using new generic xic extraction API

src/gui/xic_view/xic_box/xicbox.cpp

@@ -160,8 +160,6 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
 #if QT_VERSION >= 0x050000
   // Qt5 code
   connect(this, &XicBox::loadXic, p_worker, &XicWorkerThread::doXicLoad);
-  connect(
-    this, &XicBox::loadTimsXic, p_worker, &XicWorkerThread::doTimsXicLoad);
   connect(p_worker, &XicWorkerThread::xicLoaded, this, &XicBox::setXic);
   connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
 
@@ -405,13 +403,13 @@ XicBox::getMsRunSp()
 }
 
 void
-XicBox::setXic(std::vector<pappso::XicCstSPtr> xic_sp_list)
+XicBox::setXic(std::vector<pappso::XicCoordSPtr> xic_sp_list)
 {
   qDebug() << xic_sp_list.size() << _natural_isotope_list.size();
   ui->xic_widget->clear();
   for(std::size_t i = 0; i < xic_sp_list.size(); i++)
     {
-      _natural_isotope_list[i].xic_sp = xic_sp_list[i];
+      //_natural_isotope_list[i].xic_sp = xic_sp_list[i];
     }
   // pappso::XicWidget * xic_widget = new pappso::XicWidget(this);
   // ui->xic_list_widget->layout()->addWidget(xic_widget);
@@ -632,28 +630,36 @@ XicBox::setIsotopeMassList(
   std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list)
 {
   _natural_isotope_list.clear();
-  std::vector<pappso::pappso_double> mass_list;
+
+  pappso::XicCoordSPtr xic_coord_ref =
+    _msrun_sp.get()
+      ->getMsRunReaderSPtr()
+      .get()
+      ->newXicCoordSPtrFromSpectrumIndex(
+        _p_peptide_evidence->getSpectrumIndex(),
+        _p_xic_window->getXicExtractPrecision());
+
+  std::vector<pappso::XicCoordSPtr> mass_list;
   for(pappso::PeptideNaturalIsotopeAverageSp &natural_isotope_average :
       isotope_mass_list)
     {
       qDebug() << natural_isotope_average.get()->getMz();
-      mass_list.push_back(natural_isotope_average.get()->getMz());
-      _natural_isotope_list.push_back(
-        {nullptr, natural_isotope_average, nullptr, nullptr, {}});
-    }
+      pappso::XicCoordSPtr xic_coord =
+        xic_coord_ref.get()->initializeAndClone();
+      xic_coord.get()->mzRange =
+        pappso::MzRange(natural_isotope_average.get()->getMz(),
+                        _p_xic_window->getXicExtractPrecision());
+      mass_list.push_back(xic_coord);
 
-  if(_msrun_sp->getMzFormat() == pappso::MzFormat::brukerTims)
-    {
-      runLoadTimsXic();
-    }
-  else
-    {
-      emit loadXic(_msrun_sp,
-                   mass_list,
-                   _p_xic_window->getXicExtractPrecision(),
-                   pappso::XicExtractMethod::max);
+      _natural_isotope_list.push_back({xic_coord.get()->xicSptr,
+                                       natural_isotope_average,
+                                       nullptr,
+                                       nullptr,
+                                       {}});
     }
 
+  emit loadXic(_msrun_sp, mass_list, pappso::XicExtractMethod::max);
+
   // histogram
   if(m_theoreticalRatioBars == nullptr)
     {
@@ -735,45 +741,30 @@ XicBox::reExtractXic()
   qDebug();
   ui->xic_widget->clear();
 
-  std::vector<pappso::pappso_double> mass_list;
-  for(const XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
-    {
-      mass_list.push_back(
-        xic_isotope.peptide_natural_isotope_sp.get()->getMz());
-    }
+  pappso::XicCoordSPtr xic_coord_ref =
+    _msrun_sp.get()
+      ->getMsRunReaderSPtr()
+      .get()
+      ->newXicCoordSPtrFromSpectrumIndex(
+        _p_peptide_evidence->getSpectrumIndex(),
+        _p_xic_window->getXicExtractPrecision());
 
-  if(_msrun_sp->getMzFormat() == pappso::MzFormat::brukerTims)
-    {
-      runLoadTimsXic();
-    }
-  else
+  std::vector<pappso::XicCoordSPtr> mass_list;
+  for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
     {
-      emit loadXic(_msrun_sp,
-                   mass_list,
-                   _p_xic_window->getXicExtractPrecision(),
-                   pappso::XicExtractMethod::max);
+      pappso::XicCoordSPtr xic_coord =
+        xic_coord_ref.get()->initializeAndClone();
+      xic_coord.get()->mzRange =
+        pappso::MzRange(xic_isotope.peptide_natural_isotope_sp.get()->getMz(),
+                        _p_xic_window->getXicExtractPrecision());
+      mass_list.push_back(xic_coord);
+      xic_isotope.xic_sp = xic_coord.get()->xicSptr;
     }
-  qDebug();
-}
 
-void
-XicBox::runLoadTimsXic()
-{
-  qDebug() << "begin tims xic extraction";
-  std::vector<pappso::pappso_double> mass_list;
-  for(XicBoxNaturalIsotope isotope : _natural_isotope_list)
-    {
-      mass_list.push_back(isotope.peptide_natural_isotope_sp.get()->getMz());
-    }
-  std::size_t precursor_index = (_p_peptide_evidence->getScanNumber() / 2) + 1;
-  emit loadTimsXic(_msrun_sp,
-                   precursor_index,
-                   mass_list,
-                   _p_xic_window->getXicExtractPrecision(),
-                   pappso::XicExtractMethod::max);
-  qDebug() << "tims xic extraction sent to thread";
-}
+  emit loadXic(_msrun_sp, mass_list, pappso::XicExtractMethod::max);
 
+  qDebug();
+}
 
 void
 XicBox::setRetentionTime(double rt)

src/gui/xic_view/xic_box/xicbox.h

@@ -81,14 +81,8 @@ class XicBox : public QWidget
 
   signals:
   void loadXic(MsRunSp p_msrun,
-               std::vector<pappso::pappso_double> mz_list,
-               pappso::PrecisionPtr precision,
+               std::vector<pappso::XicCoordSPtr> mz_list,
                pappso::XicExtractMethod method);
-  void loadTimsXic(MsRunSp p_msrun,
-                   std::size_t precursor_index,
-                   std::vector<pappso::pappso_double> mz_list,
-                   pappso::PrecisionPtr precision,
-                   pappso::XicExtractMethod method);
   void computeIsotopeMassList(pappso::PeptideSp peptide_sp,
                               unsigned int charge,
                               pappso::PrecisionPtr precision,
@@ -98,7 +92,7 @@ class XicBox : public QWidget
   private slots:
   void remove();
   void reExtractXic();
-  void setXic(std::vector<pappso::XicCstSPtr> xic_sp_list);
+  void setXic(std::vector<pappso::XicCoordSPtr> xic_sp_list);
   void setIsotopeMassList(
     std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
   void error(QString error_message);
@@ -123,7 +117,6 @@ class XicBox : public QWidget
   void addCommonRt(std::vector<std::size_t> &common_peak_rt_measure_list,
                    const pappso::TracePeak *peak,
                    const pappso::Xic *xic) const;
-  void runLoadTimsXic();
 
   private:
   Ui::XicBox *ui;

src/gui/xic_view/xicworkerthread.cpp

@@ -43,24 +43,12 @@ XicWorkerThread::~XicWorkerThread()
 }
 void
 XicWorkerThread::doXicLoad(MsRunSp p_msrun,
-                           std::vector<pappso::pappso_double> mz_list,
-                           pappso::PrecisionPtr precision,
+                           std::vector<pappso::XicCoordSPtr> xic_coord_list,
                            pappso::XicExtractMethod method)
 {
 
   try
     {
-      std::vector<pappso::MzRange> mass_list;
-      for(pappso::pappso_double mass : mz_list)
-        {
-          mass_list.push_back(pappso::MzRange(mass, precision));
-        }
-      // std::vector<pappso::XicSp> xic_sp_list =
-      // SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
-
-      std::vector<pappso::XicCstSPtr> xic_sp_list;
-
-
       pappso::MsRunXicExtractorInterfaceSp extractor =
         p_msrun.get()->getMsRunXicExtractorInterfaceSp();
       if(extractor != nullptr)
@@ -70,69 +58,11 @@ XicWorkerThread::doXicLoad(MsRunSp p_msrun,
 
 
           qDebug();
-          xic_sp_list = extractor.get()->getXicCstSPtrList(mass_list);
+          extractor.get()->extractXicCoordSPtrList(xic_coord_list);
 
           qDebug();
         }
-      emit xicLoaded(xic_sp_list);
-    }
-  catch(pappso::PappsoException &error)
-    {
-      emit operationFailed(tr("Error extracting XIC for MSrun %1:\n%2")
-                             .arg(p_msrun->getFileName())
-                             .arg(error.qwhat()));
-    }
-}
-
-
-void
-XicWorkerThread::doTimsXicLoad(MsRunSp p_msrun,
-                               std::size_t precursor_index,
-                               std::vector<pappso::pappso_double> mz_list,
-                               pappso::PrecisionPtr precision,
-                               pappso::XicExtractMethod method)
-{
-  try
-    {
-      pappso::TimsMsRunReaderMs2 *tims2_reader =
-        dynamic_cast<pappso::TimsMsRunReaderMs2 *>(
-          p_msrun->getMsRunReaderSPtr().get());
-      if(tims2_reader != nullptr)
-        {
-          pappso::TimsData *tims_data = tims2_reader->getTimsDataSPtr().get();
-          qDebug() << "tims_data ok";
-
-          pappso::TimsXicStructure xic_struct =
-            tims_data->getTimsXicStructureFromPrecursorId(precursor_index,
-                                                          precision);
-          qDebug() << mz_list;
-          std::vector<pappso::TimsXicStructure> xic_struct_list;
-          std::vector<pappso::XicCstSPtr> xic_sp_list;
-          for(pappso::pappso_double mz : mz_list)
-            {
-              pappso::TimsXicStructure new_xic_struct =
-                pappso::TimsXicStructure(xic_struct);
-              new_xic_struct.mzRange = pappso::MzRange(mz, precision);
-              new_xic_struct.xicSptr = std::make_shared<pappso::Xic>();
-              xic_struct_list.push_back(new_xic_struct);
-            }
-
-          tims_data->extractXicListByTimsXicStructureList(
-            xic_struct_list, method, 100000);
-          for(pappso::TimsXicStructure xic_struct : xic_struct_list)
-            {
-              xic_sp_list.push_back(xic_struct.xicSptr);
-            }
-
-          qDebug() << "xic produced";
-          emit xicLoaded(xic_sp_list);
-        }
-      else
-        {
-          throw pappso::PappsoException(
-            tr("Error the msrun %1 isn't a timsTOF data")
-              .arg(p_msrun->getFileName()));
-        }
+      emit xicLoaded(xic_coord_list);
     }
   catch(pappso::PappsoException &error)
     {

src/gui/xic_view/xicworkerthread.h

@@ -27,8 +27,7 @@
  *implementation
  ******************************************************************************/
 
-#ifndef XICWORKERTHREAD_H
-#define XICWORKERTHREAD_H
+#pragma once
 
 #include <pappsomspp/peptide/peptidenaturalisotopelist.h>
 #include <QObject>
@@ -44,21 +43,15 @@ class XicWorkerThread : public QObject
   virtual ~XicWorkerThread();
   public slots:
   void doXicLoad(MsRunSp p_msrun,
-                 std::vector<pappso::pappso_double> mz_list,
-                 pappso::PrecisionPtr precision,
+                 std::vector<pappso::XicCoordSPtr> xic_coord_list,
                  pappso::XicExtractMethod method);
-  void doTimsXicLoad(MsRunSp p_msrun,
-                     std::size_t precursor_index,
-                     std::vector<pappso::pappso_double> mz_list,
-                     pappso::PrecisionPtr precision,
-                     pappso::XicExtractMethod method);
   void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
                                 unsigned int charge,
                                 pappso::PrecisionPtr precision,
                                 double minimum_isotope_pattern_ratio);
 
   signals:
-  void xicLoaded(std::vector<pappso::XicCstSPtr> xic_sp_list);
+  void xicLoaded(std::vector<pappso::XicCoordSPtr> xic_sp_list);
   void isotopeMassListComputed(
     std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
   void operationFailed(QString error);
@@ -66,4 +59,4 @@ class XicWorkerThread : public QObject
   private:
   std::vector<pappso::MsRunXicExtractorInterfaceSp> _extractor_list;
 };
-#endif // XICWORKERTHREAD_H
+

src/main.cpp

@@ -59,6 +59,7 @@ main(int argc, char *argv[])
   qRegisterMetaType<PtmMode>("PtmMode");
   qRegisterMetaType<std::vector<XicBox *>>("<std::vector<XicBox *>>");
   qRegisterMetaType<MassChroQRunBatch>("MassChroQRunBatch");
+  qRegisterMetaType<std::vector<pappso::XicCoordSPtr>>("std::vector<pappso::XicCoordSPtr>");
 
   // qRegisterMetaType<pappso::PeakIonIsotopeMatch>("pappso::PeakIonIsotopeMatch");