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release 2.0.8
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Jiri Novak committed Mar 11, 2020
1 parent 445ab04 commit 44ac497
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Showing 84 changed files with 4,613 additions and 3,151 deletions.
14 changes: 14 additions & 0 deletions CycloBranch/CycloBranch-Linux.pro
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ HEADERS += core/cBrick.h \
core/cDeNovoGraph.h \
core/cDeNovoGraphNode.h \
core/cFragmentIons.h \
core/cGlobalPreferences.h \
core/cImzML.h \
core/cIsotopePatternCache.h \
core/cMzML.h \
Expand Down Expand Up @@ -62,6 +63,12 @@ HEADERS += core/cBrick.h \
gui/cMultipleButtonDelegate.h \
gui/cNeutralLossesListWidget.h \
gui/cParametersWidget.h \
gui/cPreferencesDialog.h \
gui/cPreferencesIonTypeDialog.h \
gui/cPreferencesTabDataProcessing.h \
gui/cPreferencesTabDirectories.h \
gui/cPreferencesTabIonTypes.h \
gui/cPreferencesTabURLs.h \
gui/cSequenceDatabaseProxyModel.h \
gui/cSequenceDatabaseWidget.h \
gui/cSpectrumDetailProxyModel.h \
Expand All @@ -79,6 +86,7 @@ SOURCES += core/cBrick.cpp \
core/cDeNovoGraph.cpp \
core/cDeNovoGraphNode.cpp \
core/cFragmentIons.cpp \
core/cGlobalPreferences.cpp \
core/cImzML.cpp \
core/cIsotopePatternCache.cpp \
core/cMzML.cpp \
Expand Down Expand Up @@ -121,6 +129,12 @@ SOURCES += core/cBrick.cpp \
gui/cMultipleButtonDelegate.cpp \
gui/cNeutralLossesListWidget.cpp \
gui/cParametersWidget.cpp \
gui/cPreferencesDialog.cpp \
gui/cPreferencesIonTypeDialog.cpp \
gui/cPreferencesTabDataProcessing.cpp \
gui/cPreferencesTabDirectories.cpp \
gui/cPreferencesTabIonTypes.cpp \
gui/cPreferencesTabURLs.cpp \
gui/cSequenceDatabaseProxyModel.cpp \
gui/cSequenceDatabaseWidget.cpp \
gui/cSpectrumDetailProxyModel.cpp \
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14 changes: 14 additions & 0 deletions CycloBranch/CycloBranch-MacOSX.pro
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ HEADERS += core/cBrick.h \
core/cDeNovoGraph.h \
core/cDeNovoGraphNode.h \
core/cFragmentIons.h \
core/cGlobalPreferences.h \
core/cImzML.h \
core/cIsotopePatternCache.h \
core/cMzML.h \
Expand Down Expand Up @@ -64,6 +65,12 @@ HEADERS += core/cBrick.h \
gui/cMultipleButtonDelegate.h \
gui/cNeutralLossesListWidget.h \
gui/cParametersWidget.h \
gui/cPreferencesDialog.h \
gui/cPreferencesIonTypeDialog.h \
gui/cPreferencesTabDataProcessing.h \
gui/cPreferencesTabDirectories.h \
gui/cPreferencesTabIonTypes.h \
gui/cPreferencesTabURLs.h \
gui/cSequenceDatabaseProxyModel.h \
gui/cSequenceDatabaseWidget.h \
gui/cSpectrumDetailProxyModel.h \
Expand All @@ -81,6 +88,7 @@ SOURCES += core/cBrick.cpp \
core/cDeNovoGraph.cpp \
core/cDeNovoGraphNode.cpp \
core/cFragmentIons.cpp \
core/cGlobalPreferences.cpp \
core/cImzML.cpp \
core/cIsotopePatternCache.cpp \
core/cMzML.cpp \
Expand Down Expand Up @@ -123,6 +131,12 @@ SOURCES += core/cBrick.cpp \
gui/cMultipleButtonDelegate.cpp \
gui/cNeutralLossesListWidget.cpp \
gui/cParametersWidget.cpp \
gui/cPreferencesDialog.cpp \
gui/cPreferencesIonTypeDialog.cpp \
gui/cPreferencesTabDataProcessing.cpp \
gui/cPreferencesTabDirectories.cpp \
gui/cPreferencesTabIonTypes.cpp \
gui/cPreferencesTabURLs.cpp \
gui/cSequenceDatabaseProxyModel.cpp \
gui/cSequenceDatabaseWidget.cpp \
gui/cSpectrumDetailProxyModel.cpp \
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164 changes: 164 additions & 0 deletions CycloBranch/CycloBranch.vcxproj
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78 changes: 78 additions & 0 deletions CycloBranch/CycloBranch.vcxproj.filters
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Expand Up @@ -464,6 +464,63 @@
<ClCompile Include="gui\cNeutralLossesListWidget.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="gui\cPreferencesDialog.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Debug\moc_cPreferencesDialog.cpp">
<Filter>Generated Files\Debug</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Release\moc_cPreferencesDialog.cpp">
<Filter>Generated Files\Release</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Debug\moc_cPreferencesTabIonTypes.cpp">
<Filter>Generated Files\Debug</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Release\moc_cPreferencesTabIonTypes.cpp">
<Filter>Generated Files\Release</Filter>
</ClCompile>
<ClCompile Include="gui\cPreferencesTabIonTypes.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Debug\moc_cPreferencesTabURLs.cpp">
<Filter>Generated Files\Debug</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Release\moc_cPreferencesTabURLs.cpp">
<Filter>Generated Files\Release</Filter>
</ClCompile>
<ClCompile Include="gui\cPreferencesTabURLs.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="gui\cPreferencesTabDirectories.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Debug\moc_cPreferencesTabDirectories.cpp">
<Filter>Generated Files\Debug</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Release\moc_cPreferencesTabDirectories.cpp">
<Filter>Generated Files\Release</Filter>
</ClCompile>
<ClCompile Include="core\cGlobalPreferences.cpp">
<Filter>Source Files\core</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Debug\moc_cPreferencesTabDataProcessing.cpp">
<Filter>Generated Files\Debug</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Release\moc_cPreferencesTabDataProcessing.cpp">
<Filter>Generated Files\Release</Filter>
</ClCompile>
<ClCompile Include="gui\cPreferencesTabDataProcessing.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="gui\cPreferencesIonTypeDialog.cpp">
<Filter>Source Files\gui</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Debug\moc_cPreferencesIonTypeDialog.cpp">
<Filter>Generated Files\Debug</Filter>
</ClCompile>
<ClCompile Include="GeneratedFiles\Release\moc_cPreferencesIonTypeDialog.cpp">
<Filter>Generated Files\Release</Filter>
</ClCompile>
</ItemGroup>
<ItemGroup>
<CustomBuild Include="gui\cAboutWidget.h">
Expand Down Expand Up @@ -592,6 +649,24 @@
<CustomBuild Include="gui\cNeutralLossesListWidget.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
<CustomBuild Include="gui\cPreferencesDialog.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
<CustomBuild Include="gui\cPreferencesTabIonTypes.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
<CustomBuild Include="gui\cPreferencesTabURLs.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
<CustomBuild Include="gui\cPreferencesTabDirectories.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
<CustomBuild Include="gui\cPreferencesTabDataProcessing.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
<CustomBuild Include="gui\cPreferencesIonTypeDialog.h">
<Filter>Header Files\gui</Filter>
</CustomBuild>
</ItemGroup>
<ItemGroup>
<ClInclude Include="core\cBrick.h">
Expand Down Expand Up @@ -648,6 +723,9 @@
<ClInclude Include="core\cIsotopePatternCache.h">
<Filter>Header Files\core</Filter>
</ClInclude>
<ClInclude Include="core\cGlobalPreferences.h">
<Filter>Header Files\core</Filter>
</ClInclude>
</ItemGroup>
<ItemGroup>
<ResourceCompile Include="cyclobranch.rc">
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88 changes: 14 additions & 74 deletions CycloBranch/Settings/database_search/ms/peptides_test.ini
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Expand Up @@ -5,7 +5,6 @@ precursormass=0
precursormasserrortolerance=1
precursorcharge=1
fragmentmasserrortolerance=1
masserrortolerancefordeisotoping=1
minimumrelativeintensitythreshold=0
minimummz=150
brickdatabase=
Expand All @@ -18,10 +17,6 @@ maximumnumberofthreads=1
scoretype=3
hitsreported=1000
sequencetag=
fragmentiontype_0=1
fragmentiontype_1=0
fragmentiontype_2=0
clearhitswithoutparent=0
cyclicnterminus=0
cycliccterminus=0
enablescrambling=0
Expand All @@ -31,81 +26,26 @@ searchedsequence=
searchedsequenceNtermmodif=
searchedsequenceCtermmodif=
searchedsequenceTmodif=
fragmentiontype_3=0
fragmentiontype_4=0
fragmentiontype_5=0
fragmentiontype_6=0
fragmentiontype_7=0
fragmentiontype_8=0
fragmentiontype_9=0
fragmentiontype_10=0
fragmentiontype_11=0
fragmentiontype_12=0
fragmentiontype_13=0
fragmentiontype_14=0
fragmentiontype_15=0
precursoradduct=
modificationsfile=
scannumber=1
minimumabsoluteintensitythreshold=0
fwhm=0.05
similaritysearch=0
regularblocksorder=0
fragmentiontype_16=0
fragmentiontype_17=0
fragmentiontype_18=0
fragmentiontype_19=0
fragmentiontype_20=0
fragmentiontype_21=0
fragmentiontype_22=0
fragmentiontype_23=0
fragmentiontype_24=0
fragmentiontype_25=0
fragmentiontype_26=0
fragmentiontype_27=0
fragmentiontype_28=0
fragmentiontype_29=0
fragmentiontype_30=0
fragmentiontype_31=0
fragmentiontype_32=0
fragmentiontype_33=0
fragmentiontype_34=0
fragmentiontype_35=0
fragmentiontype_36=0
fragmentiontype_37=0
fragmentiontype_38=0
fragmentiontype_39=0
fragmentiontype_40=0
fragmentiontype_41=0
fragmentiontype_42=0
fragmentiontype_43=0
fragmentiontype_44=0
fragmentiontype_45=0
fragmentiontype_46=0
fragmentiontype_47=0
fragmentiontype_48=0
fragmentiontype_49=0
fragmentiontype_50=0
fragmentiontype_51=0
fragmentiontype_52=0
fragmentiontype_53=0
fragmentiontype_54=0
fragmentiontype_55=0
fragmentiontype_56=0
fragmentiontype_57=0
fragmentiontype_58=0
fragmentiontype_59=0
fragmentiontype_60=0
fragmentiontype_61=0
fragmentiontype_62=0
fragmentiontype_63=0
fragmentiontype_64=0
fragmentiontype_65=0
fragmentiontype_66=0
fragmentiontype_67=0
fragmentiontype_68=0
fragmentiontype_69=0
fragmentiontype_70=0
fragmentiontype_71=0
generateisotopepattern=0
minimumpatternsize=1
useprofiledata=0
maximummz=0
internalfragments=0
iontype_0=[M+H]+
maximumcombinedlosses=2
reportunmatchedtheoreticalpeaks=0
minimumfeaturesize=1
minimumiontypes=1
basicformulacheck=1
advancedformulacheck=1
noratiocheck=1
mzdifftolerance=0
intensitytolerance=0
searchedsequenceformula=
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