check and fix second chance for thin peaks in xicfilterdetectmatch

src/lib/quantifications/mapquanti.cpp

@@ -124,6 +124,7 @@ MapQuanti::operator()(QuantiItemBase *p_currentSearchItem)
                                                    _monitor,
                                                    _p_xic_filter.get(),
                                                    _p_detection.get(),
+                                                   _quantificator,
                                                    _matching_mode);
           filter_detect_match.filterDetectQuantify(
             *(msrun_xic_sp.get()), rt_target, p_currentSearchItem, _p_msrun);

src/lib/quantifications/mapquantirealxic.cpp

@@ -19,9 +19,6 @@
  *     You should have received a copy of the GNU General Public License
  *     along with MassChroQ.  If not, see <http://www.gnu.org/licenses/>.
  *
- * Contributors:
- *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
- *implementation
  ******************************************************************************/
 
 #include "mapquantirealxic.h"

src/lib/quantifications/mapquantirealxic.h

@@ -19,9 +19,6 @@
  *     You should have received a copy of the GNU General Public License
  *     along with MassChroQ.  If not, see <http://www.gnu.org/licenses/>.
  *
- * Contributors:
- *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
- *implementation
  ******************************************************************************/
 #pragma once
 

src/lib/quantifications/maprtrealxic.cpp

-
-/*******************************************************************************
- * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
- *
- * This file is part of the MassChroQ software.
- *
- *     MassChroQ is free software: you can redistribute it and/or modify
- *     it under the terms of the GNU General Public License as published by
- *     the Free Software Foundation, either version 3 of the License, or
- *     (at your option) any later version.
- *
- *     MassChroQ is distributed in the hope that it will be useful,
- *     but WITHOUT ANY WARRANTY; without even the implied warranty of
- *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *     GNU General Public License for more details.
- *
- *     You should have received a copy of the GNU General Public License
- *     along with MassChroQ.  If not, see <http://www.gnu.org/licenses/>.
- *
- * Contributors:
- *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
- *implementation
- ******************************************************************************/
-#include "maprtrealxic.h"
-
-#include "../quanti_items/quantiItemBase.h"
-//#include "../xic/xic_base.h"
-#include "../consoleout.h"
-#include "../xic/xicfilterdetectrealrt.h"
-#include "../xic/xictracebase.h"
-
-MapRtRealXic::MapRtRealXic(Msrun *current_msrun,
-                           McqXicType xic_type,
-                           Quantificator *quantificator,
-                           const pappso::XicFilterInterface *p_xic_filter,
-                           const pappso::XicDetectionInterface *p_detection)
-  : _xic_type(xic_type)
-{
-  _p_msrun       = current_msrun;
-  _p_xic_filter  = p_xic_filter;
-  _p_detection   = p_detection;
-  _matching_mode = quantificator->getMatchingMode();
-  _quantificator = quantificator;
-}
-
-MapRtRealXic::MapRtRealXic(const MapRtRealXic &copy) : _xic_type(copy._xic_type)
-{
-  _p_msrun       = copy._p_msrun;
-  _p_xic_filter  = copy._p_xic_filter;
-  _p_detection   = copy._p_detection;
-  _matching_mode = copy._matching_mode;
-  _quantificator = copy._quantificator;
-}
-
-MapRtRealXic::~MapRtRealXic()
-{
-}
-
-void
-MapRtRealXic::operator()(QuantiItemRtDeterminator &rt_determinator)
-{
-  try
-    {
-
-      XicFilterDetectRealRt filter_detect_real_rt_on_xic(_p_xic_filter,
-                                                         _p_detection);
-      McqXicNoConstSp _p_xic = _p_msrun->extractXic(
-        _xic_type,
-        _quantificator->getXicExtractionMethod()->getPappsoMassRange(
-          rt_determinator.getMz()));
-
-      if(_p_xic != nullptr)
-        {
-          qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-
-          filter_detect_real_rt_on_xic.filterDetect(
-            _p_xic.get(), &rt_determinator, _p_msrun);
-          qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-        }
-      else
-        {
-          qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
-                   << " _p_xic == nullptr";
-        }
-    }
-  catch(mcqError &errorException)
-    {
-      // QObject::tr("%1 CPUs used").arg(cpu_number)
-      // mcqerr() << "Oops! an error occurred in MassChroQ. Dont Panic :" <<
-      // endl; mcqerr() << error.qwhat() << endl;
-      qDebug() << " MapRtRealXic::operator " << errorException.qwhat();
-      // windaube_exit();
-      // return 1;
-    }
-}

src/lib/quantifications/maprtrealxic.h

-
-/*******************************************************************************
- * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
- *
- * This file is part of the MassChroQ software.
- *
- *     MassChroQ is free software: you can redistribute it and/or modify
- *     it under the terms of the GNU General Public License as published by
- *     the Free Software Foundation, either version 3 of the License, or
- *     (at your option) any later version.
- *
- *     MassChroQ is distributed in the hope that it will be useful,
- *     but WITHOUT ANY WARRANTY; without even the implied warranty of
- *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *     GNU General Public License for more details.
- *
- *     You should have received a copy of the GNU General Public License
- *     along with MassChroQ.  If not, see <http://www.gnu.org/licenses/>.
- *
- * Contributors:
- *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
- *implementation
- ******************************************************************************/
-#ifndef MAPRTREALXIC_H
-#define MAPRTREALXIC_H
-
-#include "../quanti_items/quantiitemrtdeterminator.h"
-#include "../quantificator.h"
-#include <pappsomspp/xic/detection/xicdetectioninterface.h>
-#include <pappsomspp/xic/filters/xicfilterinterface.h>
-
-struct MapRtRealXic
-{
-  Msrun *_p_msrun;
-  McqXicType _xic_type;
-  const pappso::XicFilterInterface *_p_xic_filter;
-  const pappso::XicDetectionInterface *_p_detection;
-  McqMatchingMode _matching_mode;
-  Quantificator *_quantificator;
-
-  MapRtRealXic(Msrun *current_msrun,
-               McqXicType xic_type,
-               Quantificator *quantificator,
-               const pappso::XicFilterInterface *p_xic_filter,
-               const pappso::XicDetectionInterface *p_detection);
-
-  MapRtRealXic(const MapRtRealXic &copy);
-
-  virtual ~MapRtRealXic();
-
-  void operator()(QuantiItemRtDeterminator &rt_determinator);
-};
-
-#endif // MAPRTREALXIC_H

src/lib/xic/xicfilterdetectmatch.cpp

+/** @file src/lib/xic/xicfilterdetectmatch.cpp
+ */
 
 /*******************************************************************************
  * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
@@ -32,20 +34,32 @@ XicFilterDetectMatch::XicFilterDetectMatch(
   MonitorSpeedInterface &monitor,
   const pappso::FilterInterface *p_xic_filter,
   const pappso::TraceDetectionInterface *p_detection,
+  Quantificator *p_quantificator,
   McqMatchingMode matching_mode)
   : _monitor(monitor)
 {
-  _p_detection   = p_detection;
-  _p_xic_filter  = p_xic_filter;
-  _p_trace       = p_trace;
-  _matching_mode = matching_mode;
+  _p_detection            = p_detection;
+  _p_xic_filter           = p_xic_filter;
+  _p_trace                = p_trace;
+  _matching_mode          = matching_mode;
+  _thin_peak_rt_tolerance = 0;
+  mp_quantificator        = p_quantificator;
   if(_matching_mode == McqMatchingMode::post_matching)
     {
       _thin_peak_rt_tolerance = 0;
     }
   else
     {
-      _thin_peak_rt_tolerance = 5;
+      if(mp_quantificator->getQuantificationMethod()->getSecondChance())
+        {
+          _thin_peak_rt_tolerance = 5;
+        }
+      else
+        {
+          // disable thin peak retention time tolerance, no second chance on
+          // thin peaks
+          _thin_peak_rt_tolerance = 0;
+        }
     }
 }
 
@@ -57,7 +71,7 @@ void
 XicFilterDetectMatch::setTracePeak(pappso::TracePeak &xic_peak)
 {
   // qDebug() << "XicFilterDetectMatch::setXicPeak begin" ;
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  qDebug();
   if(_p_trace != nullptr)
     {
       _p_trace->addXicPeak(xic_peak);
@@ -105,20 +119,24 @@ XicFilterDetectMatch::setTracePeak(pappso::TracePeak &xic_peak)
       else
         {
 
-          if(_matching_mode != McqMatchingMode::post_matching)
+          if(mp_quantificator->getQuantificationMethod()->getSecondChance())
             {
-              if((xic_peak.getLeftBoundary().x - _rt_target) < 10)
+              if(_matching_mode != McqMatchingMode::post_matching)
                 {
-                  unsigned int distance_point =
-                    _p_current_xic->getMsPointDistance(
-                      _rt_target, xic_peak.getLeftBoundary().x);
-                  if(distance_point == 0)
+                  if((xic_peak.getLeftBoundary().x - _rt_target) < 10)
                     {
-                      AlignedXicPeak aligned_peak(xic_peak, _p_current_msrun);
-                      _monitor.writeMatchedPeak(_p_current_msrun,
-                                                _p_current_search_item,
-                                                &aligned_peak);
-                      _peak_detected = true;
+                      unsigned int distance_point =
+                        _p_current_xic->getMsPointDistance(
+                          _rt_target, xic_peak.getLeftBoundary().x);
+                      if(distance_point == 0)
+                        {
+                          AlignedXicPeak aligned_peak(xic_peak,
+                                                      _p_current_msrun);
+                          _monitor.writeMatchedPeak(_p_current_msrun,
+                                                    _p_current_search_item,
+                                                    &aligned_peak);
+                          _peak_detected = true;
+                        }
                     }
                 }
             }
@@ -143,14 +161,17 @@ XicFilterDetectMatch::setTracePeak(pappso::TracePeak &xic_peak)
     }
   else
     {
-      if(std::abs(xic_peak.getMaxXicElement().y - _rt_target) <
-         _thin_peak_rt_tolerance)
+      if(mp_quantificator->getQuantificationMethod()->getSecondChance())
         {
-          // if this peak is nearby, in a 5 second range
-          _p_log_peaks.push_back(xic_peak.makeTracePeakCstSPtr());
+          if(std::abs(xic_peak.getMaxXicElement().y - _rt_target) <
+             _thin_peak_rt_tolerance)
+            {
+              // if this peak is nearby, in a 5 second range
+              _p_log_peaks.push_back(xic_peak.makeTracePeakCstSPtr());
+            }
         }
     }
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  qDebug();
   // qDebug() << "XicFilterDetectMatch::setXicPeak end" ;
 }
 
@@ -162,7 +183,7 @@ XicFilterDetectMatch::filterDetectQuantify(const pappso::Xic &xic,
 {
 
 
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  qDebug();
   _p_current_search_item = p_currentSearchItem;
   _p_current_msrun       = p_msrun;
   _rt_target             = rt_target;
@@ -177,15 +198,13 @@ XicFilterDetectMatch::filterDetectQuantify(const pappso::Xic &xic,
     }
 
 
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
-           << _rt_target;
+  qDebug() << _rt_target;
   _p_detection->detect(*_p_current_xic, *this);
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
-           << " after detect";
+  qDebug() << " after detect";
   if(_peak_detected == false)
     {
       if(_p_log_peaks.size() > 0)
-        {
+        { // second chance
           // take the nearest peak : this should be a small peak, that does not
           // cover the RT target
           const pappso::TracePeak *peak_i = _p_log_peaks.at(0).get();
@@ -230,5 +249,5 @@ XicFilterDetectMatch::filterDetectQuantify(const pappso::Xic &xic,
     }
 
 
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  qDebug();
 }

src/lib/xic/xicfilterdetectmatch.h

+/** @file src/lib/xic/xicfilterdetectmatch.h
+ */
 
 /*******************************************************************************
  * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
@@ -17,9 +19,6 @@
  *     You should have received a copy of the GNU General Public License
  *     along with MassChroQ.  If not, see <http://www.gnu.org/licenses/>.
  *
- * Contributors:
- *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
- *implementation
  ******************************************************************************/
 
 #pragma once
@@ -37,6 +36,7 @@ class XicFilterDetectMatch : public pappso::TraceDetectionSinkInterface
                        MonitorSpeedInterface &monitor,
                        const pappso::FilterInterface *p_xic_filter,
                        const pappso::TraceDetectionInterface *p_detection,
+                       Quantificator *p_quantificator,
                        McqMatchingMode matching_mode);
   ~XicFilterDetectMatch();
 
@@ -62,4 +62,5 @@ class XicFilterDetectMatch : public pappso::TraceDetectionSinkInterface
 
   std::vector<pappso::TracePeakCstSPtr> _p_log_peaks;
   pappso::pappso_double _thin_peak_rt_tolerance = 0;
+  Quantificator *mp_quantificator               = nullptr;
 };