release 1.0.739

novak-jiri · Feb 21, 2018 · 3e5d837 · 3e5d837
1 parent 642a026
commit 3e5d837
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Showing 31 changed files with 1,418 additions and 527 deletions.
diff --git a/CycloBranch/CycloBranch.vcxproj b/CycloBranch/CycloBranch.vcxproj
@@ -157,6 +157,7 @@
     <ClCompile Include="core\cParameters.cpp" />
     <ClCompile Include="core\cPeak.cpp" />
     <ClCompile Include="core\cPeaksList.cpp" />
+    <ClCompile Include="core\cSummaryFormula.cpp" />
     <ClCompile Include="core\cTheoreticalSpectrum.cpp" />
     <ClCompile Include="core\cTheoreticalSpectrumList.cpp" />
     <ClCompile Include="GeneratedFiles\Debug\moc_cAboutWidget.cpp">
@@ -187,6 +188,10 @@
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cLassoWidget.cpp">
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
+    </ClCompile>
     <ClCompile Include="GeneratedFiles\Debug\moc_cLinearWidget.cpp">
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
@@ -239,6 +244,10 @@
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cLassoWidget.cpp">
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
+      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
+    </ClCompile>
     <ClCompile Include="GeneratedFiles\Release\moc_cLinearWidget.cpp">
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
       <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
@@ -269,6 +278,7 @@
     <ClCompile Include="gui\cFragmentIonsListWidget.cpp" />
     <ClCompile Include="gui\cGraphicalSpectrumWidget.cpp" />
     <ClCompile Include="gui\cGraphWidget.cpp" />
+    <ClCompile Include="gui\cLassoWidget.cpp" />
     <ClCompile Include="gui\cLinearWidget.cpp" />
     <ClCompile Include="gui\cMainThread.cpp" />
     <ClCompile Include="gui\cMainWindow.cpp" />
@@ -289,7 +299,26 @@
     <ClInclude Include="core\cParameters.h" />
     <ClInclude Include="core\cPeak.h" />
     <ClInclude Include="core\cPeaksList.h" />
+    <ClInclude Include="core\cSummaryFormula.h" />
     <ClInclude Include="core\cTheoreticalSpectrum.h" />
+    <CustomBuild Include="gui\cLassoWidget.h">
+      <AdditionalInputs Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(QTDIR)\bin\moc.exe;%(FullPath)</AdditionalInputs>
+      <Message Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">Moc%27ing cLassoWidget.h...</Message>
+      <Outputs Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">.\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp</Outputs>
+      <Command Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">"$(QTDIR)\bin\moc.exe"  "%(FullPath)" -o ".\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp"  -DUNICODE -DWIN32 -DWIN64 -DQT_DLL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB "-I.\GeneratedFiles" "-I." "-I$(QTDIR)\include" "-I.\GeneratedFiles\$(ConfigurationName)\." "-I$(QTDIR)\include\QtCore" "-I$(QTDIR)\include\QtGui" "-I$(QTDIR)\include\QtWidgets"</Command>
+      <AdditionalInputs Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(QTDIR)\bin\moc.exe;%(FullPath)</AdditionalInputs>
+      <Message Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">Moc%27ing cLassoWidget.h...</Message>
+      <Outputs Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">.\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp</Outputs>
+      <Command Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">"$(QTDIR)\bin\moc.exe"  "%(FullPath)" -o ".\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp"  -DUNICODE -DWIN32 -DWIN64 -DQT_DLL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB "-I.\GeneratedFiles" "-I." "-I$(QTDIR)\include" "-I.\GeneratedFiles\$(ConfigurationName)\." "-I$(QTDIR)\include\QtCore" "-I$(QTDIR)\include\QtGui" "-I$(QTDIR)\include\QtWidgets"</Command>
+      <AdditionalInputs Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(QTDIR)\bin\moc.exe;%(FullPath)</AdditionalInputs>
+      <Message Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">Moc%27ing cLassoWidget.h...</Message>
+      <Outputs Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">.\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp</Outputs>
+      <Command Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">"$(QTDIR)\bin\moc.exe"  "%(FullPath)" -o ".\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp"  -DUNICODE -DWIN32 -DWIN64 -DQT_DLL -DQT_NO_DEBUG -DNDEBUG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB "-I.\GeneratedFiles" "-I." "-I$(QTDIR)\include" "-I.\GeneratedFiles\$(ConfigurationName)\." "-I$(QTDIR)\include\QtCore" "-I$(QTDIR)\include\QtGui" "-I$(QTDIR)\include\QtWidgets"</Command>
+      <AdditionalInputs Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(QTDIR)\bin\moc.exe;%(FullPath)</AdditionalInputs>
+      <Message Condition="'$(Configuration)|$(Platform)'=='Release|x64'">Moc%27ing cLassoWidget.h...</Message>
+      <Outputs Condition="'$(Configuration)|$(Platform)'=='Release|x64'">.\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp</Outputs>
+      <Command Condition="'$(Configuration)|$(Platform)'=='Release|x64'">"$(QTDIR)\bin\moc.exe"  "%(FullPath)" -o ".\GeneratedFiles\$(ConfigurationName)\moc_%(Filename).cpp"  -DUNICODE -DWIN32 -DWIN64 -DQT_DLL -DQT_NO_DEBUG -DNDEBUG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_WIDGETS_LIB "-I.\GeneratedFiles" "-I." "-I$(QTDIR)\include" "-I.\GeneratedFiles\$(ConfigurationName)\." "-I$(QTDIR)\include\QtCore" "-I$(QTDIR)\include\QtGui" "-I$(QTDIR)\include\QtWidgets"</Command>
+    </CustomBuild>
     <CustomBuild Include="gui\cLinearWidget.h">
       <AdditionalInputs Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(QTDIR)\bin\moc.exe;%(FullPath)</AdditionalInputs>
       <Message Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">Moc%27ing cLinearWidget.h...</Message>

diff --git a/CycloBranch/CycloBranch.vcxproj.filters b/CycloBranch/CycloBranch.vcxproj.filters
@@ -200,6 +200,18 @@
     <ClCompile Include="gui\cLinearWidget.cpp">
       <Filter>Source Files\gui</Filter>
     </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cLassoWidget.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cLassoWidget.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cLassoWidget.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="core\cSummaryFormula.cpp">
+      <Filter>Source Files\core</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <CustomBuild Include="gui\cAboutWidget.h">
@@ -244,6 +256,9 @@
     <CustomBuild Include="gui\cLinearWidget.h">
       <Filter>Header Files\gui</Filter>
     </CustomBuild>
+    <CustomBuild Include="gui\cLassoWidget.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="core\cBrick.h">
@@ -279,5 +294,8 @@
     <ClInclude Include="core\cCandidateSet.h">
       <Filter>Header Files\core</Filter>
     </ClInclude>
+    <ClInclude Include="core\cSummaryFormula.h">
+      <Filter>Header Files\core</Filter>
+    </ClInclude>
   </ItemGroup>
 </Project>
diff --git a/CycloBranch/core/cBricksDatabase.cpp b/CycloBranch/core/cBricksDatabase.cpp
@@ -117,6 +117,7 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 
 	bool error = false;
 	errormessage = "";
+	cSummaryFormula formula;
 
 	while (stream.good()) {
 		getline(stream,s);
@@ -182,9 +183,13 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 		if (!b.empty()) {
 
 			// calculate mass from the summary
-			b.setMass(getMassFromResidueSummary(b.getSummary(), error, errormessage));
-
-			if (error) {
+			formula.clear();
+			formula.setFormula(b.getSummary());
+			if (formula.isValid(errormessage)) {
+				b.setMass(formula.getMass());
+			}
+			else {
+				error = true;
 				break;
 			}
 
@@ -195,7 +200,6 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 			}
 
 			bricks.push_back(b);
-			//cout << b.getSummary() << " " << b.getMass() << endl;
 		}
 	}
 

diff --git a/CycloBranch/core/cBricksDatabase.h b/CycloBranch/core/cBricksDatabase.h
@@ -15,6 +15,7 @@
 
 
 #include "core/cBrick.h"
+#include "core/cSummaryFormula.h"
 
 
 using namespace std;

diff --git a/CycloBranch/core/cCandidate.cpp b/CycloBranch/core/cCandidate.cpp
@@ -487,38 +487,6 @@ int cCandidate::getBranchEnd() {
 }
 
 
-void cCandidate::getBackboneAcronyms(cBricksDatabase& bricksdatabase, vector<string>& acronyms) {
-	vector<int> bricks;
-	cBrick b;
-	b.clear();
-	b.setComposition(getComposition(), false);
-	b.explodeToIntComposition(bricks);
-
-	acronyms.clear();
-	for (int i = 0; i < (int)bricks.size(); i++) {
-		if ((branchstart >= 0) && (branchend >= 0) && ((i <= branchstart) || (i > branchend))) {
-			acronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
-		}
-	}
-}
-
-
-void cCandidate::getBranchAcronyms(cBricksDatabase& bricksdatabase, vector<string>& acronyms) {
-	vector<int> bricks;
-	cBrick b;
-	b.clear();
-	b.setComposition(getComposition(), false);
-	b.explodeToIntComposition(bricks);
-
-	acronyms.clear();
-	for (int i = 0; i < (int)bricks.size(); i++) {
-		if ((branchstart >= 0) && (branchend >= 0) && (i > branchstart) && (i <= branchend)) {
-			acronyms.push_back(bricksdatabase[bricks[i] - 1].getAcronymsAsString());
-		}
-	}
-}
-
-
 void cCandidate::getPermutationsOfBranches(vector<TRotationInfo>& tpermutations) {
 	tpermutations.resize(6);
 	for (int i = 0; i < (int)tpermutations.size(); i++) {
@@ -738,7 +706,6 @@ double cCandidate::getPrecursorMass(cBricksDatabase& brickdatabasewithcombinatio
 	}
 
 	return mass;
-
 }
 
 
@@ -906,6 +873,52 @@ void cCandidate::getLassoRotations(vector<cCandidate>& lassorotations, bool incl
 }
 
 
+string cCandidate::getSummaryFormula(cParameters& parameters) {
+	cBrick b;
+	vector<int> bricks;
+	b.setComposition(internalcomposition, false);
+	b.explodeToIntComposition(bricks);
+
+	cSummaryFormula formula;
+	string summary;
+
+	switch (parameters.peptidetype)
+	{
+	case linear:
+	case linearpolysaccharide:
+		summary = "H2O";
+		formula.addFormula(summary);
+		formula.addFormula(parameters.searchedmodifications[startmodifID].summary);
+		formula.addFormula(parameters.searchedmodifications[endmodifID].summary);
+		break;
+	case cyclic: 
+		break;
+	case branched:
+		summary = "H2O";
+		formula.addFormula(summary);
+		formula.addFormula(parameters.searchedmodifications[startmodifID].summary);
+		formula.addFormula(parameters.searchedmodifications[endmodifID].summary);
+		formula.addFormula(parameters.searchedmodifications[middlemodifID].summary);
+		break;
+	case lasso:
+		formula.addFormula(parameters.searchedmodifications[middlemodifID].summary);
+		break;
+	}
+
+	bool partial = false;
+	for (int i = 0; i < (int)bricks.size(); i++) {
+		if (bricks[i] - 1 < (int)parameters.bricksdatabase.size()) {
+			formula.addFormula(parameters.bricksdatabase[bricks[i] - 1].getSummary());
+		}
+		else {
+			partial = true;
+		}
+	}
+
+	return partial?formula.getFormula() + " (partial)":formula.getFormula();
+}
+
+
 void cCandidate::store(ofstream& os) {
 	int size;
 

diff --git a/CycloBranch/core/cCandidate.h b/CycloBranch/core/cCandidate.h
@@ -12,9 +12,9 @@
 #include <string>
 
 #include "core/cParameters.h"
-#include "core/cFragmentIons.h"
 #include "core/cBricksDatabase.h"
 #include "core/cDeNovoGraphNode.h"
+#include "core/cSummaryFormula.h"
 
 class cCandidateSet;
 
@@ -289,22 +289,6 @@ class cCandidate {
 	int getBranchEnd();
 
 
-	/**
-		\brief Get acronyms of blocks on a backbone of a branched peptide.
-		\param bricksdatabase reference to the database of bricks
-		\param acronyms an output vector of string acronyms
-	*/ 
-	void getBackboneAcronyms(cBricksDatabase& bricksdatabase, vector<string>& acronyms);
-
-
-	/**
-		\brief Get acronyms of blocks on a branch of a branched peptide.
-		\param bricksdatabase reference to the database of bricks
-		\param acronyms an output vector of string acronyms
-	*/ 
-	void getBranchAcronyms(cBricksDatabase& bricksdatabase, vector<string>& acronyms);
-
-
 	/**
 		\brief Get permutations of branches a branched peptide.
 		\param tpermutations reference to an output vector of auxiliary structures where permutations will be stored
@@ -426,6 +410,14 @@ class cCandidate {
 	void getLassoRotations(vector<cCandidate>& lassorotations, bool includerevertedrotations);
 
 
+	/**
+		\brief Get the summary formula of the peptide sequence candidate.
+		\param parameters a reference to the parameters of the application
+		\retval string the summary formula
+	*/ 
+	string getSummaryFormula(cParameters& parameters);
+
+
 	/**
 		\brief Store the structure into an output stream.
 		\param os an output stream