/z"));
+		toolbarMz->setMovable(false);
+		toolbarMz->setFloatable(false);
 
-		hidematched = new QCheckBox();
-		connect(hidematched, SIGNAL(stateChanged(int)), graphicalspectrum, SLOT(hideMatchedPeaks(int)));
+		actionMouseMzSelection = new QAction(QIcon(":/images/icons/64.png"), tr("Mouse m/z Selection Tool"), this);
+		actionMouseMzSelection->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_T));
+		actionMouseMzSelection->setToolTip("Mouse m/z Selection Tool (Ctrl + T)");
+		actionMouseMzSelection->setCheckable(true);
+		actionMouseMzSelection->setChecked(true);
+		actionMouseMzSelection->setEnabled(true);
+		toolbarMz->addAction(actionMouseMzSelection);
+		connect(actionMouseMzSelection, SIGNAL(toggled(bool)), spectrumscene, SLOT(enableMouseMzSelectionTool(bool)));
+
+		toolbarMz->addWidget(widgetmz);
+
+
+		labelrotation = new QLabel(tr("Ring break up point: "));
+		rotation = new QComboBox();
+
+		hboxrotation = new QHBoxLayout();
+		hboxrotation->addSpacing(1);
+		hboxrotation->addWidget(labelrotation);
+		hboxrotation->addSpacing(1);
+		hboxrotation->addWidget(rotation);
+		hboxrotation->addSpacing(1);
+
+		widgetrotation = new QWidget();
+		widgetrotation->setLayout(hboxrotation);
+
+
+		labeltrotation = new QLabel(tr("Linearized sequence: "));
+		trotation = new QComboBox();
+
+		hboxtrotation = new QHBoxLayout();
+		hboxtrotation->addSpacing(1);
+		hboxtrotation->addWidget(labeltrotation);
+		hboxtrotation->addSpacing(1);
+		hboxtrotation->addWidget(trotation);
+		hboxtrotation->addSpacing(1);
+
+		widgettrotation = new QWidget();
+		widgettrotation->setLayout(hboxtrotation);
 
-		formlayout = new QFormLayout();
-		formlayout->addRow(tr("Zoom: "), zoom);
-		formlayout->addRow(tr("View m/z (from - to): "), mzinterval);
-		formlayout->addRow(tr("Hide matched peaks: "), hidematched);
-		formlayout->addRow(tr("Hide unmatched peaks: "), hideunmatched);
 
 		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
 
 			// cyclic
-			if (parameters && theoreticalspectrum && (parameters->peptidetype == cyclic)) {
-				int r = (int)theoreticalspectrum->getAcronyms().size();
+			if (theoreticalspectrum && (parameters->peptidetype == cyclic)) {
+				int r = (int)theoreticalspectrum->getCandidate().getAcronyms().size();
 				int hint = (int)theoreticalspectrum->getVisualCoverage().size()/(2*r);
-
-				rotation = new QComboBox();
+				
 				rotation->addItem(tr("all"));
 
 				string s;
@@ -296,15 +403,18 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 					}
 				}
 
-				connect(rotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(rotationChanged(int)));
-				connect(rotation, SIGNAL(currentIndexChanged(QString)), graphicalspectrum, SLOT(rotationChanged(QString)));
+				connect(rotation, SIGNAL(currentIndexChanged(int)), spectrumscene, SLOT(rotationChanged(int)));
+				connect(rotation, SIGNAL(currentIndexChanged(QString)), spectrumscene, SLOT(rotationChanged(QString)));
 				connect(rotation, SIGNAL(currentIndexChanged(int)), cyclicwidget, SLOT(rotationChanged(int)));
-				formlayout->addRow(tr("Ring break up point: "), rotation);
+
+				toolbarRotation = addToolBar(tr("Ring break up point"));
+				toolbarRotation->addWidget(widgetrotation);
+				toolbarRotation->setMovable(false);
+				toolbarRotation->setFloatable(false);
 			}
 
 			// branched
-			if (parameters && (parameters->peptidetype == branched)) {
-				trotation = new QComboBox();
+			if (parameters->peptidetype == branched) {
 				trotation->addItem(tr("all"));
 				trotation->addItem(tr("1 (left-to-right)"));
 				trotation->addItem(tr("2 (top-to-right)"));
@@ -313,17 +423,20 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 				trotation->addItem(tr("5 (top-to-left)"));
 				trotation->addItem(tr("6 (right-to-top)"));
 
-				connect(trotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(trotationChanged(int)));
+				connect(trotation, SIGNAL(currentIndexChanged(int)), spectrumscene, SLOT(trotationChanged(int)));
 				connect(trotation, SIGNAL(currentIndexChanged(int)), branchedwidget, SLOT(trotationChanged(int)));
-				formlayout->addRow(tr("Linearized sequence: "), trotation);
+
+				toolbarTrotation = addToolBar(tr("Linearized sequence"));
+				toolbarTrotation->addWidget(widgettrotation);
+				toolbarTrotation->setMovable(false);
+				toolbarTrotation->setFloatable(false);
 			}
 
-			// lasso
+			// branch-cyclic
 			if (parameters && theoreticalspectrum && (parameters->peptidetype == lasso)) {
-				int r = (int)theoreticalspectrum->getAcronyms().size() - (int)theoreticalspectrum->getCandidate().getBranchSize();
+				int r = (int)theoreticalspectrum->getCandidate().getAcronyms().size() - (int)theoreticalspectrum->getCandidate().getBranchSize();
 				int hint = (int)theoreticalspectrum->getVisualCoverage().size()/(2*r);
 
-				rotation = new QComboBox();
 				rotation->addItem(tr("all"));
 
 				string s;
@@ -334,12 +447,15 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 					}
 				}
 
-				connect(rotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(rotationChanged(int)));
-				connect(rotation, SIGNAL(currentIndexChanged(QString)), graphicalspectrum, SLOT(rotationChanged(QString)));
+				connect(rotation, SIGNAL(currentIndexChanged(int)), spectrumscene, SLOT(rotationChanged(int)));
+				connect(rotation, SIGNAL(currentIndexChanged(QString)), spectrumscene, SLOT(rotationChanged(QString)));
 				connect(rotation, SIGNAL(currentIndexChanged(int)), lassowidget, SLOT(rotationChanged(int)));
-				formlayout->addRow(tr("Ring break up point: "), rotation);
 
-				trotation = new QComboBox();
+				toolbarRotation = addToolBar(tr("Ring break up point"));
+				toolbarRotation->addWidget(widgetrotation);
+				toolbarRotation->setMovable(false);
+				toolbarRotation->setFloatable(false);
+
 				trotation->addItem(tr("all"));
 				trotation->addItem(tr("1 (left-to-right)"));
 				trotation->addItem(tr("2 (top-to-right)"));
@@ -348,62 +464,41 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 				trotation->addItem(tr("5 (top-to-left)"));
 				trotation->addItem(tr("6 (right-to-top)"));
 
-				connect(trotation, SIGNAL(currentIndexChanged(int)), graphicalspectrum, SLOT(trotationChanged(int)));
+				connect(trotation, SIGNAL(currentIndexChanged(int)), spectrumscene, SLOT(trotationChanged(int)));
 				connect(trotation, SIGNAL(currentIndexChanged(int)), lassowidget, SLOT(trotationChanged(int)));
-				formlayout->addRow(tr("Linearized sequence: "), trotation);
+				
+				toolbarTrotation = addToolBar(tr("Linearized sequence"));
+				toolbarTrotation->addWidget(widgettrotation);
+				toolbarTrotation->setMovable(false);
+				toolbarTrotation->setFloatable(false);
 			}
 
 		}
 
-		formwidget = new QWidget();
-		formwidget->setLayout(formlayout);
+		hsplitter1->addWidget(spectrumscene);
+		hsplitter2->addWidget(textbrowser);
 
-		vsplitter1->addWidget(graphicalspectrumscroll);
-		vsplitter1->addWidget(textbrowser);
-		vsplitter1->setStretchFactor(0, 7);
-		vsplitter1->setStretchFactor(1, 3);
+		QList<int> sizes;
+		sizes.push_back(100);
+		sizes.push_back(100);
 
-		if (parameters && ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch))) {
+		if ((parameters->mode == denovoengine) || (parameters->mode == singlecomparison) || (parameters->mode == databasesearch)) {
 
 			switch (peptidetype)
 			{
 			case linear:
-				vsplitter2->addWidget(formwidget);
-				vsplitter2->addWidget(linearwidget);
-				vsplitter2->addWidget(textedit);
-				vsplitter2->setStretchFactor(0, 2);
-				vsplitter2->setStretchFactor(1, 3);
-				vsplitter2->setStretchFactor(2, 5);
+				hsplitter1->addWidget(linearwidget);
 				break;
 			case cyclic:
-				vsplitter2->addWidget(formwidget);
-				vsplitter2->addWidget(cyclicwidget);
-				vsplitter2->addWidget(textedit);
-				vsplitter2->setStretchFactor(0, 2);
-				vsplitter2->setStretchFactor(1, 3);
-				vsplitter2->setStretchFactor(2, 5);
+				hsplitter1->addWidget(cyclicwidget);
 				break;
 			case branched:
-				vsplitter2->addWidget(formwidget);
-				vsplitter2->addWidget(branchedwidget);
-				vsplitter2->addWidget(textedit);
-				vsplitter2->setStretchFactor(0, 2);
-				vsplitter2->setStretchFactor(1, 3);
-				vsplitter2->setStretchFactor(2, 5);
+				hsplitter1->addWidget(branchedwidget);
 				break;
 			case lasso:
-				vsplitter2->addWidget(formwidget);
-				vsplitter2->addWidget(lassowidget);
-				vsplitter2->addWidget(textedit);
-				vsplitter2->setStretchFactor(0, 2);
-				vsplitter2->setStretchFactor(1, 3);
-				vsplitter2->setStretchFactor(2, 5);
+				hsplitter1->addWidget(lassowidget);
 				break;
 			case linearpolysaccharide:
-				vsplitter2->addWidget(formwidget);
-				vsplitter2->addWidget(textedit);
-				vsplitter2->setStretchFactor(0, 2);
-				vsplitter2->setStretchFactor(1, 8);
 				break;
 			case other:
 				break;
@@ -411,20 +506,20 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 				break;
 			}
 
-		}
+			hsplitter2->addWidget(textedit);
+
+			hsplitter1->setSizes(sizes);
+			hsplitter2->setSizes(sizes);
 
-		if (parameters && (parameters->mode == dereplication)) {
-			vsplitter2->addWidget(formwidget);
 		}
 
-		hsplitter->addWidget(vsplitter1);
-		hsplitter->addWidget(vsplitter2);
-		hsplitter->setStretchFactor(0, 6);
-		hsplitter->setStretchFactor(1, 4);
-		
-		mainbox = new QHBoxLayout();
-		mainbox->addWidget(hsplitter);
-		setLayout(mainbox);
+		vsplitter->addWidget(hsplitter1);
+		vsplitter->addWidget(hsplitter2);
+
+		vsplitter->setSizes(sizes);
+
+		setCentralWidget(vsplitter);
+		centralWidget()->setContentsMargins(10, 10, 10, 10);
 
 		resize(1280, 700);
 
@@ -453,12 +548,12 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 				default:
 					break;
 				}
-			
-				textedit->setHtml(theoreticalspectrum->getCoverageBySeries().c_str());
 
+				textedit->setHtml(theoreticalspectrum->getCoverageBySeries().c_str());
+			
 			}
 
-			graphicalspectrum->initialize(parameters, theoreticalspectrum);
+			spectrumscene->initialize(parameters, theoreticalspectrum);
 			textbrowser->setHtml(getDetailsAsHTMLString().c_str());
 		}
 
@@ -468,6 +563,17 @@ void cSpectrumDetailWidget::prepareToShow(peptideType peptidetype) {
 }
 
 
+void cSpectrumDetailWidget::keyPressEvent(QKeyEvent *event) {
+	if(event->key() == Qt::Key_Escape) {
+		hide();
+    }
+	
+	if(event->key() == Qt::Key_Enter) {
+		setMZInterval();
+    }
+}
+
+
 void cSpectrumDetailWidget::updateMZInterval(double minmz, double maxmz) {
 	this->minmz->setValue(minmz);
 	this->maxmz->setValue(maxmz);
@@ -478,3 +584,189 @@ void cSpectrumDetailWidget::setMZInterval() {
 	emit emitMZInterval(minmz->value(), maxmz->value());
 }
 
+
+void cSpectrumDetailWidget::exportSpectrum() {
+	#if OS_TYPE == UNX
+		QString filename = QFileDialog::getSaveFileName(this, tr("Export Spectrum..."), "./", "PDF Files (*.pdf);; PS Files (*.ps);; PNG Files (*.png);; SVG Files (*.svg)");
+	#else
+		QString filename = QFileDialog::getSaveFileName(this, tr("Export Spectrum..."), "./", "PDF Files (*.pdf);; PS Files (*.ps);; PNG Files (*.png)");
+	#endif
+	if (!filename.isEmpty()) {
+		regex rx;
+		bool selected = false;
+
+		rx = ".+\\.pdf$";
+		if (!selected && (regex_search(filename.toStdString(), rx))) {
+			spectrumscene->exportToPDF(filename, false);
+			selected = true;
+		}
+
+		rx = ".+\\.ps$";
+		if (!selected && (regex_search(filename.toStdString(), rx))) {
+			spectrumscene->exportToPDF(filename, true);
+			selected = true;
+		}
+
+		rx = ".+\\.png$";
+		if (!selected && (regex_search(filename.toStdString(), rx))) {
+			spectrumscene->exportToPNG(filename);
+			selected = true;
+		}
+
+		#if OS_TYPE == UNX
+			rx = ".+\\.svg$";
+			if (!selected && (regex_search(filename.toStdString(), rx))) {
+				spectrumscene->exportToSVG(filename);
+				selected = true;
+			}
+		#endif
+
+		if (!selected) {
+			QMessageBox msgBox;
+			QString errstr = "Unsupported file format.";
+			msgBox.setText(errstr);
+			msgBox.exec();
+		}
+	}
+}
+
+
+void cSpectrumDetailWidget::exportPeptide() {
+	#if OS_TYPE == UNX
+		QString filename = QFileDialog::getSaveFileName(this, tr("Export Peptide..."), "./", "PDF Files (*.pdf);; PS Files (*.ps);; PNG Files (*.png);; SVG Files (*.svg)");
+	#else
+		QString filename = QFileDialog::getSaveFileName(this, tr("Export Peptide..."), "./", "PDF Files (*.pdf);; PS Files (*.ps);; PNG Files (*.png)");
+	#endif
+	if (!filename.isEmpty() && parameters) {
+		regex rx;
+		bool selected = false;
+
+		switch ((peptideType)parameters->peptidetype) {
+			case linear:
+				rx = ".+\\.pdf$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					linearwidget->exportToPDF(filename, false);
+					selected = true;
+				}
+
+				rx = ".+\\.ps$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					linearwidget->exportToPDF(filename, true);
+					selected = true;
+				}
+
+				rx = ".+\\.png$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					linearwidget->exportToPNG(filename);
+					selected = true;
+				}
+
+				#if OS_TYPE == UNX
+					rx = ".+\\.svg$";
+					if (!selected && (regex_search(filename.toStdString(), rx))) {
+						linearwidget->exportToSVG(filename);
+						selected = true;
+					}
+				#endif
+				break;
+			case cyclic:
+				rx = ".+\\.pdf$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					cyclicwidget->exportToPDF(filename, false);
+					selected = true;
+				}
+
+				rx = ".+\\.ps$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					cyclicwidget->exportToPDF(filename, true);
+					selected = true;
+				}
+
+
+				rx = ".+\\.png$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					cyclicwidget->exportToPNG(filename);
+					selected = true;
+				}
+
+				#if OS_TYPE == UNX
+					rx = ".+\\.svg$";
+					if (!selected && (regex_search(filename.toStdString(), rx))) {
+						cyclicwidget->exportToSVG(filename);
+						selected = true;
+					}
+				#endif
+				break;
+			case branched:
+				rx = ".+\\.pdf$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					branchedwidget->exportToPDF(filename, false);
+					selected = true;
+				}
+
+				rx = ".+\\.ps$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					branchedwidget->exportToPDF(filename, true);
+					selected = true;
+				}
+
+
+				rx = ".+\\.png$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					branchedwidget->exportToPNG(filename);
+					selected = true;
+				}
+
+				#if OS_TYPE == UNX
+					rx = ".+\\.svg$";
+					if (!selected && (regex_search(filename.toStdString(), rx))) {
+						branchedwidget->exportToSVG(filename);
+						selected = true;
+					}
+				#endif
+				break;
+			case lasso:
+				rx = ".+\\.pdf$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					lassowidget->exportToPDF(filename, false);
+					selected = true;
+				}
+
+				rx = ".+\\.ps$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					lassowidget->exportToPDF(filename, true);
+					selected = true;
+				}
+
+
+				rx = ".+\\.png$";
+				if (!selected && (regex_search(filename.toStdString(), rx))) {
+					lassowidget->exportToPNG(filename);
+					selected = true;
+				}
+
+				#if OS_TYPE == UNX
+					rx = ".+\\.svg$";
+					if (!selected && (regex_search(filename.toStdString(), rx))) {
+						lassowidget->exportToSVG(filename);
+						selected = true;
+					}
+				#endif
+				break;
+			case linearpolysaccharide:
+				break;
+			case other:
+				break;
+			default:
+				break;
+		}
+
+		if (!selected) {
+			QMessageBox msgBox;
+			QString errstr = "Unsupported file format.";
+			msgBox.setText(errstr);
+			msgBox.exec();
+		}
+	}
+}
+
diff --git a/CycloBranch/gui/cSpectrumDetailWidget.h b/CycloBranch/gui/cSpectrumDetailWidget.h
index 01c528f..6c0063c 100644
--- a/CycloBranch/gui/cSpectrumDetailWidget.h
+++ b/CycloBranch/gui/cSpectrumDetailWidget.h
@@ -8,12 +8,13 @@
 #define _CSPECTRUMDETAILWIDGET_H
 
 #include <QWidget>
+#include <QMainWindow>
 #include "core/cTheoreticalSpectrum.h"
 #include "gui/cLinearWidget.h"
 #include "gui/cCyclicWidget.h"
 #include "gui/cBranchedWidget.h"
 #include "gui/cLassoWidget.h"
-#include "gui/cGraphicalSpectrumWidget.h"
+#include "gui/cSpectrumSceneWidget.h"
 
 
 // forward declaration
@@ -22,18 +23,20 @@ class QTextBrowser;
 class QHBoxLayout;
 class QVBoxLayout;
 class QFormLayout;
-class QScrollArea;
 class QCheckBox;
 class QPushButton;
 class QSplitter;
 class QComboBox;
 class QDoubleSpinBox;
+class QToolBar;
+class QAction;
+class QLabel;
 
 
 /**
 	\brief The class representing a widget for visualisation of a detail of a spectrum (opened after doubleclick on a row when results are reported).
 */
-class cSpectrumDetailWidget : public QWidget
+class cSpectrumDetailWidget : public QMainWindow
 {
 	Q_OBJECT
 
@@ -53,6 +56,13 @@ class cSpectrumDetailWidget : public QWidget
 	cSpectrumDetailWidget(const cSpectrumDetailWidget& sd);
 
 
+	/**
+		\brief Overloaded operator=.
+		\param sd reference to a cSpectrumDetailWidget
+	*/ 
+	cSpectrumDetailWidget& operator=(const cSpectrumDetailWidget& sd);
+
+
 	/**
 		\brief The destructor.
 	*/ 
@@ -95,26 +105,54 @@ class cSpectrumDetailWidget : public QWidget
 	void prepareToShow(peptideType peptidetype);
 
 
+protected:
+
+
+	/**
+		\brief Handle a key press event.
+		\param event pointer to QKeyEvent
+	*/ 
+	void keyPressEvent(QKeyEvent *event);
+
+
 private:
-	QHBoxLayout* zoom;
-	QHBoxLayout* mzinterval;
-
-	QSplitter* hsplitter;
-	QSplitter* vsplitter1;
-	QSplitter* vsplitter2;
-
-	QWidget* formwidget;
-	QFormLayout* formlayout;
-	QPushButton* zoomin;
-	QPushButton* zoomout;
-	QPushButton* normalsize;
+	QToolBar* toolbarExport;
+	QToolBar* toolbarZoom;
+	QToolBar* toolbarHide;
+	QToolBar* toolbarMz;
+	QToolBar* toolbarRotation;
+	QToolBar* toolbarTrotation;
+
+	QAction* actionExportSpectrum;
+	QAction* actionExportPeptide;
+	QAction* actionZoomIn;
+	QAction* actionZoomOut;
+	QAction* actionZoomReset;
+	QAction* actionHideMatched;
+	QAction* actionHideUnmatched;
+	QAction* actionHideScrambled;
+	QAction* actionMouseMzSelection;
+
+	QSplitter* hsplitter1;
+	QSplitter* hsplitter2;
+	QSplitter* vsplitter;
+
+	QWidget* widgetmz;
+	QHBoxLayout* hboxmz;
+	QLabel* labelmz;
 	QDoubleSpinBox* minmz;
 	QDoubleSpinBox* maxmz;
 	QPushButton* setmzinterval;
 	QPushButton* resetmzinterval;
-	QCheckBox* hideunmatched;
-	QCheckBox* hidematched;
+
+	QWidget* widgetrotation;
+	QHBoxLayout* hboxrotation;
+	QLabel* labelrotation;
 	QComboBox* rotation;
+
+	QWidget* widgettrotation;
+	QHBoxLayout* hboxtrotation;
+	QLabel* labeltrotation;
 	QComboBox* trotation;
 
 	QTextEdit* textedit;
@@ -124,16 +162,14 @@ class cSpectrumDetailWidget : public QWidget
 	cBranchedWidget* branchedwidget;
 	cLassoWidget* lassowidget;
 
-	QScrollArea* graphicalspectrumscroll;
-	cGraphicalSpectrumWidget* graphicalspectrum;
+	cSpectrumSceneWidget* spectrumscene;
 
 	cTheoreticalSpectrum* theoreticalspectrum;
 
-	QHBoxLayout* mainbox;
-
 	bool preparedToShow;
 	cParameters* parameters;
 
+
 signals:
 
 	/**
@@ -143,12 +179,17 @@ class cSpectrumDetailWidget : public QWidget
 	*/ 
 	void emitMZInterval(double minmz, double maxmz);
 
+
 private slots:
 
 	void updateMZInterval(double minmz, double maxmz);
 
 	void setMZInterval();
 
+	void exportSpectrum();
+
+	void exportPeptide();
+
 };
 
 #endif
\ No newline at end of file
diff --git a/CycloBranch/gui/cSpectrumSceneWidget.cpp b/CycloBranch/gui/cSpectrumSceneWidget.cpp
new file mode 100644
index 0000000..eaa1420
--- /dev/null
+++ b/CycloBranch/gui/cSpectrumSceneWidget.cpp
@@ -0,0 +1,646 @@
+#include "gui/cSpectrumSceneWidget.h"
+
+#include <QTextEdit>
+#include <QVBoxLayout>
+#include <QPainter>
+#include <QPaintEvent>
+#include <QMessageBox>
+#include <QPrinter>
+#include <QGraphicsSimpleTextItem>
+#include <QGraphicsView>
+#include <QGraphicsScene>
+#include <QScrollBar>
+#include <QMatrix>
+#include <QGraphicsItemGroup>
+#include <QGraphicsRectItem>
+#include <QGraphicsSimpleTextItem>
+#include <QSvgGenerator>
+#include <QImage>
+
+
+cSpectrumSceneWidget::cSpectrumSceneWidget(QWidget* parent) {
+	this->parent = parent;
+	parameters = 0;
+	theoreticalspectrum = 0;
+	origwidth = 500;
+	origheight = 200;
+	currentscale = 1;
+	hideunmatched = false;
+	hidematched = false;
+	hidescrambled = false;
+	factor = 0.2;
+	coloredrotationid = -1;
+	coloredrotationstring = "";
+	coloredtrotationid = -1;
+	pressedx = -1;
+	pressedy = -1;
+	currentx = 0;
+	currenty = 0;
+	minmzratio = 0;
+	maxmzratio = 0;
+
+	topmargin = 0;
+	bottommargin = 0;
+	leftmargin = 0;
+	rightmargin = 0;
+
+	firstshow = true;
+	enablemousemzselection = true;
+
+	scene = new QGraphicsScene(this);
+
+	zoomgroup = new QGraphicsItemGroup();
+	zoomrect = new QGraphicsRectItem();
+	zoomgroup->addToGroup(zoomrect);
+	zoomsimpletextitem = new QGraphicsSimpleTextItem();
+	zoomgroup->addToGroup(zoomsimpletextitem);
+	scene->addItem(zoomgroup);
+}
+
+
+cSpectrumSceneWidget::~cSpectrumSceneWidget() {
+	delete scene;
+}
+
+
+void cSpectrumSceneWidget::initialize(cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum) {
+	this->parameters = parameters;
+	this->theoreticalspectrum = theoreticalspectrum;
+
+	if (parameters->mode == dereplication) {
+		origwidth = 800;
+	}
+
+	minmzratio = 0;
+	maxmzratio = theoreticalspectrum->getExperimentalSpectrum().getMaximumMZRatio();
+	emit updateMZInterval(minmzratio, maxmzratio);
+
+	setScene(scene);
+	redrawScene();
+	originalmatrix = matrix();
+}
+
+
+void cSpectrumSceneWidget::exportToPDF(QString filename, bool postscript) {
+	QPrinter printer;
+	if (postscript) {
+		printer.setPaperSize(QSizeF(scene->width() + 100, scene->height() + 100), QPrinter::DevicePixel);
+		printer.setPageMargins (50, 50, 50, 50, QPrinter::DevicePixel);
+	}
+	else {
+		printer.setPaperSize(QSizeF(scene->width(), scene->height()), QPrinter::DevicePixel);
+		printer.setPageMargins (0, 0, 0, 0, QPrinter::DevicePixel);
+	}
+	printer.setOutputFormat(QPrinter::NativeFormat);
+	printer.setOutputFileName(filename);
+
+	QPainter painter;
+	if (!painter.begin(&printer)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		#if OS_TYPE == UNX
+			errstr += "\nDo you have a properly configured print server (sudo apt-get install cups-pdf) ?";
+			errstr += "\nIf you cannot create a ps file, you can create a pdf file and then use pdf2ps tool.";
+		#endif
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	painter.setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing|QPainter::SmoothPixmapTransform);
+	scene->render(&painter);
+	painter.end();
+}
+
+
+void cSpectrumSceneWidget::exportToSVG(QString filename) {
+	QSvgGenerator generator;
+	generator.setFileName(filename);
+	generator.setSize(QSize(scene->width(), scene->height()));
+	generator.setViewBox(QRect(0, 0, scene->width(), scene->height()));
+
+	QPainter painter;
+	if (!painter.begin(&generator)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	scene->render(&painter);
+	painter.end();
+}
+
+
+void cSpectrumSceneWidget::exportToPNG(QString filename) {
+	QImage image(scene->width(), scene->height(), QImage::Format_ARGB32);
+	image.fill(Qt::white);
+
+	QPainter painter;
+	if (!painter.begin(&image)) {
+		QMessageBox msgBox;
+		QString errstr = "The file cannot be created.";
+		msgBox.setText(errstr);
+		msgBox.exec();
+		return;
+	}
+
+	scene->render(&painter);
+	painter.end();
+	image.save(filename);
+}
+
+
+void cSpectrumSceneWidget::wheelEvent(QWheelEvent *event) {
+	if (event->delta() > 0) {
+		zoomIn();
+	}
+	else {
+		zoomOut();
+	}
+}
+
+
+void cSpectrumSceneWidget::mouseMoveEvent(QMouseEvent *event) {
+	QGraphicsView::mouseMoveEvent(event);
+
+	if (enablemousemzselection && (pressedx != -1) && (pressedy != -1)) {
+		QPointF p = mapToScene(event->x(), event->y());
+		currentx = (int)p.x();
+		currenty = (int)p.y();
+
+		updateZoomGroup();
+	}
+}
+
+
+void cSpectrumSceneWidget::mouseReleaseEvent(QMouseEvent *event) {
+	QGraphicsView::mouseReleaseEvent(event);
+
+	if (enablemousemzselection) {
+		if (pressedx == currentx) {
+			pressedx = -1;
+			currentx = -1;
+
+			redrawScene();
+		}
+    
+		if ((event->button() == Qt::LeftButton) && (pressedx != -1) && (pressedy != -1)) {
+			if (pressedx < leftmargin) {
+				pressedx = leftmargin;
+			}
+
+			if (pressedx > origwidth - rightmargin) {
+				pressedx = origwidth - rightmargin;
+			}
+
+			if (currentx < leftmargin) {
+				currentx = leftmargin;
+			}
+
+			if (currentx > origwidth - rightmargin) {
+				currentx = origwidth - rightmargin;
+			}
+
+			double tmpminmzratio = getMZRatioFromXPosition((pressedx < currentx)?pressedx:currentx, origwidth);
+			double tmpmaxmzratio = getMZRatioFromXPosition((pressedx < currentx)?currentx:pressedx, origwidth);
+
+			minmzratio = tmpminmzratio;
+			maxmzratio = tmpmaxmzratio;
+
+			emit updateMZInterval(minmzratio, maxmzratio);
+
+			pressedx = -1;
+			pressedy = -1;
+
+			redrawScene();
+		}
+	}
+}
+
+
+void cSpectrumSceneWidget::mousePressEvent(QMouseEvent *event) {
+	QGraphicsView::mousePressEvent(event);
+
+	if (enablemousemzselection) {
+		if (event->button() == Qt::LeftButton) {
+			QPointF p = mapToScene(event->x(), event->y());
+			pressedx = (int)p.x();
+			pressedy = (int)p.y();
+
+			currentx = pressedx;
+			currenty = pressedy;
+
+			updateZoomGroup();
+		}
+
+		if (event->button() == Qt::RightButton) {
+			pressedx = -1;
+			pressedy = -1;
+
+			redrawScene();
+		}
+
+		if (event->button() == Qt::MiddleButton) {
+			pressedx = -1;
+			pressedy = -1;
+
+			resetMZInterval();
+
+			redrawScene();
+		}
+	}
+}
+
+
+void cSpectrumSceneWidget::showEvent(QShowEvent *event) {
+	if (firstshow) {
+		normalSize();
+		firstshow = false;
+	}
+}
+
+
+double cSpectrumSceneWidget::getMZRatioFromXPosition(int x, int w) {
+	return (double)(x - leftmargin)/(double)(w - leftmargin - rightmargin)*(maxmzratio - minmzratio) + minmzratio;
+}
+
+
+int cSpectrumSceneWidget::getXPositionFromMZRatio(double mzratio, int w) {
+	double val = mzratio - minmzratio;
+	val /= maxmzratio - minmzratio;
+	val *= double(w - leftmargin - rightmargin);
+	return (int)val + leftmargin;
+}
+
+
+void cSpectrumSceneWidget::redrawScene() {
+
+	QGraphicsSimpleTextItem* simpletext;
+	QGraphicsTextItem* text;
+
+	int x;
+	double y;
+	qreal tx, ty, tw, th, sumh;
+
+	char tmpbuf[30];
+	string s;
+
+	int w = origwidth;
+	int h = origheight;
+
+	cPeaksList visiblepeaks;
+	visiblepeaks.clear();
+
+	QList<QGraphicsItem *> hiddenitems;
+
+	vector<string> hits;
+
+	QFont myFont("Arial", 8);
+	QFontMetrics fm(myFont);
+
+	// maximum intensity in the interval <minmzratio, maxmzratio>
+	double maxintensity = theoreticalspectrum->getExperimentalSpectrum().getMaximumIntensityFromMZInterval(minmzratio, maxmzratio);
+
+	scene->removeItem(zoomgroup);
+	scene->clear();
+	zoomgroup->setVisible(false);
+	scene->addItem(zoomgroup);
+
+	// x axis
+	scene->addLine(leftmargin, h - bottommargin, w - rightmargin, h - bottommargin, QPen(Qt::black, 2, Qt::SolidLine));
+
+	// x axis ruler
+	scene->addLine(leftmargin, h - bottommargin, leftmargin, h - bottommargin + 10, QPen(Qt::black, 2, Qt::SolidLine));
+	scene->addLine(w - rightmargin, h - bottommargin, w - rightmargin, h - bottommargin + 10, QPen(Qt::black, 2, Qt::SolidLine));
+
+	simpletext = scene->addSimpleText(QString::number(minmzratio), myFont);
+	simpletext->setPos(QPointF(leftmargin - 2, h - bottommargin + 12));
+
+	simpletext = scene->addSimpleText(QString::number(maxmzratio), myFont);
+	simpletext->setPos(QPointF(w - rightmargin - 2, h - bottommargin + 12));
+
+	// y axis
+	scene->addLine(leftmargin, h - bottommargin, leftmargin, h - bottommargin - std::max(h - topmargin - bottommargin, 5), QPen(Qt::black, 2, Qt::SolidLine));
+	
+	// y axis ruler
+	scene->addLine(leftmargin - 10, h - bottommargin - std::max(h - topmargin - bottommargin, 5), leftmargin, h - bottommargin - std::max(h - topmargin - bottommargin, 5), QPen(Qt::black, 2, Qt::SolidLine));
+	scene->addLine(leftmargin - 10, h - bottommargin, leftmargin, h - bottommargin, QPen(Qt::black, 2, Qt::SolidLine));
+
+	simpletext = scene->addSimpleText(QString::number(0), myFont);
+	simpletext->setPos(QPointF(leftmargin - 25, h - bottommargin + 2));
+	simpletext->setRotation(-90);
+
+	simpletext = scene->addSimpleText(QString::number(maxintensity), myFont);
+	simpletext->setPos(QPointF(leftmargin - 25, h - bottommargin - std::max(h - topmargin - bottommargin, 5) + 2));
+	simpletext->setRotation(-90);
+
+	// all experimental peaks
+	for (int i = 0; i < (int)theoreticalspectrum->getExperimentalSpectrum().size(); i++) {
+
+		// skip peaks which are out of range
+		if ((theoreticalspectrum->getExperimentalSpectrum()[i].mzratio < minmzratio) || (theoreticalspectrum->getExperimentalSpectrum()[i].mzratio > maxmzratio)) {
+			continue;
+		}
+
+		// hide unmatched peaks
+		if (hideunmatched && (theoreticalspectrum->getExperimentalSpectrum()[i].matched <= 0)) {
+			continue;
+		}
+
+		// hide matched peaks
+		if (hidematched && (theoreticalspectrum->getExperimentalSpectrum()[i].matched > 0)) {
+			continue;
+		}
+
+		visiblepeaks.add(theoreticalspectrum->getExperimentalSpectrum()[i]);
+
+	}
+
+	visiblepeaks.sortbyIntensityDesc();
+
+	// visible peaks only
+	for (int i = 0; i < (int)visiblepeaks.size(); i++) {
+
+		x = getXPositionFromMZRatio(visiblepeaks[i].mzratio, origwidth);
+
+		y = visiblepeaks[i].intensity/maxintensity * (h - topmargin - bottommargin);
+
+		string coloredtrotationstring;
+		if (coloredtrotationid != -1) {
+			if (parameters->peptidetype == branched) {
+				coloredtrotationstring = " " + to_string(coloredtrotationid + 1) + "_";
+			}
+			if (parameters->peptidetype == lasso) {
+				coloredtrotationstring = "_" + to_string(coloredtrotationid + 1) + "_";
+			}
+		}
+
+		hits.clear();
+
+		s = visiblepeaks[i].description;
+		int position = (int)s.find(',');
+		while (position != (int)string::npos) {
+			hits.push_back(s.substr(0, position));
+			s = s.substr(position + 1);
+
+			if (parameters->peptidetype == cyclic) {
+				if (visiblepeaks[i].scrambled) {
+					if (hidescrambled) {
+						hits.pop_back();
+					}
+				}
+				else {
+					if ((coloredrotationid != -1) && (hits.back().find(coloredrotationstring) == string::npos)) {
+						hits.pop_back();
+					}
+				}	
+			}
+
+			if ((parameters->peptidetype == branched) && (coloredtrotationid != -1) && (hits.back().find(coloredtrotationstring) == string::npos)) {
+				hits.pop_back();
+			}
+
+			if ((parameters->peptidetype == lasso) && (((coloredrotationid != -1) && (hits.back().find(coloredrotationstring) == string::npos)) || ((coloredtrotationid != -1) && (hits.back().find(coloredtrotationstring) == string::npos)))) {
+				hits.pop_back();
+			}
+
+			position = (int)s.find(',');
+		}
+
+		if (s.size() > 0) {
+			hits.push_back(s);
+
+			if (parameters->peptidetype == cyclic) {
+				if (visiblepeaks[i].scrambled) {
+					if (hidescrambled) {
+						hits.pop_back();
+					}
+				}
+				else {
+					if ((coloredrotationid != -1) && (hits.back().find(coloredrotationstring) == string::npos)) {
+						hits.pop_back();
+					}
+				}	
+			}
+
+			if ((parameters->peptidetype == branched) && (coloredtrotationid != -1) && (hits.back().find(coloredtrotationstring) == string::npos)) {
+				hits.pop_back();
+			}
+
+			if ((parameters->peptidetype == lasso) && (((coloredrotationid != -1) && (hits.back().find(coloredrotationstring) == string::npos)) || ((coloredtrotationid != -1) && (hits.back().find(coloredtrotationstring) == string::npos)))) {
+				hits.pop_back();
+			}
+		}
+
+		sprintf_s(tmpbuf,"%.3f\0",visiblepeaks[i].mzratio);
+		s = tmpbuf;
+		hits.push_back(s);
+
+		if (hits.size() > 1) {
+			scene->addLine(x, h - bottommargin - 2, x, h - bottommargin - std::max((int)y, 5), QPen(Qt::red, 2, Qt::SolidLine));
+			
+			hiddenitems.clear();
+			sumh = 0;
+			for (vector<string>::reverse_iterator rit = hits.rbegin(); rit != hits.rend(); ++rit) {
+				text = scene->addText("");
+				text->setDefaultTextColor(QColor(Qt::red));
+				text->setFont(myFont);
+				if (parameters->mode == dereplication) {
+					text->setTextInteractionFlags(Qt::TextBrowserInteraction);
+					text->setOpenExternalLinks(true);
+				}
+				text->setHtml(rit->c_str());
+				tw = text->boundingRect().width();
+				th = text->boundingRect().height();
+				sumh += th + 1;
+				tx = x - 2 - 4;
+				ty = h - bottommargin - std::max((int)y, 5) - sumh - 4;
+				text->setPos(tx, ty);
+
+				hiddenitems.append(text);
+				
+				if (scene->items(tx, ty, tw, th, Qt::IntersectsItemBoundingRect, Qt::AscendingOrder).size() > 1) {
+					for (int k = 0; k < (int)hiddenitems.size(); k++) {
+						scene->removeItem(hiddenitems[k]);
+					}
+					break;
+				}
+			}
+		}
+		else {
+			scene->addLine(x, h - bottommargin - 2, x, h - bottommargin - std::max((int)y, 5), QPen(Qt::black, 2, Qt::SolidLine));
+
+			simpletext = scene->addSimpleText(hits[0].c_str(), myFont);
+			tw = simpletext->boundingRect().width();
+			th = simpletext->boundingRect().height();
+			tx = x - 2;
+			ty = h - bottommargin - std::max((int)y, 5) - th - 1 - 4;
+			simpletext->setPos(tx, ty);
+			simpletext->setBrush(Qt::black);
+	
+			if (scene->items(tx, ty, tw, th, Qt::IntersectsItemBoundingRect, Qt::AscendingOrder).size() > 1) {
+				scene->removeItem(simpletext);
+			}
+		}
+
+	}
+
+	// fix the scene rectangle
+	scene->setSceneRect(scene->itemsBoundingRect());
+	
+}
+
+
+void cSpectrumSceneWidget::updateZoomGroup() {
+	qreal rx1, rx2, ry1, ry2;
+	QFont myFont("Arial", 8);
+
+	if (currentx < pressedx) {
+		rx1 = currentx;
+		rx2 = pressedx;
+	}
+	else {
+		rx1 = pressedx;
+		rx2 = currentx;
+	}
+
+	if (currenty < pressedy) {
+		ry1 = currenty;
+		ry2 = pressedy;
+	}
+	else {
+		ry1 = pressedy;
+		ry2 = currenty;
+	}
+
+	zoomrect->setPen(QPen(Qt::black, 1, Qt::DashLine));
+	zoomrect->setRect(QRectF(QPointF(rx1, ry1), QPointF(rx2, ry2)));
+		
+	QString qstr = "m/z: ";
+	qstr += QString::number(getMZRatioFromXPosition((pressedx < currentx)?pressedx:currentx, origwidth));
+	qstr += "-";
+	qstr += QString::number(getMZRatioFromXPosition((pressedx < currentx)?currentx:pressedx, origwidth));
+		
+	zoomsimpletextitem->setFont(myFont);
+	zoomsimpletextitem->setText(qstr);
+	zoomsimpletextitem->setPos(QPointF(pressedx, pressedy - 2));
+
+	zoomgroup->setVisible(true);
+}
+
+
+void cSpectrumSceneWidget::hideUnmatchedPeaks(bool state) {
+	if (state == false) {
+		hideunmatched = false;
+	}
+	else {
+		hideunmatched = true;
+	}
+
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::hideMatchedPeaks(bool state) {
+	if (state == false) {
+		hidematched = false;
+	}
+	else {
+		hidematched = true;
+	}
+
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::hideScrambledPeaks(bool state) {
+	if (state == false) {
+		hidescrambled = false;
+	}
+	else {
+		hidescrambled = true;
+	}
+
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::zoomIn() {
+	if (currentscale < 32) {
+		currentscale += factor;
+		setMatrix(originalmatrix);
+		scale(currentscale, currentscale);
+		verticalScrollBar()->setSliderPosition(verticalScrollBar()->maximum());
+	}
+}
+
+
+void cSpectrumSceneWidget::zoomOut() {
+	if (currentscale > 1) {
+		currentscale -= factor;
+		setMatrix(originalmatrix);
+		scale(currentscale, currentscale);
+		verticalScrollBar()->setSliderPosition(verticalScrollBar()->maximum());
+	}
+}
+
+
+void cSpectrumSceneWidget::normalSize() {
+	currentscale = 1;
+	setMatrix(originalmatrix);
+	verticalScrollBar()->setSliderPosition(verticalScrollBar()->maximum());
+}
+
+
+void cSpectrumSceneWidget::setMZInterval(double minmz, double maxmz) {
+	if (maxmz < minmz) {
+		double tmp = maxmz;
+		maxmz = minmz;
+		minmz = tmp;
+	}
+
+	minmzratio = std::max(0.0, minmz);
+	maxmzratio = std::min(maxmz, theoreticalspectrum->getExperimentalSpectrum().getMaximumMZRatio());
+	emit updateMZInterval(minmzratio, maxmzratio);
+
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::resetMZInterval() {
+	minmzratio = 0;
+	maxmzratio = theoreticalspectrum->getExperimentalSpectrum().getMaximumMZRatio();
+	emit updateMZInterval(minmzratio, maxmzratio);
+
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::rotationChanged(int index) {
+	coloredrotationid = index - 1;
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::trotationChanged(int index) {
+	coloredtrotationid = index - 1;
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::rotationChanged(QString text) {
+	coloredrotationstring = " " + text.toStdString() + "_";
+	redrawScene();
+}
+
+
+void cSpectrumSceneWidget::enableMouseMzSelectionTool(bool enable) {
+	enablemousemzselection = enable;
+	pressedx = -1;
+	pressedy = -1;
+
+	redrawScene();
+}
+
diff --git a/CycloBranch/gui/cSpectrumSceneWidget.h b/CycloBranch/gui/cSpectrumSceneWidget.h
new file mode 100644
index 0000000..83fc912
--- /dev/null
+++ b/CycloBranch/gui/cSpectrumSceneWidget.h
@@ -0,0 +1,210 @@
+/**
+	\file cSpectrumSceneWidget.h
+	\brief The implementation of a widget painting a 2D mass spectrum.
+*/
+
+
+#ifndef _CSPECTRUMSCENEWIDGET_H
+#define _CSPECTRUMSCENEWIDGET_H
+
+#include <iostream>
+#include <QWidget>
+#include <QGraphicsView>
+
+#include "core/cTheoreticalSpectrum.h"
+
+
+using namespace std;
+
+
+// forward declaration
+class QPaintEvent;
+class QGraphicsScene;
+class QMatrix;
+class QGraphicsItemGroup;
+class QGraphicsRectItem;
+class QGraphicsSimpleTextItem;
+
+
+/**
+	\brief The widget representing a 2D mass spectrum.
+*/
+class cSpectrumSceneWidget : public QGraphicsView
+{
+	Q_OBJECT
+
+public:
+
+
+	/**
+		\brief The constructor.
+		\param parent pointer to a parent widget
+	*/ 
+	cSpectrumSceneWidget(QWidget* parent = 0);
+
+
+	/**
+		\brief The destructor.
+	*/ 
+	~cSpectrumSceneWidget();
+
+
+	/**
+		\brief Initialize the widget.
+		\param parameters a pointer to parameters
+		\param theoreticalspectrum a pointer to a theoretical spectrum
+	*/ 
+	void initialize(cParameters* parameters, cTheoreticalSpectrum* theoreticalspectrum);
+
+
+	/**
+		\brief Export spectrum scene into a PDF or a PS file.
+		\param filename filename
+		\param postscript if true then PS file is generated instead of PDF
+	*/ 
+	void exportToPDF(QString filename, bool postscript);
+
+
+	/**
+		\brief Export spectrum scene into a SVG file.
+		\param filename filename
+	*/ 
+	void exportToSVG(QString filename);
+
+
+	/**
+		\brief Export spectrum scene into a PNG file.
+		\param filename filename
+	*/ 
+	void exportToPNG(QString filename);
+
+
+protected:
+
+
+	/**
+		\brief Handle the mouse wheel event.
+		\param event pointer to QWheelEvent
+	*/ 
+	void wheelEvent(QWheelEvent *event);
+
+
+	/**
+		\brief Handle the mouse move event.
+		\param event pointer to QMouseEvent
+	*/ 
+	void mouseMoveEvent(QMouseEvent *event);
+
+
+	/**
+		\brief Handle the mouse release event.
+		\param event pointer to QMouseEvent
+	*/ 
+	void mouseReleaseEvent(QMouseEvent *event);
+
+
+	/**
+		\brief Handle the mouse press event.
+		\param event pointer to QMouseEvent
+	*/ 
+	void mousePressEvent(QMouseEvent *event);
+
+
+	/**
+		\brief Handle the widget show event.
+		\param event pointer to QShowEvent
+	*/ 
+	void showEvent(QShowEvent *event);
+
+
+private:
+	QWidget* parent;
+	QGraphicsScene* scene;
+	QMatrix originalmatrix;
+
+	QGraphicsItemGroup* zoomgroup;
+	QGraphicsRectItem* zoomrect;
+	QGraphicsSimpleTextItem* zoomsimpletextitem;
+
+	cParameters* parameters;
+	cTheoreticalSpectrum* theoreticalspectrum;
+
+	qreal currentscale;
+	qreal factor;
+
+	int origwidth;
+	int origheight;
+
+	int coloredrotationid;
+	string coloredrotationstring;
+	int coloredtrotationid;
+
+	bool hideunmatched;
+	bool hidematched;
+	bool hidescrambled;
+
+	int pressedx;
+	int pressedy;
+
+	int currentx;
+	int currenty;
+
+	double minmzratio;
+	double maxmzratio;
+
+	int topmargin;
+	int bottommargin;
+	int leftmargin;
+	int rightmargin;
+
+	bool firstshow;
+	bool enablemousemzselection;
+
+
+	double getMZRatioFromXPosition(int x, int w);
+
+	int getXPositionFromMZRatio(double mzratio, int w);
+
+	void redrawScene();
+
+	void updateZoomGroup();
+
+
+signals:
+
+	/**
+		\brief The signal is emitted when the range of m/z ratios has been changed.
+		\param minmz a minimum threshold of m/z ratio
+		\param maxmz a maximum threshold of m/z ratio
+	*/ 
+	void updateMZInterval(double minmz, double maxmz);
+
+private slots:
+
+	void hideUnmatchedPeaks(bool state);
+
+	void hideMatchedPeaks(bool state);
+
+	void hideScrambledPeaks(bool state);
+
+	void zoomIn();
+
+	void zoomOut();
+
+	void normalSize();
+
+	void setMZInterval(double minmz, double maxmz);
+
+	void resetMZInterval();
+
+	void rotationChanged(int index);
+
+	void trotationChanged(int index);
+
+	void rotationChanged(QString text);
+
+	void enableMouseMzSelectionTool(bool enable);
+
+};
+
+#endif
diff --git a/CycloBranch/images.qrc b/CycloBranch/images.qrc
new file mode 100644
index 0000000..74aa3b2
--- /dev/null
+++ b/CycloBranch/images.qrc
@@ -0,0 +1,32 @@
+<RCC>
+    <qresource prefix="/">
+        <file>images/icons/2.png</file>
+        <file>images/icons/3.png</file>
+        <file>images/icons/4.png</file>
+        <file>images/icons/22.png</file>
+        <file>images/icons/26.png</file>
+        <file>images/icons/32.png</file>
+        <file>images/icons/33.png</file>
+        <file>images/icons/48.png</file>
+        <file>images/icons/52.png</file>
+        <file>images/icons/61.png</file>
+        <file>images/icons/62.png</file>
+        <file>images/icons/68.png</file>
+        <file>images/icons/73.png</file>
+        <file>images/icons/77.png</file>
+        <file>images/icons/89.png</file>
+        <file>images/icons/93.png</file>
+        <file>images/icons/96.png</file>
+        <file>images/splash.png</file>
+        <file>images/cb.png</file>
+        <file>images/icons/20.png</file>
+        <file>images/icons/81.png</file>
+        <file>images/icons/82.png</file>
+        <file>images/icons/83.png</file>
+        <file>images/icons/84.png</file>
+        <file>images/icons/80.png</file>
+        <file>images/icons/57.png</file>
+        <file>images/icons/54.png</file>
+        <file>images/icons/64.png</file>
+    </qresource>
+</RCC>
diff --git a/CycloBranch/images/cb.cdr b/CycloBranch/images/cb.cdr
new file mode 100644
index 0000000000000000000000000000000000000000..6efd8530fb072565eef570aeebdcb4734e4b862b
GIT binary patch
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diff --git a/CycloBranch/images/icons/33.png b/CycloBranch/images/icons/33.png
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GIT binary patch
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diff --git a/CycloBranch/images/icons/52.png b/CycloBranch/images/icons/52.png
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GIT binary patch
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GIT binary patch
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diff --git a/CycloBranch/licence.txt b/CycloBranch/licence.txt
new file mode 100644
index 0000000..818433e
--- /dev/null
+++ b/CycloBranch/licence.txt
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
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+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
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+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
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+  Some devices are designed to deny users access to install or run
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+  The precise terms and conditions for copying, distribution and
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+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
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+  "The Program" refers to any copyrightable work licensed under this
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+extent that warranties are provided), that licensees may convey the
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diff --git a/CycloBranch/main.cpp b/CycloBranch/main.cpp
index cbfb6ab..e4c75dc 100644
--- a/CycloBranch/main.cpp
+++ b/CycloBranch/main.cpp
@@ -1,7 +1,11 @@
 #include <QApplication>
 #include <QLabel>
 #include <QMetaType>
+#include <QPixmap>
+#include <QSplashScreen>
+#include <QThread>
 
+#include "core/utilities.h"
 #include "gui/cMainWindow.h"
 
 
@@ -12,9 +16,14 @@
 	\retval int 0 when the application finished successfully
 */ 
 int main(int argc, char** argv) {
-
+	
 	QApplication app(argc, argv);
-	qRegisterMetaType<cTheoreticalSpectrum>("cTheoreticalSpectrum");
+	Q_INIT_RESOURCE(images);
+
+	#if OS_TYPE == UNX
+		setlocale(LC_NUMERIC,"C");
+		chdir(linuxinstalldir.toStdString().c_str());
+	#endif
 	qRegisterMetaType<cParameters>("cParameters");
 	qRegisterMetaType<vector<fragmentIonType> >("vector<fragmentIonType>");
 	qRegisterMetaType<peptideType>("peptideType");
@@ -22,9 +31,25 @@ int main(int argc, char** argv) {
 	qRegisterMetaType<string>("string");
 	qRegisterMetaType<cFragmentIons>("cFragmentIons");
 
+	QPixmap pixmap(":/images/splash.png");
+	QSplashScreen splash(pixmap);
+	if(!pixmap.isNull()) {
+		splash.show();
+		splash.showMessage(QObject::tr(QString(appname + " " + appversion + " is starting ...").toStdString().c_str()), Qt::AlignLeft | Qt::AlignBottom, Qt::black);
+		for (int i = 0; i < 50; i++) {
+			if (!splash.isVisible()) {
+				break;
+			}
+			QThread::msleep(100);
+			app.processEvents();
+		}
+	}
+
 	cMainWindow mwin;
 	mwin.show();
 
+	splash.finish(&mwin);
+
 	return app.exec();
 
 }
diff --git a/CycloBranch/parallel/cGraphReaderThread.cpp b/CycloBranch/parallel/cGraphReaderThread.cpp
index 17f4316..8c9e5da 100644
--- a/CycloBranch/parallel/cGraphReaderThread.cpp
+++ b/CycloBranch/parallel/cGraphReaderThread.cpp
@@ -3,7 +3,7 @@
 #include "gui/cMainThread.h"
 
 
-int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector<string>& composition, double precursormass, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector<nodeEdge>& perspectivepath, double cummass, bool* terminatecomputation) {
+int cGraphReaderThread::getCandidatesIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector<string>& composition, double precursormass, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector<nodeEdge>& perspectivepath, double cummass, bool* terminatecomputation) {
 	nodeEdge ne;
 	int tmpmiddlemodifID = 0;
 	int finish;
@@ -18,10 +18,19 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
 		return 0;
 	}
 
+	if ((parameters->peptidetype == lasso) && (startmodifID > 0) && (middlemodifID > 0)) {
+		return 0;
+	}
+
 	if ((*graph)[nodeid].size() > 0) {
 
 		for (int i = 0; i < (int)(*graph)[nodeid].size(); i++) {
 
+			// target charge of an edge must be equal to the source charge of a following edge
+			if ((perspectivepath.size() > 0) && ((*graph)[nodeid][i].sourcecharge != (*graph)[perspectivepath.back().nodeid][perspectivepath.back().edgeid].targetcharge)) {
+				continue;
+			}
+
 			// accumulation of middle modifications is not allowed
 			if (((parameters->peptidetype == branched) || (parameters->peptidetype == lasso)) && (middlemodifID != 0) && ((*graph)[nodeid][i].middlemodifID != 0)) {
 				continue;
@@ -39,7 +48,7 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
 			if (cycle) {
 				continue;
 			}
-			
+
 			ne.nodeid = nodeid;
 			ne.edgeid = i;	
 			perspectivepath.push_back(ne);
@@ -52,7 +61,7 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
 			}
 
 			composition.push_back((*graph)[nodeid][i].composition);
-			finish = getTheoreticalSpectraIter(cterminalstartingnode, candidates, (*graph)[nodeid][i].targetnode, composition, precursormass, startmodifID, (*graph)[nodeid][i].endmodifID, tmpmiddlemodifID, middlepos, perspectivepath, cummass + (*graph)[nodeid][i].massdifference, terminatecomputation);
+			finish = getCandidatesIter(cterminalstartingnode, candidates, (*graph)[nodeid][i].targetnode, composition, precursormass, startmodifID, (*graph)[nodeid][i].endmodifID, tmpmiddlemodifID, middlepos, perspectivepath, cummass + (*graph)[nodeid][i].massdifference, terminatecomputation);
 			composition.pop_back();
 
 			perspectivepath.pop_back();
@@ -77,7 +86,7 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
 
 				if ((parameters->peptidetype == branched) || (parameters->peptidetype == lasso)) {
 					result.getSet().clear();
-					candidate.prepareBranchedCandidate(result, parameters->peptidetype, terminatecomputation);
+					candidate.prepareBranchedCandidates(result, parameters->peptidetype, terminatecomputation);
 					if (scanmode == 0) {
 						candidates->lock();
 						for (auto i = result.getSet().begin(); i != result.getSet().end(); ++i) {
@@ -132,18 +141,6 @@ int cGraphReaderThread::getTheoreticalSpectraIter(bool cterminalstartingnode, cC
 }
 
 
-int cGraphReaderThread::reverseCTerminalCandidates(int nodeid, cCandidateSet* candidates, double precursormass, int startmodifID, bool* terminatecomputation) {
-	vector<string> composition;
-	vector<nodeEdge> perspectivepath;
-
-	if (getTheoreticalSpectraIter((*graph)[nodeid].checkIonAnnotation(y_ion), candidates, nodeid, composition, precursormass, startmodifID, 0, 0, -1, perspectivepath, (*graph)[nodeid].getMZRatio(), terminatecomputation) == -1) {
-		return -1;
-	}
-
-	return 0;
-}
-
-
 cGraphReaderThread::cGraphReaderThread() {
 	graph = 0;
 	bricksdatabasewithcombinations = 0;
@@ -177,12 +174,12 @@ void cGraphReaderThread::run() {
 	vector<string> composition;
 	vector<nodeEdge> perspectivepath;
 	int startmodifID = 0;
-	double unchargedprecursormass = uncharge(parameters->precursormass, parameters->precursorcharge);
+	double unchargedprecursormass = charge(uncharge(parameters->precursormass, parameters->precursorcharge), (parameters->precursorcharge > 0)?1:-1);
 
 	switch (parameters->peptidetype)
 	{
 	case cyclic:
-		if (getTheoreticalSpectraIter(false, candidates, 0, composition, unchargedprecursormass, 0, 0, 0, -1, perspectivepath, (*graph)[0].getMZRatio(), terminatecomputation) == -1) {
+		if (getCandidatesIter(false, candidates, 0, composition, unchargedprecursormass, 0, 0, 0, -1, perspectivepath, (*graph)[0].getMZRatio(), terminatecomputation) == -1) {
 			// terminated
 			return;
 		}
@@ -193,7 +190,7 @@ void cGraphReaderThread::run() {
 			if (i - 2 > 0) {
 				startmodifID = i - 2;
 			}
-			if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, startmodifID, terminatecomputation) == -1) {
+			if (getCandidatesIter((*graph)[i].checkIonAnnotation(y_ion), candidates, i, composition, unchargedprecursormass, startmodifID, 0, 0, -1, perspectivepath, (*graph)[i].getMZRatio(), terminatecomputation) == -1) {
 				// terminated
 				return;
 			}
@@ -204,9 +201,11 @@ void cGraphReaderThread::run() {
 			if (i - 1/*2*/ > 0) {
 				startmodifID = i - 1/*2*/;
 			}
-			if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, startmodifID, terminatecomputation) == -1) {
-				// terminated
-				return;
+			if (parameters->searchedmodifications[startmodifID].nterminal) {
+				if (getCandidatesIter((*graph)[i].checkIonAnnotation(y_ion), candidates, i, composition, unchargedprecursormass, startmodifID, 0, 0, -1, perspectivepath, (*graph)[i].getMZRatio(), terminatecomputation) == -1) {
+					// terminated
+					return;
+				}
 			}
 		}
 		break;
@@ -215,7 +214,7 @@ void cGraphReaderThread::run() {
 			if (i - 1 > 0) {
 				startmodifID = i - 1;
 			}
-			if (reverseCTerminalCandidates(i, candidates, unchargedprecursormass, startmodifID, terminatecomputation) == -1) {
+			if (getCandidatesIter((*graph)[i].checkIonAnnotation(y_ion), candidates, i, composition, unchargedprecursormass, startmodifID, 0, 0, -1, perspectivepath, (*graph)[i].getMZRatio(), terminatecomputation) == -1) {
 				// terminated
 				return;
 			}
diff --git a/CycloBranch/parallel/cGraphReaderThread.h b/CycloBranch/parallel/cGraphReaderThread.h
index fbaa489..81457e8 100644
--- a/CycloBranch/parallel/cGraphReaderThread.h
+++ b/CycloBranch/parallel/cGraphReaderThread.h
@@ -44,9 +44,7 @@ class cGraphReaderThread : public QThread {
 	int scanmode;
 	bool* terminatecomputation;
 
-	int getTheoreticalSpectraIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector<string>& composition, double precursormass, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector<nodeEdge>& perspectivepath, double cummass, bool* terminatecomputation);
-
-	int reverseCTerminalCandidates(int nodeid, cCandidateSet* candidates, double precursormass, int startmodifID, bool* terminatecomputation);
+	int getCandidatesIter(bool cterminalstartingnode, cCandidateSet* candidates, int nodeid, vector<string>& composition, double precursormass, int startmodifID, int endmodifID, int middlemodifID, int middlepos, vector<nodeEdge>& perspectivepath, double cummass, bool* terminatecomputation);
 
 public:
 
diff --git a/CycloBranch/parallel/cSpectrumComparatorThread.cpp b/CycloBranch/parallel/cSpectrumComparatorThread.cpp
index f519934..0a9b202 100644
--- a/CycloBranch/parallel/cSpectrumComparatorThread.cpp
+++ b/CycloBranch/parallel/cSpectrumComparatorThread.cpp
@@ -3,7 +3,7 @@
 #include "core/cTheoreticalSpectrumList.h"
 
 
-bool compareBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
+bool compareBandAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
 	if (a.getNumberOfMatchedPeaks(b_ion) > b.getNumberOfMatchedPeaks(b_ion)) {
 		return true;
 	}
@@ -17,11 +17,11 @@ bool compareBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
 }
 
 
-bool compareBBwaterLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
-	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_water_loss) > b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_water_loss)) {
+bool compareBBwaterLossAndAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
+	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_dehydrated) > b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_dehydrated)) {
 		return true;
 	}
-	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_water_loss) < b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_water_loss)) {
+	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_dehydrated) < b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_dehydrated)) {
 		return false;
 	}
 	if (a.getNumberOfMatchedPeaks() > b.getNumberOfMatchedPeaks()) {
@@ -31,11 +31,11 @@ bool compareBBwaterLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpect
 }
 
 
-bool compareBBammoniaLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
-	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_ammonia_loss) > b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_ammonia_loss)) {
+bool compareBBammoniaLossAndAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
+	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_deamidated) > b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_deamidated)) {
 		return true;
 	}
-	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_ammonia_loss) < b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_ammonia_loss)) {
+	if (a.getNumberOfMatchedPeaks(b_ion) + a.getNumberOfMatchedPeaks(b_ion_deamidated) < b.getNumberOfMatchedPeaks(b_ion) + b.getNumberOfMatchedPeaks(b_ion_deamidated)) {
 		return false;
 	}
 	if (a.getNumberOfMatchedPeaks() > b.getNumberOfMatchedPeaks()) {
@@ -45,7 +45,7 @@ bool compareBBammoniaLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpe
 }
 
 
-bool compareYBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
+bool compareYBandAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
 	if (a.getNumberOfMatchedPeaksYB() > b.getNumberOfMatchedPeaksYB()) {
 		return true;
 	}
@@ -59,7 +59,7 @@ bool compareYBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
 }
 
 
-bool compareYandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
+bool compareYandAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
 	if (a.getNumberOfMatchedPeaks(y_ion) > b.getNumberOfMatchedPeaks(y_ion)) {
 		return true;
 	}
@@ -73,17 +73,17 @@ bool compareYandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
 }
 
 
-bool compareWeightedIntensityDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
+bool compareWeightedIntensityDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
 	return (a.getWeightedIntensityScore() > b.getWeightedIntensityScore());
 }
 
 
-bool compareNumberOfMatchedPeaksDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
+bool compareNumberOfMatchedPeaksDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
 	return (a.getNumberOfMatchedPeaks() > b.getNumberOfMatchedPeaks());
 }
 
 
-bool compareNumberOfMatchedBricksDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b) {
+bool compareNumberOfMatchedBricksDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b) {
 	return (a.getNumberOfMatchedBricks() > b.getNumberOfMatchedBricks());
 }
 
@@ -161,11 +161,11 @@ void cSpectrumComparatorThread::run() {
 		case b_ions:
 			score = tsp.getNumberOfMatchedPeaks(b_ion);
 			break;
-		case b_ions_and_b_water_loss_ions:
-			score = tsp.getNumberOfMatchedPeaks(b_ion) + tsp.getNumberOfMatchedPeaks(b_ion_water_loss);
+		case b_ions_and_b_dehydrated_ions:
+			score = tsp.getNumberOfMatchedPeaks(b_ion) + tsp.getNumberOfMatchedPeaks(b_ion_dehydrated);
 			break;
-		case b_ions_and_b_ammonia_loss_ions:
-			score = tsp.getNumberOfMatchedPeaks(b_ion) + tsp.getNumberOfMatchedPeaks(b_ion_ammonia_loss);
+		case b_ions_and_b_deamidated_ions:
+			score = tsp.getNumberOfMatchedPeaks(b_ion) + tsp.getNumberOfMatchedPeaks(b_ion_deamidated);
 			break;
 		case y_ions_and_b_ions:
 			score = tsp.getNumberOfMatchedPeaksYB();
diff --git a/CycloBranch/parallel/cSpectrumComparatorThread.h b/CycloBranch/parallel/cSpectrumComparatorThread.h
index 5431536..c7c7a23 100644
--- a/CycloBranch/parallel/cSpectrumComparatorThread.h
+++ b/CycloBranch/parallel/cSpectrumComparatorThread.h
@@ -22,7 +22,7 @@ class cTheoreticalSpectrumList;
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareBandAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -31,7 +31,7 @@ bool compareBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareBBwaterLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareBBwaterLossAndAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -40,7 +40,7 @@ bool compareBBwaterLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpect
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareBBammoniaLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareBBammoniaLossAndAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -49,7 +49,7 @@ bool compareBBammoniaLossAndAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpe
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareYBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareYBandAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -58,7 +58,7 @@ bool compareYBandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareYandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareYandAllIonsDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -67,7 +67,7 @@ bool compareYandAllIonsDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareWeightedIntensityDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareWeightedIntensityDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -76,7 +76,7 @@ bool compareWeightedIntensityDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum&
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareNumberOfMatchedPeaksDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareNumberOfMatchedPeaksDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
@@ -85,7 +85,7 @@ bool compareNumberOfMatchedPeaksDesc(cTheoreticalSpectrum& a, cTheoreticalSpectr
 	\param b second theoretical spectrum
 	\retval bool true if the score of \a a is greater than the score of \a b
 */ 
-bool compareNumberOfMatchedBricksDesc(cTheoreticalSpectrum& a, cTheoreticalSpectrum& b);
+bool compareNumberOfMatchedBricksDesc(const cTheoreticalSpectrum& a, const cTheoreticalSpectrum& b);
 
 
 /**
diff --git a/CycloBranch/readme-linux-compile.txt b/CycloBranch/readme-linux-compile.txt
new file mode 100644
index 0000000..d47dbc1
--- /dev/null
+++ b/CycloBranch/readme-linux-compile.txt
@@ -0,0 +1,12 @@
+1) Required packages:
+g++
+libboost-all-dev
+qt5-default
+libqt5svg5*
+
+2) Execute the following commands in the directory where CycloBranch is unpacked:
+mkdir build
+mkdir moc
+qmake
+make
+
diff --git a/readme.txt b/readme.txt
index 571ce70..43fa1a7 100644
--- a/readme.txt
+++ b/readme.txt
@@ -1,3 +1,3 @@
 CycloBranch.sln 
 - project for MS Visual Studio 2012
-- requires Qt 5.1.1 installed
+- requires Qt 5.2.1 and Boost 1.57 installed