release 1.2.660

novak-jiri · Feb 21, 2018 · 2622b24 · 2622b24
1 parent 115eed4
commit 2622b24
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Showing 57 changed files with 4,983 additions and 1,162 deletions.
diff --git a/CycloBranch/CycloBranch-Linux.pro b/CycloBranch/CycloBranch-Linux.pro
@@ -6,7 +6,7 @@ TEMPLATE = app
 TARGET = CycloBranch
 QT += core gui widgets printsupport svg
 INCLUDEPATH += . core gui parallel
-QMAKE_CXXFLAGS += -std=c++0x -DLINUX -m64
+QMAKE_CXXFLAGS += -std=c++11 -DLINUX -m64
 QMAKE_LIBS += -lboost_regex -lxerces-c
 OBJECTS_DIR = build/
 MOC_DIR = moc/
@@ -21,6 +21,7 @@ HEADERS += core/cBrick.h \
            core/cDeNovoGraphNode.h \
            core/cFragmentIons.h \
            core/cImzML.h \
+           core/cIsotopePatternCache.h \
            core/cMzML.h \
            core/cParameters.h \
            core/cPeak.h \
@@ -78,6 +79,7 @@ SOURCES += core/cBrick.cpp \
            core/cDeNovoGraphNode.cpp \
            core/cFragmentIons.cpp \
            core/cImzML.cpp \
+           core/cIsotopePatternCache.cpp \
            core/cMzML.cpp \
            core/cParameters.cpp \
            core/cPeak.cpp \

diff --git a/CycloBranch/CycloBranch-MacOSX.pro b/CycloBranch/CycloBranch-MacOSX.pro
@@ -6,7 +6,7 @@ TEMPLATE = app
 TARGET = CycloBranch
 QT += core gui widgets printsupport svg
 INCLUDEPATH += . core gui parallel /usr/local/opt/boost/include /usr/local/opt/xerces-c/include
-QMAKE_CXXFLAGS += -std=c++0x -DMACOSX -m64
+QMAKE_CXXFLAGS += -std=c++11 -DMACOSX -m64
 QMAKE_LIBS += -lboost_regex -lxerces-c
 QMAKE_LIBDIR = /usr/local/opt/boost/lib /usr/local/opt/xerces-c/lib
 OBJECTS_DIR = build/
@@ -23,6 +23,7 @@ HEADERS += core/cBrick.h \
            core/cDeNovoGraphNode.h \
            core/cFragmentIons.h \
            core/cImzML.h \
+           core/cIsotopePatternCache.h \
            core/cMzML.h \
            core/cParameters.h \
            core/cPeak.h \
@@ -80,6 +81,7 @@ SOURCES += core/cBrick.cpp \
            core/cDeNovoGraphNode.cpp \
            core/cFragmentIons.cpp \
            core/cImzML.cpp \
+           core/cIsotopePatternCache.cpp \
            core/cMzML.cpp \
            core/cParameters.cpp \
            core/cPeak.cpp \

diff --git a/CycloBranch/CycloBranch.desktop b/CycloBranch/CycloBranch.desktop
@@ -1,5 +1,5 @@
 [Desktop Entry]
-Comment=A tool for de novo sequencing of nonribosomal peptides from accurate product ion mass spectra. 
+Comment=CycloBranch 
 Exec=CycloBranch
 Icon=/usr/share/cyclobranch/images/cb.png
 Name=CycloBranch

diff --git a/CycloBranch/CycloBranch.vcxproj b/CycloBranch/CycloBranch.vcxproj
@@ -155,6 +155,7 @@
     <ClCompile Include="core\cDeNovoGraphNode.cpp" />
     <ClCompile Include="core\cFragmentIons.cpp" />
     <ClCompile Include="core\cImzML.cpp" />
+    <ClCompile Include="core\cIsotopePatternCache.cpp" />
     <ClCompile Include="core\cMzML.cpp" />
     <ClCompile Include="core\cParameters.cpp" />
     <ClCompile Include="core\cPeak.cpp" />
@@ -529,6 +530,7 @@
     <ClInclude Include="core\cDeNovoGraphNode.h" />
     <ClInclude Include="core\cFragmentIons.h" />
     <ClInclude Include="core\cImzML.h" />
+    <ClInclude Include="core\cIsotopePatternCache.h" />
     <ClInclude Include="core\cMzML.h" />
     <ClInclude Include="core\cParameters.h" />
     <ClInclude Include="core\cPeak.h" />

diff --git a/CycloBranch/CycloBranch.vcxproj.filters b/CycloBranch/CycloBranch.vcxproj.filters
@@ -452,6 +452,9 @@
     <ClCompile Include="gui\cChromatogramWindowWidget.cpp">
       <Filter>Source Files\gui</Filter>
     </ClCompile>
+    <ClCompile Include="core\cIsotopePatternCache.cpp">
+      <Filter>Source Files\core</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <CustomBuild Include="gui\cAboutWidget.h">
@@ -630,6 +633,9 @@
     <ClInclude Include="core\cMzML.h">
       <Filter>Header Files\core</Filter>
     </ClInclude>
+    <ClInclude Include="core\cIsotopePatternCache.h">
+      <Filter>Header Files\core</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ResourceCompile Include="cyclobranch.rc">

diff --git a/CycloBranch/core/cBrick.cpp b/CycloBranch/core/cBrick.cpp
@@ -1,5 +1,7 @@
 #include "core/cBrick.h"
 
+#include "core/cSummaryFormula.h"
+
 
 int getNumberOfBricks(const string& composition) {
 	if (composition.size() == 0) {
@@ -26,6 +28,7 @@ void cBrick::clear() {
 	acronyms.clear();
 	references.clear();
 	summary = "";
+	summarymap.clear();
 	mass = 0;
 	composition = "";
 	artificial = false;
@@ -54,6 +57,11 @@ string& cBrick::getSummary() {
 }
 
 
+map<string, int>& cBrick::getSummaryMap() {
+	return summarymap;
+}
+
+
 vector<string>& cBrick::getAcronyms() {
 	return acronyms;
 }
@@ -106,6 +114,12 @@ void cBrick::setSummary(const string& summary) {
 }
 
 
+void cBrick::createSummaryMap() {
+	summarymap.clear();
+	addStringFormulaToMap(summary, summarymap);
+}
+
+
 void cBrick::setAcronyms(const string& acronyms) {
 	this->acronyms.clear();
 	string s = "";
@@ -360,6 +374,7 @@ void cBrick::store(ofstream& os) {
 	storeStringVector(acronyms, os);
 	storeStringVector(references, os);
 	storeString(summary, os);
+	storeStringIntMap(summarymap, os);
 	os.write((char *)&mass, sizeof(double));
 	storeString(composition, os);
 	os.write((char *)&artificial, sizeof(bool));
@@ -372,6 +387,7 @@ void cBrick::load(ifstream& is) {
 	loadStringVector(acronyms, is);
 	loadStringVector(references, is);
 	loadString(summary, is);
+	loadStringIntMap(summarymap, is);
 	is.read((char *)&mass, sizeof(double));
 	loadString(composition, is);
 	is.read((char *)&artificial, sizeof(bool));

diff --git a/CycloBranch/core/cBrick.h b/CycloBranch/core/cBrick.h
@@ -12,6 +12,7 @@
 #include <string>
 #include <vector>
 #include <algorithm>
+#include <map>
 #include "core/utilities.h"
 
 using namespace std;
@@ -42,6 +43,7 @@ class cBrick {
 	vector<string> acronyms;
 	vector<string> references;
 	string summary;
+	map<string, int> summarymap;
 	double mass;
 	string composition;
 	bool artificial;
@@ -89,6 +91,13 @@ class cBrick {
 	string& getSummary();
 
 
+	/**
+		\brief Access to a map which stores a summary molecular formula of the brick.
+		\retval map<string, int> reference to a map
+	*/
+	map<string, int>& getSummaryMap();
+
+
 	/**
 		\brief Access to a vector of strings which stores acronyms of all izomers corresponding to the brick.
 		\retval reference to a vector of strings
@@ -142,10 +151,16 @@ class cBrick {
 	/**
 		\brief Set the summary molecular formula of the brick.
 		\param summary reference to a string
-	*/ 
+	*/
 	void setSummary(const string& summary);
 
 
+	/**
+		\brief Create an internal map of atoms from the summary formula.
+	*/
+	void createSummaryMap();
+
+
 	/**
 		\brief Set acronyms of all izomers corresponding to the brick.
 		\param acronyms reference to a string where the acronyms are separated by '/'

diff --git a/CycloBranch/core/cBricksDatabase.cpp b/CycloBranch/core/cBricksDatabase.cpp
@@ -1,6 +1,5 @@
 #include "core/cBricksDatabase.h"
 
-
 #include "gui/cMainThread.h"
 
 
@@ -184,6 +183,7 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 		pos = s.find('\t');
 		if (pos != string::npos) {
 			b.setSummary(s.substr(0, pos));
+			b.createSummaryMap();
 			s = s.substr(pos + 1);
 		}
 		else {

diff --git a/CycloBranch/core/cCandidate.cpp b/CycloBranch/core/cCandidate.cpp
@@ -885,7 +885,7 @@ bool cCandidate::compare(cCandidate& candidate) {
 }
 
 
-vector<nodeEdge> cCandidate::getPath() {
+vector<nodeEdge>& cCandidate::getPath() {
 	return path;
 }
 

diff --git a/CycloBranch/core/cCandidate.h b/CycloBranch/core/cCandidate.h
@@ -391,7 +391,7 @@ class cCandidate {
 		\brief Get a path in the de novo graph corresponding to the peptide sequence candidate.
 		\retval vector<nodeEdge> vector of pairs node and edge
 	*/ 
-	vector<nodeEdge> getPath();
+	vector<nodeEdge>& getPath();
 
 
 	/**

diff --git a/CycloBranch/core/cDeNovoGraph.cpp b/CycloBranch/core/cDeNovoGraph.cpp
@@ -162,13 +162,17 @@ int cDeNovoGraph::createGraph(bool& terminatecomputation) {
 	sortedpeaklist.removeChargeVariants(parameters->precursorcharge, parameters->fragmentmasserrortolerance);
 	*os << "Number of nodes after deconvolution: " << sortedpeaklist.size() << endl;
 
-	// remove dehydrated peaks
-	sortedpeaklist.removeNeutralLoss(- H2O, parameters->precursorcharge, parameters->fragmentmasserrortolerance);
-	*os << "Number of nodes when dehydrated ions are removed: " << sortedpeaklist.size() << endl;
+	//if (!parameters->generateisotopepattern) {
 
-	// remove deamidated peaks
-	sortedpeaklist.removeNeutralLoss(- NH3, parameters->precursorcharge, parameters->fragmentmasserrortolerance);
-	*os << "Number of nodes when deamidated ions are removed: " << sortedpeaklist.size() << endl;	
+		// remove dehydrated peaks
+		sortedpeaklist.removeNeutralLoss(-H2O, parameters->precursorcharge, parameters->fragmentmasserrortolerance);
+		*os << "Number of nodes when dehydrated ions are removed: " << sortedpeaklist.size() << endl;
+
+		// remove deamidated peaks
+		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*(H - e);
 	string negativeshiftsummary = (parameters->precursorcharge > 0)?"":"H-2+-2";

diff --git a/CycloBranch/core/cDeNovoGraphNode.cpp b/CycloBranch/core/cDeNovoGraphNode.cpp
@@ -13,6 +13,11 @@ void nodeEdge::load(ifstream& is) {
 }
 
 
+bool operator == (nodeEdge const& a, nodeEdge const& b) {
+	return (a.nodeid == b.nodeid) && (a.edgeid == b.edgeid);
+}
+
+
 bool operator == (cEdge const& a, cEdge const& b) {
 	return (a.targetnode == b.targetnode) && (a.brickid == b.brickid) && (a.sourceion == b.sourceion) && (a.targetion == b.targetion);
 }

diff --git a/CycloBranch/core/cDeNovoGraphNode.h b/CycloBranch/core/cDeNovoGraphNode.h
@@ -50,6 +50,15 @@ struct nodeEdge {
 };
 
 
+/**
+	\brief Overloaded operator ==.
+	\param a first nodeEdge
+	\param b second nodeEdge
+	\retval bool true when nodeEdges are equal
+*/
+bool operator == (nodeEdge const& a, nodeEdge const& b);
+
+
 /**
 	\brief The structure representing an outgoing edge from a node.
 */