development version 1.3.0

novak-jiri · May 11, 2018 · 2e3d4db · 2e3d4db
1 parent 331e441
commit 2e3d4db
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Showing 38 changed files with 1,014 additions and 289 deletions.
diff --git a/CycloBranch/CycloBranch.vcxproj b/CycloBranch/CycloBranch.vcxproj
@@ -136,7 +136,7 @@
       <EnableParallelCodeGeneration>true</EnableParallelCodeGeneration>
     </ClCompile>
     <Link>
-      <SubSystem>Windows</SubSystem>
+      <SubSystem>Console</SubSystem>
       <OutputFile>$(OutDir)\$(ProjectName).exe</OutputFile>
       <AdditionalLibraryDirectories>$(QTDIR)\lib;C:\boost_1_57_0\lib64-msvc-11.0;C:\xerces-c-3.1.1\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
       <GenerateDebugInformation>false</GenerateDebugInformation>

diff --git a/CycloBranch/External/windows/any2mgf.bat b/CycloBranch/External/windows/any2mgf.bat
@@ -1,2 +1,2 @@
-SET PATH=%PATH%
+SET PATH=%PATH:C:\Xcalibur\system\programs;=%
 FileConverter.exe -in %1 -out %1.mgf
diff --git a/CycloBranch/External/windows/baf2profile.bat b/CycloBranch/External/windows/baf2profile.bat
@@ -0,0 +1,11 @@
+@echo off
+set PATH=%PATH%
+del "%~f1_converted*.csv" 2>NUL
+del "%~f1.profile.*.csv" 2>NUL
+"%programfiles(x86)%\Bruker Daltonik\CompassXport\CompassXport.exe" -mode 4 -raw 1 -a "%~f1" -o "%~f1_converted" 1>NUL
+setlocal enabledelayedexpansion
+set count=0
+for %%i in ("%~f1_converted_*.csv") do (
+set /a count=!count!+1
+move "%%i" "%~f1.profile.!count!.csv" 1>NUL
+)
diff --git a/CycloBranch/External/windows/mis2csv.bat b/CycloBranch/External/windows/mis2csv.bat
@@ -7,7 +7,7 @@ del "%~f1.baf.txt" 2>NUL
 
 for /R %%f in (analysis.baf) do if exist "%%f" (
 del "%%f_converted*.csv" 2>NUL
-CompassXport.exe -mode 4 -a "%%f" -o "%%f_converted" 1>NUL
+"%programfiles(x86)%\Bruker Daltonik\CompassXport\CompassXport.exe" -mode 4 -a "%%f" -o "%%f_converted" 1>NUL
 (type "%%f_converted*.csv" 2>NUL) >> "%~f1.baf.csv"
 del "%%f_converted*.csv" 2>NUL
 )

diff --git a/CycloBranch/External/windows/raw2peaks.bat b/CycloBranch/External/windows/raw2peaks.bat
@@ -1,5 +1,5 @@
 @echo off
-SET PATH=%PATH%
+SET PATH=%PATH:C:\Xcalibur\system\programs;=%
 
 (type NUL 2>NUL) > "%~1mgf"
 for %%f in ("%~d1%~p1%~n1.00*.mgf") do (

diff --git a/CycloBranch/External/windows/ser2csv.bat b/CycloBranch/External/windows/ser2csv.bat
@@ -7,7 +7,7 @@ del "%~f1.txt" 2>NUL
 
 for /R %%f in (fid) do if exist "%%f" (
 del "%%f_converted*.csv" 2>NUL
-CompassXport.exe -mode 4 -a "%%f" -o "%%f_converted" -raw 1 1>NUL
+"%programfiles(x86)%\Bruker Daltonik\CompassXport\CompassXport.exe" -mode 4 -a "%%f" -o "%%f_converted" -raw 1 1>NUL
 (type "%%f_converted*.csv" 2>NUL) >> "%~f1.csv"
 del "%%f_converted*.csv" 2>NUL
 echo %%f >> "%~f1.txt"

diff --git a/CycloBranch/core/cParameters.cpp b/CycloBranch/core/cParameters.cpp
@@ -15,6 +15,8 @@ void cParameters::clear() {
 	iondefinitions.recalculateFragments(false, false, s);
 	peptidetype = linear;
 	peaklistfilename = "";
+	useprofiledata = false;
+	convertprofiledata = true;
 	peaklistfileformat = txt;
 	peaklistseries.clear();
 	scannumber = 1;
@@ -242,7 +244,9 @@ int cParameters::checkAndPrepare(bool& terminatecomputation) {
 				break;
 			case baf:
 				#if OS_TYPE == WIN
-					*os << "Converting the file " + peaklistfilename + " ... ";
+					*os << "Processing the file " + peaklistfilename + ":" << endl;
+
+					*os << "centroid spectra ... ";
 					s = "External\\windows\\baf2csv.bat \"" + peaklistfilename + "\"";
 					if (system(s.c_str()) != 0) {
 						error = true;
@@ -255,18 +259,39 @@ int cParameters::checkAndPrepare(bool& terminatecomputation) {
 					}
 
 					if (!error) {
-						*os << "ok" << endl << endl;
+						*os << "ok" << endl;
 						peakliststream.open(peaklistfilename + ".csv");
 					}
+
+					if (useprofiledata && convertprofiledata) {
+						*os << "profile spectra ... ";
+						s = "External\\windows\\baf2profile.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 'baf2profile.bat' file located in the 'External/windows' folder ?\n";
+						}
+
+						if (!error) {
+							*os << "ok" << endl;
+						}
+					}
+
+					*os << endl;
 				#endif
 				break;
 			case raw:
 				#if OS_TYPE == WIN
-					* os << "Converting the file " + peaklistfilename + " ... ";
+					*os << "Converting the file " + peaklistfilename + " ... ";
 					s = "External\\windows\\raw2mzml.bat \"" + peaklistfilename + "\"";
 					if (system(s.c_str()) != 0) {
 						error = true;
 						errormessage = "The file cannot be converted.\n";
+						errormessage += "Is the file '" + peaklistfilename + "' opened elsewhere ?\n";
 						errormessage += "Does the file '" + peaklistfilename + "' exist ?\n";
 						errormessage += "Is the directory with the file '" + peaklistfilename + "' writable ?\n";
 						errormessage += "Do you have msconvert.exe installed (OpenMS 2.x including ProteoWizard must be installed) ?\n";
@@ -753,7 +778,7 @@ string cParameters::printToString() {
 		s += "De Novo Search Engine";
 		break;
 	case singlecomparison:
-		s += "Compare Peaklist with Spectrum of Searched Sequence";
+		s += "Compare Peaklist(s) with Spectrum of Searched Sequence";
 		break;
 	case databasesearch:
 		s += "Compare Peaklist with Database - MS/MS data";
@@ -797,6 +822,11 @@ string cParameters::printToString() {
 	s += "\n";
 
 	s += "File: " + peaklistfilename + "\n";
+
+	s += "Use Profile Data: ";
+	s += useprofiledata ? "on" : "off";
+	s += "\n";
+
 	s += "Scan no.: " + to_string(scannumber) + "\n";
 	s += "Precursor m/z Ratio: " + to_string(precursormass) + "\n";
 	s += "Precursor Ion Adduct: " + precursoradduct + "\n";
@@ -1130,6 +1160,9 @@ void cParameters::store(ofstream& os) {
 	os.write((char *)&peaklistfileformat, sizeof(ePeakListFileFormat));
 	peaklistseries.store(os);
 
+	os.write((char *)&useprofiledata, sizeof(bool));
+	os.write((char *)&convertprofiledata, sizeof(bool));
+
 	os.write((char *)&scannumber, sizeof(int));
 	os.write((char *)&precursormass, sizeof(double));
 
@@ -1251,6 +1284,9 @@ void cParameters::load(ifstream& is) {
 	is.read((char *)&peaklistfileformat, sizeof(ePeakListFileFormat));
 	peaklistseries.load(is);
 
+	is.read((char *)&useprofiledata, sizeof(bool));
+	is.read((char *)&convertprofiledata, sizeof(bool));
+
 	is.read((char *)&scannumber, sizeof(int));
 	is.read((char *)&precursormass, sizeof(double));
 

diff --git a/CycloBranch/core/cParameters.h b/CycloBranch/core/cParameters.h
@@ -79,6 +79,18 @@ class cParameters {
     string peaklistfilename;
 
 
+	/**
+		\brief Use profile data.
+	*/
+	bool useprofiledata;
+
+
+	/**
+		\brief Convert profile data.
+	*/
+	bool convertprofiledata;
+
+
 	/**
 		\brief A file format of peak list.
     */

diff --git a/CycloBranch/core/cPeakListSeries.cpp b/CycloBranch/core/cPeakListSeries.cpp
@@ -30,6 +30,11 @@ void cPeakListSeries::clear() {
 }
 
 
+void cPeakListSeries::resize(int size) {
+	peaklists.resize(size);
+}
+
+
 void cPeakListSeries::addPeakList(cPeaksList& peaklist) {
 	peaklists.push_back(peaklist);
 }
@@ -193,7 +198,14 @@ int cPeakListSeries::loadFromMZMLStream(string& mzmlfilename, ifstream &mzmlstre
 		string convertedmzmlfilename;
 		string mgfname = mzmlfilename.substr(0, (int)mzmlfilename.size() - 4);
 
-		*os << "ok" << endl << "Total number of spectra: " << peaklists.size() << endl << endl << "Converting raw data to peaklists... ";
+		*os << "ok" << endl;
+		if (mode == dereplication) {
+			*os << "Total number of MS spectra: ";
+		}
+		else {
+			*os << "Total number of MS/MS spectra: ";
+		}
+		*os << peaklists.size() << endl << endl << "Converting raw data to peaklists... ";
 
 		string s;
 		#if OS_TYPE == UNX
@@ -240,7 +252,14 @@ int cPeakListSeries::loadFromMZMLStream(string& mzmlfilename, ifstream &mzmlstre
 	}
 	else {
 
-		*os << "ok" << endl << endl;
+		*os << "ok" << endl;
+		if (mode == dereplication) {
+			*os << "Total number of MS spectra: ";
+		}
+		else {
+			*os << "Total number of MS/MS spectra: ";
+		}
+		*os << peaklists.size() << endl << endl;
 
 	}
 

diff --git a/CycloBranch/core/cPeakListSeries.h b/CycloBranch/core/cPeakListSeries.h
@@ -59,6 +59,13 @@ class cPeakListSeries {
 	void clear();
 
 
+	/**
+		\brief Resize the peaklist series.
+		\param size new size
+	*/
+	void resize(int size);
+
+
 	/**
 		\brief Add a peaklist.
 		\param peaklist peaklist which will be added

diff --git a/CycloBranch/core/cPeaksList.cpp b/CycloBranch/core/cPeaksList.cpp
@@ -347,11 +347,13 @@ int cPeaksList::normalizeIntenzity() {
 	}
 
 	double maximum = 0.0f;
+
 	for (int i = 0; i < (int)peaks.size(); i++) {
 		if (peaks[i].absoluteintensity > maximum) {
 			maximum = peaks[i].absoluteintensity;
 		}
 	}
+
 	if (maximum > 0) {
 		for (int i = 0; i < (int)peaks.size(); i++) {
 			peaks[i].relativeintensity = peaks[i].absoluteintensity/maximum*100.0f;
@@ -362,6 +364,19 @@ int cPeaksList::normalizeIntenzity() {
 }
 
 
+void cPeaksList::normalizeIntenzityByValue(double value) {
+	if (peaks.size() == 0) {
+		return;
+	}
+
+	if (value > 0) {
+		for (int i = 0; i < (int)peaks.size(); i++) {
+			peaks[i].relativeintensity = peaks[i].absoluteintensity / value * 100.0f;
+		}
+	}
+}
+
+
 void cPeaksList::cropRelativeIntenzity(double minimumrelativeintensitythreshold) {
 	sortbyRelativeIntensityDesc();
 
@@ -696,6 +711,17 @@ double cPeaksList::getMaximumAbsoluteIntensityFromMZInterval(double minmz, doubl
 }
 
 
+double cPeaksList::getMaximumAbsoluteIntensity() {
+	double intensity = 0;
+	for (int i = 0; i < (int)peaks.size(); i++) {
+		if (peaks[i].absoluteintensity > intensity) {
+			intensity = peaks[i].absoluteintensity;
+		}
+	}
+	return intensity;
+}
+
+
 void cPeaksList::setCoordinates(int x, int y) {
 	this->x = x;
 	this->y = y;

diff --git a/CycloBranch/core/cPeaksList.h b/CycloBranch/core/cPeaksList.h
@@ -197,6 +197,13 @@ class cPeaksList {
 	int normalizeIntenzity();
 
 
+	/**
+		\brief Normalize intensities of peaks using a value.
+		\param value normalization value
+	*/
+	void normalizeIntenzityByValue(double value);
+
+
 	/**
 		\brief Remove peaks with relative intensities lower than the threshold.
 		\param minimumrelativeintensitythreshold minimum threshold of relative intensity
@@ -338,6 +345,13 @@ class cPeaksList {
 	double getMaximumAbsoluteIntensityFromMZInterval(double minmz, double maxmz, bool hidematched, bool hideunmatched, ePeptideType peptidetype, bool hidescrambled);
 
 
+	/**
+		\brief Get the maximum absolute intensity.
+		\retval double maximum absolute intensity
+	*/
+	double getMaximumAbsoluteIntensity();
+
+
 	/**
 		\brief Set the coordinates.
 		\param x X coordinate

diff --git a/CycloBranch/core/cTheoreticalSpectrum.cpp b/CycloBranch/core/cTheoreticalSpectrum.cpp
@@ -822,7 +822,7 @@ void cTheoreticalSpectrum::removeUnmatchedIsotopePatterns(cPeaksList& theoretica
 		return;
 	}
 
-	int minimumenvelopepeaks = (parameters->mode == dereplication)?parameters->minimumpatternsize:1;
+	int minimumenvelopepeaks = parameters->minimumpatternsize;
 
 	int groupid = theoreticalpeaks[0].groupid;
 	int start = 0;

diff --git a/CycloBranch/core/cTheoreticalSpectrumList.cpp b/CycloBranch/core/cTheoreticalSpectrumList.cpp
@@ -225,7 +225,10 @@ int cTheoreticalSpectrumList::parallelCompareAndStore(cCandidateSet& candidates,
 	else {
 
 		cTheoreticalSpectrum t(parameters, (cCandidate &)(*candidates.getSet().begin()));
-		theoreticalspectra.push_back(t);
+		int cnt = parameters->peaklistseries.size();
+		for (int i = 0; i < cnt; i++) {
+			theoreticalspectra.push_back(t);
+		}
 
 	}
 
@@ -246,6 +249,7 @@ int cTheoreticalSpectrumList::parallelCompareAndStore(cCandidateSet& candidates,
 
 	// fill descriptions of peaks
 	cPeaksList unmatchedpeaksinmatchedpatterns;
+	cPeaksList tmppeaklist;
 	resultspectra.resize(theoreticalspectra.size());
 	for (int i = 0; i < (int)theoreticalspectra.size(); i++) {
 
@@ -257,24 +261,32 @@ int cTheoreticalSpectrumList::parallelCompareAndStore(cCandidateSet& candidates,
 
 		unmatchedpeaksinmatchedpatterns.clear();
 
+		if (parameters->mode == singlecomparison) {
+			tmppeaklist = parameters->peaklistseries[i];
+			tmppeaklist.sortbyMass();
+		}
+		else {
+			tmppeaklist = peaklist;
+		}
+
 		switch (parameters->peptidetype) {
 			case linear:
-				theoreticalpeaksrealsize = tsp.compareLinear(peaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
+				theoreticalpeaksrealsize = tsp.compareLinear(tmppeaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
 				break;
 			case cyclic:
-				theoreticalpeaksrealsize = tsp.compareCyclic(peaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
+				theoreticalpeaksrealsize = tsp.compareCyclic(tmppeaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
 				break;
 			case branched:
-				theoreticalpeaksrealsize = tsp.compareBranched(peaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
+				theoreticalpeaksrealsize = tsp.compareBranched(tmppeaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
 				break;
 			case branchcyclic:
-				theoreticalpeaksrealsize = tsp.compareBranchCyclic(peaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
+				theoreticalpeaksrealsize = tsp.compareBranchCyclic(tmppeaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
 				break;
 			case linearpolyketide:
-				theoreticalpeaksrealsize = tsp.compareLinearPolyketide(peaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
+				theoreticalpeaksrealsize = tsp.compareLinearPolyketide(tmppeaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
 				break;
 			case cyclicpolyketide:
-				theoreticalpeaksrealsize = tsp.compareCyclicPolyketide(peaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
+				theoreticalpeaksrealsize = tsp.compareCyclicPolyketide(tmppeaklist, *bricksdb, true, rxsequencetag, rxsearchedsequence, unmatchedpeaksinmatchedpatterns, &isotopeformuladesctoid);
 				break;
 			case other:
 				break;
@@ -412,7 +424,7 @@ double cTheoreticalSpectrumList::updatekNNList(cTheoreticalSpectrum& theoretical
 				break;
 		}
 
-		if ((currentscore == score) && (it1->getCandidate().getPath() == theoreticalspectrum.getCandidate().getPath())) {
+		if ((parameters->mode == denovoengine) && (currentscore == score) && (it1->getCandidate().getPath() == theoreticalspectrum.getCandidate().getPath())) {
 			if (!it1->isValid() && theoreticalspectrum.isValid()) {
 				*it1 = theoreticalspectrum;
 				it1->resizePeakList(theoreticalpeaksrealsize);

diff --git a/CycloBranch/core/utilities.cpp b/CycloBranch/core/utilities.cpp
@@ -4,7 +4,7 @@
 
 
 QString appname = "CycloBranch";
-QString appversion = "v. 1.2.748 (64-bit)";
+QString appversion = "v. 1.3.0 (64-bit)";
 
 
 #if OS_TYPE == UNX