release 1.1.170

novak-jiri · Feb 21, 2018 · 587b546 · 587b546
1 parent 50ca5e2
commit 587b546
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Showing 49 changed files with 2,770 additions and 789 deletions.
diff --git a/CycloBranch/CycloBranch-Linux.pro b/CycloBranch/CycloBranch-Linux.pro
@@ -45,6 +45,8 @@ HEADERS += core/cAllocator.h \
            gui/cFragmentIonsListWidget.h \
            gui/cGraphWidget.h \
            gui/cHTMLExportDialog.h \
+           gui/cImageWindow.h \
+           gui/cImageWindowWidget.h \
            gui/cLinearWidget.h \
            gui/cMainThread.h \
            gui/cMainWindow.h \
@@ -53,6 +55,7 @@ HEADERS += core/cAllocator.h \
            gui/cSequenceDatabaseWidget.h \
            gui/cSpectrumDetailWidget.h \
            gui/cSpectrumSceneWidget.h \
+           gui/cSummaryPeaksTableWidget.h \
            parallel/cGraphReaderThread.h \
            parallel/cSpectrumComparatorThread.h
 SOURCES += core/cBrick.cpp \
@@ -86,6 +89,8 @@ SOURCES += core/cBrick.cpp \
            gui/cFragmentIonsListWidget.cpp \
            gui/cGraphWidget.cpp \
            gui/cHTMLExportDialog.cpp \
+           gui/cImageWindow.cpp \
+           gui/cImageWindowWidget.cpp \
            gui/cLinearWidget.cpp \
            gui/cMainThread.cpp \
            gui/cMainWindow.cpp \
@@ -94,6 +99,7 @@ SOURCES += core/cBrick.cpp \
            gui/cSequenceDatabaseWidget.cpp \
            gui/cSpectrumDetailWidget.cpp \
            gui/cSpectrumSceneWidget.cpp \
+           gui/cSummaryPeaksTableWidget.cpp \
            parallel/cGraphReaderThread.cpp \
            parallel/cSpectrumComparatorThread.cpp \
            main.cpp
diff --git a/CycloBranch/CycloBranch-MacOSX.pro b/CycloBranch/CycloBranch-MacOSX.pro
@@ -53,6 +53,8 @@ HEADERS += core/cAllocator.h \
            gui/cFragmentIonsListWidget.h \
            gui/cGraphWidget.h \
            gui/cHTMLExportDialog.h \
+           gui/cImageWindow.h \
+           gui/cImageWindowWidget.h \
            gui/cLinearWidget.h \
            gui/cMainThread.h \
            gui/cMainWindow.h \
@@ -61,6 +63,7 @@ HEADERS += core/cAllocator.h \
            gui/cSequenceDatabaseWidget.h \
            gui/cSpectrumDetailWidget.h \
            gui/cSpectrumSceneWidget.h \
+           gui/cSummaryPeaksTableWidget.h \
            parallel/cGraphReaderThread.h \
            parallel/cSpectrumComparatorThread.h
 SOURCES += core/cBrick.cpp \
@@ -94,6 +97,8 @@ SOURCES += core/cBrick.cpp \
            gui/cFragmentIonsListWidget.cpp \
            gui/cGraphWidget.cpp \
            gui/cHTMLExportDialog.cpp \
+           gui/cImageWindow.cpp \
+           gui/cImageWindowWidget.cpp \
            gui/cLinearWidget.cpp \
            gui/cMainThread.cpp \
            gui/cMainWindow.cpp \
@@ -102,6 +107,7 @@ SOURCES += core/cBrick.cpp \
            gui/cSequenceDatabaseWidget.cpp \
            gui/cSpectrumDetailWidget.cpp \
            gui/cSpectrumSceneWidget.cpp \
+           gui/cSummaryPeaksTableWidget.cpp \
            parallel/cGraphReaderThread.cpp \
            parallel/cSpectrumComparatorThread.cpp \
            main.cpp
diff --git a/CycloBranch/CycloBranch.vcxproj b/CycloBranch/CycloBranch.vcxproj
diff --git a/CycloBranch/CycloBranch.vcxproj.filters b/CycloBranch/CycloBranch.vcxproj.filters
@@ -314,6 +314,33 @@
     <ClCompile Include="core\cImzML.cpp">
       <Filter>Source Files\core</Filter>
     </ClCompile>
+    <ClCompile Include="gui\cSummaryPeaksTableWidget.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cSummaryPeaksTableWidget.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cSummaryPeaksTableWidget.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cImageWindow.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cImageWindow.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cImageWindow.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Debug\moc_cImageWindowWidget.cpp">
+      <Filter>Generated Files\Debug</Filter>
+    </ClCompile>
+    <ClCompile Include="GeneratedFiles\Release\moc_cImageWindowWidget.cpp">
+      <Filter>Generated Files\Release</Filter>
+    </ClCompile>
+    <ClCompile Include="gui\cImageWindowWidget.cpp">
+      <Filter>Source Files\gui</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <CustomBuild Include="gui\cAboutWidget.h">
@@ -394,6 +421,15 @@
     <CustomBuild Include="gui\cHTMLExportDialog.h">
       <Filter>Header Files\gui</Filter>
     </CustomBuild>
+    <CustomBuild Include="gui\cSummaryPeaksTableWidget.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
+    <CustomBuild Include="gui\cImageWindow.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
+    <CustomBuild Include="gui\cImageWindowWidget.h">
+      <Filter>Header Files\gui</Filter>
+    </CustomBuild>
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="core\cBrick.h">

diff --git a/CycloBranch/core/cBrick.cpp b/CycloBranch/core/cBrick.cpp
@@ -50,7 +50,7 @@ void cBrick::clear() {
 	mass = 0;
 	composition = "";
 	artificial = false;
-	residuelosstype = water;
+	residuelosstype = h2o_loss;
 }
 
 

diff --git a/CycloBranch/core/cBrick.h b/CycloBranch/core/cBrick.h
@@ -21,9 +21,18 @@ using namespace std;
 	\brief Residue loss types.
 */
 enum eResidueLossType {
-	water = 0,
-	h2,
-	h2o2
+	h2o_loss = 0,
+	h2_loss
+};
+
+
+/**
+	\brief Precursor loss types.
+*/
+enum eKetidePrecursorType {
+	ketide_precursor_h2o = 0,
+	ketide_precursor_h2,
+	ketide_precursor_h2o2
 };
 
 

diff --git a/CycloBranch/core/cBricksDatabase.cpp b/CycloBranch/core/cBricksDatabase.cpp
@@ -67,7 +67,7 @@ bool cBricksDatabase::nextCombination(vector<int>& combarray, int numberofbasicb
 		combarray[pointer]++;
 
 		// set combarray[pointer] to the maximum value when outside of the mass range
-		mass = getMassOfComposition(combarray);
+		mass = getMassOfComposition(combarray, numberofbasicbricks);
 
 		if ((cyFlag == 0) && (combarray[pointer] <= numberofbasicbricks) && (((maximumcumulativemass > 0) && (mass > maximumcumulativemass)) || (mass > neutralprecursormass))) {
 			combarray[pointer] = numberofbasicbricks + 1;
@@ -82,7 +82,7 @@ bool cBricksDatabase::nextCombination(vector<int>& combarray, int numberofbasicb
 				}
 
 				// skip combinations outside of the mass range
-				mass = getMassOfComposition(combarray);
+				mass = getMassOfComposition(combarray, numberofbasicbricks);
 
 				while ((combarray[pointer] <= numberofbasicbricks) && (pointer < maximumbricksincombination - 1) && (((maximumcumulativemass > 0) && (mass > maximumcumulativemass)) || (mass > neutralprecursormass))) {
 					pointer++;
@@ -92,7 +92,7 @@ bool cBricksDatabase::nextCombination(vector<int>& combarray, int numberofbasicb
 						combarray[i] = combarray[pointer];
 					}
 
-					mass = getMassOfComposition(combarray);
+					mass = getMassOfComposition(combarray, numberofbasicbricks);
 				}
 
 				if ((combarray[pointer] > numberofbasicbricks) || ((maximumcumulativemass > 0) && (mass > maximumcumulativemass)) || (mass > neutralprecursormass)) {
@@ -128,7 +128,7 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 	size_t pos;
 	double mass;
 
-#if POLYKETIDE_SIDEROPHORES == 1
+#if OLIGOKETIDES == 1
 	regex rx;
 	string name;
 #endif
@@ -165,17 +165,12 @@ int cBricksDatabase::loadFromPlainTextStream(ifstream &stream, string& errormess
 			break;
 		}
 
-#if POLYKETIDE_SIDEROPHORES == 1
+#if OLIGOKETIDES == 1
 		name = b.getName();
 
 		rx = "^\\(-2H\\) ";
 		if (regex_search(name, rx)) {
-			b.setResidueLossType(h2);
-		}
-
-		rx = "^\\(-2OH\\) ";
-		if (regex_search(name, rx)) {
-			b.setResidueLossType(h2o2);
+			b.setResidueLossType(h2_loss);
 		}
 #endif
 
@@ -284,11 +279,11 @@ cBrick& cBricksDatabase::operator[](int position) {
 }
 
 
-double cBricksDatabase::getMassOfComposition(vector<int>& combarray) {
+double cBricksDatabase::getMassOfComposition(vector<int>& combarray, int numberofbasicbricks) {
 	double mass = 0;
 	int i = 0;
 	while (i < (int)combarray.size()) {
-		if (combarray[i] > 0) {
+		if ((combarray[i] > 0) && (combarray[i] <= numberofbasicbricks)) {
 			mass += bricks[combarray[i] - 1].getMass();
 		}
 		i++;
@@ -554,31 +549,37 @@ void cBricksDatabase::load(ifstream& is) {
 }
 
 
-#if POLYKETIDE_SIDEROPHORES == 1
+#if OLIGOKETIDES == 1
 
 
-bool cBricksDatabase::checkPolyketideBlocks(cBrick& brickseries) {
+bool cBricksDatabase::checkKetideBlocks(cBrick& brickseries) {
 	vector<int> intcomposition;
 	brickseries.explodeToIntComposition(intcomposition);
 
 	if (intcomposition.size() == 0) {
 		return false;
 	}
 
-	int hydrogens = 0;
-	int hydroxyls = 0;
+	int h2_blocks = 0;
+	int h2o_blocks = 0;
 	for (int i = 0; i < (int)intcomposition.size(); i++) {
-		if (bricks[intcomposition[i] - 1].getResidueLossType() == h2) {
-			hydrogens++;
+		if (bricks[intcomposition[i] - 1].getResidueLossType() == h2_loss) {
+			h2_blocks++;
 		}
-		if (bricks[intcomposition[i] - 1].getResidueLossType() == h2o2) {
-			hydroxyls++;
+		if (bricks[intcomposition[i] - 1].getResidueLossType() == h2o_loss) {
+			h2o_blocks++;
 		}
 	}
 
-	if ((hydrogens == hydroxyls) || (hydrogens == hydroxyls + 1) || (hydrogens + 1 == hydroxyls)) {
+	if ((h2_blocks == h2o_blocks) || (h2_blocks == h2o_blocks + 1) || (h2_blocks + 1 == h2o_blocks)) {
+		return true;
+	}
+
+	/*
+	if ((h2_blocks == 0) && (h2o_blocks == (int)intcomposition.size())) {
 		return true;
 	}
+	*/
 
 	return false;
 }

diff --git a/CycloBranch/core/cBricksDatabase.h b/CycloBranch/core/cBricksDatabase.h
@@ -134,9 +134,10 @@ class cBricksDatabase {
 	/**
 		\brief Get the mass of a composition of bricks.
 		\param combarray reference to an input integer vector of ids
+		\param numberofbasicbricks number of basic building blocks
 		\retval double cumulative mass of the bricks in the \a combarray
 	*/ 
-	double getMassOfComposition(vector<int>& combarray);
+	double getMassOfComposition(vector<int>& combarray, int numberofbasicbricks);
 
 
 	/**
@@ -223,15 +224,15 @@ class cBricksDatabase {
 	void load(ifstream& is);
 
 
-#if POLYKETIDE_SIDEROPHORES == 1
+#if OLIGOKETIDES == 1
 
 
 	/**
-		\brief Check if the numbers of hydrogen and hydroxyl blocks are correct.
+		\brief Check if the numbers of H2 loss and H2O loss blocks are correct.
 		\param brickseries a tested combination of building blocks
 		\retval bool true when the numbers of blocks are correct
 	*/ 
-	bool checkPolyketideBlocks(cBrick& brickseries);
+	bool checkKetideBlocks(cBrick& brickseries);
 
 
 #endif