cleaning up for new relese

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2257 e4b6dbb4-9209-464b-83f7-6257456c460c

masschroq/src/CMakeLists.txt

@@ -127,36 +127,36 @@ SET(VIEWXIC_MOC_HDRS
   ./qtquanti/choose_mz_precision_widget.h
   )  
 
-SET(GUI_SRCS
-  ./gui/mainwindow.cpp
-  ./gui/masschroq_gui.cpp
-  ./gui/xicSelectionWidget.cpp
-  ./gui/filterBackgroundWidget.cpp
-  ./gui/plotStyle.cpp
-  ./gui/xicProfile.cpp
-  ./gui/xicPlot.cpp
-  ./gui/plot.cpp
-  ./gui/mcqThread.cpp
-  ./gui/msrunLoaderThread.cpp
-  ./gui/runningBarr.cpp
-  )
-
-# another list, this time it includes all header files that should be treated with moc
-SET(GUI_MOC_HDRS
-  ./gui/mainwindow.h
-  ./gui/xicSelectionWidget.h
-  ./gui/filterBackgroundWidget.h
-  ./gui/xicProfile.h
-  ./gui/plot.h
-  ./gui/mcqThread.h
-  ./gui/msrunLoaderThread.h
-  ./gui/runningBarr.h
-  )  
+# SET(GUI_SRCS
+#   ./gui/mainwindow.cpp
+#   ./gui/masschroq_gui.cpp
+#   ./gui/xicSelectionWidget.cpp
+#   ./gui/filterBackgroundWidget.cpp
+#   ./gui/plotStyle.cpp
+#   ./gui/xicProfile.cpp
+#   ./gui/xicPlot.cpp
+#   ./gui/plot.cpp
+#   ./gui/mcqThread.cpp
+#   ./gui/msrunLoaderThread.cpp
+#   ./gui/runningBarr.cpp
+#   )
+
+# # another list, this time it includes all header files that should be treated with moc
+# SET(GUI_MOC_HDRS
+#   ./gui/mainwindow.h
+#   ./gui/xicSelectionWidget.h
+#   ./gui/filterBackgroundWidget.h
+#   ./gui/xicProfile.h
+#   ./gui/plot.h
+#   ./gui/mcqThread.h
+#   ./gui/msrunLoaderThread.h
+#   ./gui/runningBarr.h
+#   )  
 
 set(CMAKE_MODULE_PATH ${masschroq_SOURCE_DIR}/modules)
 
-set(Qwt5_DIR ${masschroq_SOURCE_DIR}/Modules)
-FIND_PACKAGE(Qwt5 REQUIRED) 
+# set(Qwt5_DIR ${masschroq_SOURCE_DIR}/Modules)
+# FIND_PACKAGE(Qwt5 REQUIRED) 
 
   
 # this command will generate rules that will run rcc on all files from SAMPLE_RCS
@@ -168,14 +168,13 @@ FIND_PACKAGE(Qwt5 REQUIRED)
   
 # and finally this will run moc:
 
-QT4_WRAP_CPP( VIEWXIC_MOC_SRCS ${VIEWXIC_MOC_HDRS} )
-
-QT4_WRAP_CPP( GUI_MOC_SRCS ${GUI_MOC_HDRS} )
+# QT4_WRAP_CPP( VIEWXIC_MOC_SRCS ${VIEWXIC_MOC_HDRS} )
+# QT4_WRAP_CPP( GUI_MOC_SRCS ${GUI_MOC_HDRS} )
   
 # we need this to be able to include headers produced by uic in our code
 # (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
 
-INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR} ${Qwt5_INCLUDE_DIR})
+# INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR} ${Qwt5_INCLUDE_DIR})
 
 IF (WIN32)
 
@@ -209,11 +208,11 @@ INSTALL(TARGETS ${MASSCHROQ_LIB_NAME} LIBRARY DESTINATION lib)
 # if lib quanti is graphical
 #TARGET_LINK_LIBRARIES(masschroq libmasschroq ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
 
-ADD_EXECUTABLE(viewxic qtquanti/viewxic.cpp ${VIEWXIC_SRCS} ${VIEWXIC_MOC_SRCS})
-TARGET_LINK_LIBRARIES(viewxic ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
+# ADD_EXECUTABLE(viewxic qtquanti/viewxic.cpp ${VIEWXIC_SRCS} ${VIEWXIC_MOC_SRCS})
+# TARGET_LINK_LIBRARIES(viewxic ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
 
-ADD_EXECUTABLE(mcq_gui gui/gui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS})
-TARGET_LINK_LIBRARIES(mcq_gui ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
+# ADD_EXECUTABLE(mcq_gui gui/gui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS})
+# TARGET_LINK_LIBRARIES(mcq_gui ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
 
 
 #ADD_EXECUTABLE(visualqms visualqms.cpp ${VIEWXIC_SRCS} ${VIEWXIC_MOC_SRCS} ${SAXLIB_SRCS} ${OBWARP_SRCS})

masschroq/src/lib/quantificator.cpp

@@ -14,295 +14,318 @@
 #include <QStringList>
 #include <algorithm>
 
-Quantificator::Quantificator(const QString & xml_id, const msRunHashGroup * quanti_group, 
-			     QuantificationMethod * quanti_method) 
-  :
-  _xml_id(xml_id)
+Quantificator::Quantificator(const QString & xml_id,
+							 const msRunHashGroup * quanti_group, 
+							 QuantificationMethod * quanti_method) 
+	:
+	_xml_id(xml_id)
 {
-  set_quanti_group(quanti_group);
-  set_quanti_method(quanti_method);
-  _quanti_items = new std::vector<QuantiItemBase *>;
-  const mcq_double coeff_match_range = 
-    (_quanti_method->getDetectionMethod())->get_coeff_detect_range();
-  _peak_matcher = new PeakMatcher(coeff_match_range);
+	set_quanti_group(quanti_group);
+	set_quanti_method(quanti_method);
+	_quanti_items = new std::vector<QuantiItemBase *>;
+	const mcq_double coeff_match_range = 
+		(_quanti_method->getDetectionMethod())->get_coeff_detect_range();
+	_peak_matcher = new PeakMatcher(coeff_match_range);
 }
 
 Quantificator::~Quantificator() {
-  std::vector<QuantiItemBase *>::iterator it;
-  for (it = _quanti_items->begin(); 
-       it != _quanti_items->end(); 
-       ++it) {
-    if (*it != 0) {
-      delete (*it);
-      *it = 0;
-    }
-  }
+	std::vector<QuantiItemBase *>::iterator it;
+	for (it = _quanti_items->begin(); 
+		 it != _quanti_items->end(); 
+		 ++it)
+	{
+		if (*it != 0)
+		{
+			delete (*it);
+			*it = 0;
+		}
+	}
   
-  if (_quanti_items != 0) {
-    delete _quanti_items;
-    _quanti_items = 0;
-  }
+	if (_quanti_items != 0)
+	{
+		delete _quanti_items;
+		_quanti_items = 0;
+	}
 
-  if (_peak_matcher != 0) {
-    delete _peak_matcher;
-    _peak_matcher = 0;
-  }
+	if (_peak_matcher != 0)
+	{
+		delete _peak_matcher;
+		_peak_matcher = 0;
+	}
   
 }
 
 void 
-Quantificator::set_quanti_group(const msRunHashGroup * quanti_group) {
-  _group_to_quantify = quanti_group;
+Quantificator::set_quanti_group(const msRunHashGroup * quanti_group)
+{
+	_group_to_quantify = quanti_group;
 }
 
 void 
-Quantificator::set_quanti_method(QuantificationMethod * quanti_method) {
-  _quanti_method = quanti_method;
+Quantificator::set_quanti_method(QuantificationMethod * quanti_method)
+{
+	_quanti_method = quanti_method;
 }
 
 void 
-Quantificator::set_matching_mode(const mcq_matching_mode & match_mode) {
-  _peak_matcher->set_matching_mode(match_mode);
+Quantificator::set_matching_mode(const mcq_matching_mode & match_mode)
+{
+	_peak_matcher->set_matching_mode(match_mode);
 }
 
 const QString & 
-Quantificator::get_quanti_group_id() const {
-  return (_group_to_quantify->getXmlId());
+Quantificator::get_quanti_group_id() const
+{
+	return (_group_to_quantify->getXmlId());
 }
 
 void
-Quantificator::add_peptide_quanti_items(vector<const Peptide *> & isotope_peptides) {
+Quantificator::add_peptide_quanti_items(vector<const Peptide *> & isotope_peptides)
+{
 
-   XicExtractionMethodBase * extraction_method = 
-    _quanti_method->getXicExtractionMethod();
+	XicExtractionMethodBase * extraction_method = 
+		_quanti_method->getXicExtractionMethod();
   
-  QuantiItemBase * quanti_item;
-  vector<const Peptide *>::const_iterator itpep;
-  /// for each peptide (or isotope in the vector), we will create a peptide quanti item
-  for (itpep = isotope_peptides.begin(); 
-       itpep != isotope_peptides.end(); 
-       ++itpep) {
+	QuantiItemBase * quanti_item;
+	vector<const Peptide *>::const_iterator itpep;
+	/// for each peptide (or isotope in the vector), we will create a peptide quanti item
+	for (itpep = isotope_peptides.begin(); 
+		 itpep != isotope_peptides.end(); 
+		 ++itpep)
+	{
     
-    /// get the set of charges z the peptide is observed in the current group,
-    /// and construct a quantification item for each peptide/z
+		/// get the set of charges z the peptide is observed in the current group,
+		/// and construct a quantification item for each peptide/z
         
-    std::set<unsigned int> * s_charges = (*itpep)->getCharges(*_group_to_quantify);
+		std::set<unsigned int> * s_charges = (*itpep)->getCharges(*_group_to_quantify);
     
-    // for each z do
+		// for each z do
     
-    std::set<unsigned int>::const_iterator itz;
-    for (itz = s_charges->begin(); 
-	 itz != s_charges->end(); 
-	 ++itz) {
-      /// calculate the mean bestRt for this peptide/z   
-      mcq_double rt((*itpep)->getMeanBestRt(*_group_to_quantify));
-      /// this test is not necessary here
-      if (rt != -1) {
-	extraction_method->setMz((*itpep)->getMz(*itz));
-	quanti_item = new QuantiItemPeptide(*extraction_method,
+		std::set<unsigned int>::const_iterator itz;
+		for (itz = s_charges->begin(); 
+			 itz != s_charges->end(); 
+			 ++itz)
+		{
+			/// calculate the mean bestRt for this peptide/z   
+			mcq_double rt((*itpep)->getMeanBestRt(*_group_to_quantify));
+			/// this test is not necessary here
+			if (rt != -1)
+			{
+				extraction_method->setMz((*itpep)->getMz(*itz));
+				quanti_item = new QuantiItemPeptide(*extraction_method,
 					    *itpep, 
 					    *itz,
 					    *_group_to_quantify,
 					    _peak_matcher->get_match_mode());
-	_quanti_items->push_back(quanti_item);
-      }
-    }
-    delete (s_charges);
-  }
+				_quanti_items->push_back(quanti_item);
+			}
+		}
+		delete (s_charges);
+	}
 }
 
 void 
-Quantificator::add_mz_quanti_items(const QStringList & mz_list) {
+Quantificator::add_mz_quanti_items(const QStringList & mz_list)
+{
  
-  XicExtractionMethodBase * extraction_method = 
-    _quanti_method->getXicExtractionMethod();
+	XicExtractionMethodBase * extraction_method = 
+		_quanti_method->getXicExtractionMethod();
   
-  QuantiItemBase * quanti_item;
+	QuantiItemBase * quanti_item;
   
-  QStringList::const_iterator it;
+	QStringList::const_iterator it;
   
-  for (it = mz_list.begin(); it != mz_list.end(); ++it) {
-    
-    extraction_method->setMz(it->toDouble());
-    quanti_item = new QuantiItemBase(*extraction_method);
-    _quanti_items->push_back(quanti_item);
-  }
+	for (it = mz_list.begin(); it != mz_list.end(); ++it)
+	{
+		extraction_method->setMz(it->toDouble());
+		quanti_item = new QuantiItemBase(*extraction_method);
+		_quanti_items->push_back(quanti_item);
+	}
 }
 
 void 
-Quantificator::add_mzrt_quanti_item(const QString & mz, const QString & rt) {
+Quantificator::add_mzrt_quanti_item(const QString & mz, const QString & rt)
+{
  
-  XicExtractionMethodBase * extraction_method = 
-    _quanti_method->getXicExtractionMethod();
+	XicExtractionMethodBase * extraction_method = 
+		_quanti_method->getXicExtractionMethod();
   
-  extraction_method->setMz(mz.toDouble());
+	extraction_method->setMz(mz.toDouble());
 
-  QuantiItemBase * quanti_item =
-    new QuantiItemMzRt(*extraction_method,
-		       rt.toDouble());
-  _quanti_items->push_back(quanti_item);
+	QuantiItemBase * quanti_item =
+		new QuantiItemMzRt(*extraction_method,
+						   rt.toDouble());
+	_quanti_items->push_back(quanti_item);
 }
 
 void 
-Quantificator::setMonitor(MonitorBase * monitor) {
-  _monitor = monitor;
+Quantificator::setMonitor(MonitorBase * monitor)
+{
+	_monitor = monitor;
 }
 
-struct CmpQuantiItems {
-  bool operator() (const QuantiItemBase * l1, const QuantiItemBase * l2)  { 
-    const mcq_double mz1 = l1->get_mz();
-    const mcq_double mz2 = l2->get_mz();
-    return (mz1 < mz2);
-  }
+struct CmpQuantiItems
+{
+	bool operator() (const QuantiItemBase * l1, const QuantiItemBase * l2)
+		{ 
+			const mcq_double mz1 = l1->get_mz();
+			const mcq_double mz2 = l2->get_mz();
+			return (mz1 < mz2);
+		}
 } QuantiItemsCmp;
 
 
 void
-Quantificator::sortQuantiItems() {
-  sort(_quanti_items->begin(), _quanti_items->end(), QuantiItemsCmp);  
+Quantificator::sortQuantiItems()
+{
+	sort(_quanti_items->begin(), _quanti_items->end(), QuantiItemsCmp);  
 }
 
 void
-Quantificator::quantify() {
+Quantificator::quantify()
+{
   
-  sortQuantiItems();
+	sortQuantiItems();
   
-  QString group_id =  _group_to_quantify->getXmlId();
-  QString quanti_method_id =  _quanti_method->getXmlId();
-  XicExtractionMethodBase * xic_extraction_method = _quanti_method->getXicExtractionMethod();
-  const mcq_xic_type xic_type = _quanti_method->getXicType();
-  const vector<const filterBase *> xic_filters = _quanti_method->getXicFilters();
-  peakDetectionBase * detection_method = _quanti_method->getDetectionMethod();
-  const peakExtractor * peak_extractor = new peakExtractor(detection_method);
+	QString group_id =  _group_to_quantify->getXmlId();
+	QString quanti_method_id =  _quanti_method->getXmlId();
+	XicExtractionMethodBase * xic_extraction_method = _quanti_method->getXicExtractionMethod();
+	const mcq_xic_type xic_type = _quanti_method->getXicType();
+	const vector<const filterBase *> xic_filters = _quanti_method->getXicFilters();
+	peakDetectionBase * detection_method = _quanti_method->getDetectionMethod();
+	const peakExtractor * peak_extractor = new peakExtractor(detection_method);
   
-  cout << "MS run group '" << group_id.toStdString() 
-	    << "': quantification method '" << quanti_method_id.toStdString()
-	    << "': quantification begin" << endl;
-  _quanti_method->printInfos(cout);
+	cout << "MS run group '" << group_id.toStdString() 
+		 << "': quantification method '" << quanti_method_id.toStdString()
+		 << "': quantification begin" << endl;
+	_quanti_method->printInfos(cout);
       
-  _monitor->setCurrentQuantify(_xml_id);
-  _monitor->setCurrentGroup(_group_to_quantify);
+	_monitor->setCurrentQuantify(_xml_id);
+	_monitor->setCurrentGroup(_group_to_quantify);
   
-  // launch quantification in group
-  Msrun * current_msrun;
-  msRunHashGroup::const_iterator itmsrun;
-  unsigned int count_msruns(1);
-  QuantiItemBase * current_mz;
-  vector<QuantiItemBase *>::const_iterator itmz;
-  xicBase * current_xic;
-  unsigned int quanti_items_size = _quanti_items->size();
+	// launch quantification in group
+	Msrun * current_msrun;
+	msRunHashGroup::const_iterator itmsrun;
+	unsigned int count_msruns(1);
+	QuantiItemBase * current_mz;
+	vector<QuantiItemBase *>::const_iterator itmz;
+	xicBase * current_xic;
+	unsigned int quanti_items_size = _quanti_items->size();
   
-  for (itmsrun = _group_to_quantify->begin(); 
-       itmsrun != _group_to_quantify->end(); 
-       ++itmsrun, ++count_msruns) 
+	for (itmsrun = _group_to_quantify->begin(); 
+		 itmsrun != _group_to_quantify->end(); 
+		 ++itmsrun, ++count_msruns) 
     {
-      current_msrun = itmsrun->second;
-      cout << "\tQuantifying in MS run '"
-	   << (current_msrun->getXmlId()).toStdString() 
-	   << "' : " << count_msruns << "/" << _group_to_quantify->size() 
-	   << " in group '" << group_id.toStdString() 
-	   << "'" << endl;
+		current_msrun = itmsrun->second;
+		cout << "\tQuantifying in MS run '"
+			 << (current_msrun->getXmlId()).toStdString() 
+			 << "' : " << count_msruns << "/" << _group_to_quantify->size() 
+			 << " in group '" << group_id.toStdString() 
+			 << "'" << endl;
       
-      _monitor->setCurrentMsrun(current_msrun);
-      current_msrun->prepareSpectraForQuantification(xic_extraction_method);
+		_monitor->setCurrentMsrun(current_msrun);
+		current_msrun->prepareSpectraForQuantification(xic_extraction_method);
       
-      int count_xic(1);
-      for (itmz = _quanti_items->begin();
-	   itmz != _quanti_items->end(); 
-	   ++itmz, ++count_xic) 
-	{
+		int count_xic(1);
+		for (itmz = _quanti_items->begin();
+			 itmz != _quanti_items->end(); 
+			 ++itmz, ++count_xic) 
+		{
 	  
-	  cout << "\r\t\textracting XIC and detecting peaks on XIC "
-	       << count_xic << "/" << quanti_items_size;
+			cout << "\r\t\textracting XIC and detecting peaks on XIC "
+				 << count_xic << "/" << quanti_items_size;
 	  
-	  current_mz = *itmz;
-	  _monitor->setCurrentSearchItem(current_mz);
+			current_mz = *itmz;
+			_monitor->setCurrentSearchItem(current_mz);
 	  
-	  current_xic = current_msrun->extractXic(xic_type, current_mz);
+			current_xic = current_msrun->extractXic(xic_type, current_mz);
 	  
-	  if (current_xic == 0) {
-	    qDebug() << "detectAndQuantify null xic ";
-	  }
+			if (current_xic == 0)
+				qDebug() << "detectAndQuantify null xic ";
 	  
-	  current_xic->setMonitor(*_monitor);
-	  _monitor->setXic(current_xic);
-	  // apply filters to the extracted Xic
-	  // monitor is passed to Xic class which calls 
-	  // monitor.setFilteredXics() method
-	  current_xic->applyFilters(xic_filters);
+			current_xic->setMonitor(*_monitor);
+			_monitor->setXic(current_xic);
+			// apply filters to the extracted Xic
+			// monitor is passed to Xic class which calls 
+			// monitor.setFilteredXics() method
+			current_xic->applyFilters(xic_filters);
 	  
-	  // extract all peaks from xic
-	  vector<xicPeak *> * all_peaks_list = 
-	    peak_extractor->newAllPeaksList(current_xic);
-	  _monitor->setAllPeaks(all_peaks_list);
-	  delete (current_xic);
+			// extract all peaks from xic
+			vector<xicPeak *> * all_peaks_list = 
+				peak_extractor->newAllPeaksList(current_xic);
+			_monitor->setAllPeaks(all_peaks_list);
+			delete (current_xic);
 
-	  // match the peaks	  
-	  vector<xicPeak *> * matched_peak_list = 
-	    _peak_matcher->newMatchedPeaks(current_mz, all_peaks_list, current_msrun);
+			// match the peaks	  
+			vector<xicPeak *> * matched_peak_list = 
+				_peak_matcher->newMatchedPeaks(current_mz, all_peaks_list, current_msrun);
 	  
-	  _monitor->setMatchedPeaks(matched_peak_list);
-       	  _monitor->setEndCurrentSearchItem();
+			_monitor->setMatchedPeaks(matched_peak_list);
+			_monitor->setEndCurrentSearchItem();
 	  
-	  // clean up
-	  if (matched_peak_list != 0) {
-	    delete matched_peak_list;
-	    matched_peak_list = 0;
-	  }
-	}
-      cout << endl;
-      current_msrun->doneWithSpectra();
-      _monitor->setEndCurrentMsrun();
+			// clean up
+			if (matched_peak_list != 0)
+			{
+				delete matched_peak_list;
+				matched_peak_list = 0;
+			}
+		}
+		cout << endl;
+		current_msrun->doneWithSpectra();
+		_monitor->setEndCurrentMsrun();
     }
-  delete (peak_extractor);
+	delete (peak_extractor);
   
-  cout << "MS run group '" << group_id.toStdString() 
-       << "': quantification method '" << quanti_method_id.toStdString()
-       << "': quantification finished" << endl;
+	cout << "MS run group '" << group_id.toStdString() 
+		 << "': quantification method '" << quanti_method_id.toStdString()
+		 << "': quantification finished" << endl;
   
-  cout << "MS run group '" << group_id.toStdString() 
-       << "': post matching begin" << endl;
-
-  performPostMatching();
-  _monitor->setEndCurrentGroup();	  
+	performPostMatching();
+	_monitor->setEndCurrentGroup();	  
   
 }
 
 void
-Quantificator::performPostMatching() {
-  if (_peak_matcher->isPostMatchingRequired()) {
-    _monitor->setPostMatchingOn();
-    QString group_id =  _group_to_quantify->getXmlId();
-    vector<QuantiItemBase *>::const_iterator itmz;
-    Msrun * current_msrun;
-    unsigned int count_msruns(1);
-    msRunHashGroup::const_iterator itmsrun;
-    for (itmsrun = _group_to_quantify->begin(); 
-	 itmsrun != _group_to_quantify->end(); 
-	 ++itmsrun, ++count_msruns) 
-      {
-	current_msrun = itmsrun->second;
-	cout << "\tPost matching in MS run '"
-	     << (current_msrun->getXmlId()).toStdString() 
-	     << "' : " << count_msruns << "/" << _group_to_quantify->size() 
-	     << " in group '" << group_id.toStdString() 
-	     << "'" << endl;
+Quantificator::performPostMatching()
+{
+	if (_peak_matcher->isPostMatchingRequired())
+	{
+		QString group_id =  _group_to_quantify->getXmlId();
+		cout << "MS run group '" << group_id.toStdString() 
+			 << "': post matching begin" << endl;
+	  
+		_monitor->setPostMatchingOn();
+		vector<QuantiItemBase *>::const_iterator itmz;
+		Msrun * current_msrun;
+		unsigned int count_msruns(1);
+		msRunHashGroup::const_iterator itmsrun;
+		for (itmsrun = _group_to_quantify->begin(); 
+			 itmsrun != _group_to_quantify->end(); 
+			 ++itmsrun, ++count_msruns) 
+		{
+			current_msrun = itmsrun->second;
+			cout << "\tPost matching in MS run '"
+				 << (current_msrun->getXmlId()).toStdString() 
+				 << "' : " << count_msruns << "/" << _group_to_quantify->size() 
+				 << " in group '" << group_id.toStdString() 
+				 << "'" << endl;
 	
-	_monitor->setCurrentMsrun(current_msrun);
-	for (itmz = _quanti_items->begin();
-	     itmz != _quanti_items->end(); 
-	     ++itmz) {
-	  vector<xicPeak *> * post_matched_peaks = 
-	    _peak_matcher->newPostMatchedPeaks(*itmz, current_msrun);
-	  _monitor->setPostMatchedPeaks(*itmz, post_matched_peaks);
-	  delete (post_matched_peaks);
-	}
-	_monitor->setEndCurrentMsrun(); 
-      }
-    _monitor->setPostMatchingOff();
-     cout << "MS run group '" << group_id.toStdString() 
-       << "': post matching end" << endl;