release 1.3.1

CycloBranch/External/linux/correctprofile.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+SAVEIFS=$IFS
+IFS=$',' read name fwhm <<< $@
+IFS=$SAVEIFS
+FileConverter -in "$name"".mgf" -out "$name"".FileConverter.mzML"
+NoiseFilterGaussian -in "$name"".FileConverter.mzML" -out "$name"".NoiseFilterGaussian.mzML" -algorithm:gaussian_width $fwhm
+rm "$name"".mzML"
+BaselineFilter -in "$name"".NoiseFilterGaussian.mzML" -out "$name"".mzML"
+rm "$name"".mgf"
+rm "$name"".FileConverter.mzML"
+rm "$name"".NoiseFilterGaussian.mzML"

CycloBranch/External/macosx/correctprofile.sh

@@ -0,0 +1 @@
+SAVEIFS=$IFSIFS=$',' read name fwhm <<< $@IFS=$SAVEIFSFileConverter -in "$name"".mgf" -out "$name"".FileConverter.mzML"NoiseFilterGaussian -in "$name"".FileConverter.mzML" -out "$name"".NoiseFilterGaussian.mzML" -algorithm:gaussian_width $fwhmrm "$name"".mzML"BaselineFilter -in "$name"".NoiseFilterGaussian.mzML" -out "$name"".mzML"rm "$name"".mgf"rm "$name"".FileConverter.mzML"rm "$name"".NoiseFilterGaussian.mzML"

CycloBranch/External/windows/correctprofile.bat

@@ -0,0 +1,11 @@
+@echo off
+SET PATH=%PATH:C:\Xcalibur\system\programs;=%
+
+FileConverter.exe -in "%~f1.mgf" -out "%~f1.FileConverter.mzML" 1>NUL
+NoiseFilterGaussian.exe -in "%~f1.FileConverter.mzML" -out "%~f1.NoiseFilterGaussian.mzML" -algorithm:gaussian_width %2 1>NUL
+del "%~f1.mzML" 2>NUL
+BaselineFilter.exe -in "%~f1.NoiseFilterGaussian.mzML" -out "%~f1.mzML" 1>NUL
+
+del "%~f1.mgf" 2>NUL
+del "%~f1.FileConverter.mzML" 2>NUL
+del "%~f1.NoiseFilterGaussian.mzML" 2>NUL

CycloBranch/core/cMzML.cpp

@@ -329,11 +329,13 @@ int cMzML::parse(string& filename, vector<cPeaksList>& peaklists, eModeType mode
 															mgfofstream.open(ss.str());
 														}
 
-														if ((count + 1) % 100 == 0) {
-															*os << count + 1 << " ";
-														}
-														if ((count + 1) % 2500 == 0) {
-															*os << endl;
+														if (os) {
+															if ((count + 1) % 100 == 0) {
+																*os << count + 1 << " ";
+															}
+															if ((count + 1) % 2500 == 0) {
+																*os << endl;
+															}
 														}
 
 														mgfofstream << "BEGIN IONS" << endl;

CycloBranch/core/cParameters.cpp

@@ -17,6 +17,7 @@ void cParameters::clear() {
 	peaklistfilename = "";
 	useprofiledata = false;
 	convertprofiledata = true;
+	profiledatafilename = "";
 	peaklistfileformat = txt;
 	peaklistseries.clear();
 	scannumber = 1;
@@ -1163,6 +1164,8 @@ void cParameters::store(ofstream& os) {
 	os.write((char *)&useprofiledata, sizeof(bool));
 	os.write((char *)&convertprofiledata, sizeof(bool));
 
+	storeString(profiledatafilename, os);
+
 	os.write((char *)&scannumber, sizeof(int));
 	os.write((char *)&precursormass, sizeof(double));
 
@@ -1287,6 +1290,8 @@ void cParameters::load(ifstream& is) {
 	is.read((char *)&useprofiledata, sizeof(bool));
 	is.read((char *)&convertprofiledata, sizeof(bool));
 
+	loadString(profiledatafilename, is);
+
 	is.read((char *)&scannumber, sizeof(int));
 	is.read((char *)&precursormass, sizeof(double));
 

CycloBranch/core/cParameters.h

@@ -91,6 +91,12 @@ class cParameters {
 	bool convertprofiledata;
 
 
+	/**
+		\brief Profile data file name.
+	*/
+	string profiledatafilename;
+
+
 	/**
 		\brief A file format of peak list.
     */

CycloBranch/core/cPeaksList.cpp

@@ -143,10 +143,6 @@ void cPeaksList::loadFromIBDStream(cImzMLItem& imzmlitem, ifstream &ibdstream, b
 		}
 	}
 
-	if (imzmlitem.mzlength != imzmlitem.intensitylength) {
-		return;
-	}
-
 	// intensities
 	if (use_64bit_float_intensity_precision) {
 		start = imzmlitem.intensitystart;

CycloBranch/core/utilities.cpp

@@ -4,7 +4,7 @@
 
 
 QString appname = "CycloBranch";
-QString appversion = "v. 1.3.0 (64-bit)";
+QString appversion = "v. 1.3.1 (64-bit)";
 
 
 #if OS_TYPE == UNX

CycloBranch/gui/cMainWindow.cpp

@@ -329,7 +329,11 @@ cMainWindow::cMainWindow() {
 	spectradetails.clear();
 
 	parameters.clear();
+
 	rawdata.clear();
+	imzmlprofilemetadata.clear();
+	profilemz64precision = false;
+	profileintensity64precision = false;
 
 	resultsbasecolumncount = 9;
 	resultsspecificcolumncount = 0;
@@ -736,13 +740,20 @@ void cMainWindow::run() {
 	spectradetails.clear();
 
 	parameters.clear();
+
 	rawdata.clear();
+	imzmlprofilemetadata.clear();
+	profilemz64precision = false;
+	profileintensity64precision = false;
 
 	cParameters localparameters = parameterswidget->getParameters();
 
 	regex rx;
 	rx = "\\.[iI][mM][zZ][mM][lL]$";
+	localparameters.profiledatafilename = "";
 	if (regex_search(localparameters.peaklistfilename, rx)) {
+		localparameters.profiledatafilename = localparameters.peaklistfilename;
+
 		string convertedimzml = localparameters.peaklistfilename.substr(0, (int)localparameters.peaklistfilename.size() - 6);
 		string convertedibd = convertedimzml;
 		convertedimzml += "_converted_fwhm_";
@@ -1140,13 +1151,39 @@ void cMainWindow::reportSpectra() {
 
 	results->resizeColumnsToContents();
 
-	if (parameters.useprofiledata && (parameters.peaklistfileformat == baf)) {
-		if ((parameters.mode == denovoengine) || (parameters.mode == databasesearch)) {
-			rawdata.resize(1);
+	if (parameters.useprofiledata) {
+
+		if (parameters.peaklistfileformat == baf) {
+			if ((parameters.mode == denovoengine) || (parameters.mode == databasesearch)) {
+				rawdata.resize(1);
+			}
+			else {
+				rawdata.resize(theoreticalspectrumlist.size());
+			}
 		}
-		else {
+
+		if ((parameters.peaklistfileformat == imzML) && (parameters.mode == dereplication)) {
 			rawdata.resize(theoreticalspectrumlist.size());
+			imzmlprofilemetadata.clear();
+			profilemz64precision = false;
+			profileintensity64precision = false;
+
+			cImzML imzml;
+			int defaultmaxx;
+			int defaultmaxy;
+			int defaultpixelsizex;
+			int defaultpixelsizey;
+			eVendorType vendor;
+
+			if (imzml.parse(parameters.profiledatafilename, defaultmaxx, defaultmaxy, defaultpixelsizex, defaultpixelsizey, vendor) == 0) {
+				if (imzml.hasProfileSpectra()) {
+					imzmlprofilemetadata = imzml.getItems();
+					profilemz64precision = imzml.use64BitMzPrecision();
+					profileintensity64precision = imzml.use64BitIntensityPrecision();
+				}
+			}
 		}
+
 	}
 
 	QProgressDialog progress("Preparing the report...", /*"Cancel"*/0, 0, theoreticalspectrumlist.size(), this);
@@ -1247,7 +1284,7 @@ void cMainWindow::rowDoubleClicked(const QModelIndex& item) {
 	int row = resultsproxymodel->mapToSource(item).row();
 	int rowid = resultsmodel->item(row, 1)->data(Qt::DisplayRole).toInt() - 1;
 
-	spectradetails[rowid].prepareToShow(&rawdata, actionShowIsomers);
+	spectradetails[rowid].prepareToShow(actionShowIsomers, &rawdata, &imzmlprofilemetadata, profilemz64precision, profileintensity64precision);
 	spectradetails[rowid].show();
 	spectradetails[rowid].activateWindow();
 	if (spectradetails[rowid].isMinimized()) {
@@ -1741,8 +1778,12 @@ void cMainWindow::openResultsFile() {
 			spectradetails.clear();
 
 			parameters.clear();
+
 			rawdata.clear();
-
+			imzmlprofilemetadata.clear();
+			profilemz64precision = false;
+			profileintensity64precision = false;
+
 			// load graph window
 			graph->load(infile);
 			graph->updateView(actionShowIsomers->isChecked());
@@ -1898,7 +1939,7 @@ void cMainWindow::summaryPeaksTableCancelled() {
 
 
 void cMainWindow::summaryPeaksTableRowDoubleClicked(int rowid, double experimentalmz) {
-	spectradetails[rowid].prepareToShow(&rawdata, actionShowIsomers);
+	spectradetails[rowid].prepareToShow(actionShowIsomers, &rawdata, &imzmlprofilemetadata, profilemz64precision, profileintensity64precision);
 	spectradetails[rowid].show();
 	spectradetails[rowid].activateWindow();
 	if (spectradetails[rowid].isMinimized()) {

CycloBranch/gui/cMainWindow.h

@@ -131,7 +131,11 @@ class cMainWindow : public QMainWindow
 	vector<cSpectrumDetailWidget> spectradetails;
 
 	cParameters parameters;
+
 	cPeakListSeries rawdata;
+	vector<cImzMLItem> imzmlprofilemetadata;
+	bool profilemz64precision;
+	bool profileintensity64precision;
 
 	QTextEdit* logWindow;
 	QSplitter* splitter;