Merge branch 'renne' into 'master'

Allow to use TDF raw data to load MGF spectrum

See merge request !26

src/core/identification_sources/identificationdatasource.cpp

@@ -29,6 +29,7 @@
 #include <QFileInfo>
 #include "../msrun.h"
 #include "../peptideevidence.h"
+#include <pappsomspp/msrun/private/timsmsrunreaderms2.h>
 
 IdentificationDataSource::IdentificationDataSource(const QString resource_name)
 {
@@ -216,6 +217,7 @@ IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
   if(_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF)
     {
       scan_number = scan_number - 1;
+      qDebug() << "MGF format";
     }
   pappso::MsRunReaderSPtr msrun_reader_sp =
     _ms_run_sp.get()->getMsRunReaderSPtr();
@@ -259,6 +261,89 @@ IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
   return spectrum_sp;
 }
 
+pappso::MassSpectrumCstSPtr
+IdentificationDataSource::getMassSpectrumCstSPtrMgfToTdf(
+  unsigned int scan_number,
+  QString tdf_file,
+  int charge,
+  double mz_val,
+  double rt_sec,
+  double k0) const
+{
+  qDebug() << "scan=" << scan_number;
+  if(_ms_run_sp.get()->getMzFormat() != pappso::MzFormat::MGF)
+    {
+      throw pappso::ExceptionNotFound(
+        QObject::tr("mz data \"%1\" not a MGF format")
+          .arg(_ms_run_sp.get()->getFileName()));
+    }
+
+  scan_number = scan_number - 1;
+
+  pappso::MsRunReaderSPtr msrun_reader_sp =
+    _ms_run_sp.get()->getMsRunReaderSPtrMgfToTdf(tdf_file);
+
+  if(msrun_reader_sp == nullptr)
+    {
+      msrun_reader_sp = _ms_run_sp.get()->findMsRunFile();
+      if(msrun_reader_sp == nullptr)
+        {
+          throw pappso::ExceptionNotFound(
+            QObject::tr("mz data \"%1\" file not found").arg(tdf_file));
+        }
+    }
+  msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSPtrMgfToTdf(tdf_file);
+  if(msrun_reader_sp == nullptr)
+    {
+      throw pappso::ExceptionNotFound(
+        QObject::tr("mz data \"%1\" file not found").arg(tdf_file));
+    }
+
+
+  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__  <<
+  // _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
+
+
+  std::size_t spectrum_index = scan_number;
+  qDebug();
+  if(msrun_reader_sp.get()->hasScanNumbers())
+    {
+      qDebug() << "HAS SCAN NUMBERS";
+      spectrum_index =
+        msrun_reader_sp.get()->scanNumber2SpectrumIndex(scan_number);
+    }
+  std::vector<std::size_t> spectrum_result;
+
+  pappso::TimsMsRunReaderMs2 *tims2_reader =
+    dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader_sp.get());
+  if(tims2_reader != nullptr)
+    {
+      spectrum_result =
+        tims2_reader->getPrecursorsIDFromMzRt(charge, mz_val, rt_sec, k0);
+    }
+
+  qDebug() << spectrum_result.size();
+  if(spectrum_result.size() == 0)
+    {
+      throw pappso::ExceptionNotFound(
+        QObject::tr("The SQL request doesn't found any TDF scan "
+                    "associated"));
+    }
+  if(spectrum_result.size() > 1)
+    {
+      throw pappso::ExceptionNotFound(
+        QObject::tr("The SQL request found more than 1 TDF scan "
+                    "associated"));
+    }
+  spectrum_index = spectrum_result[0] * 2 - 1;
+  qDebug() << " spectrum index=" << spectrum_index;
+  pappso::MassSpectrumCstSPtr spectrum_sp =
+    msrun_reader_sp.get()->massSpectrumCstSPtr(spectrum_index);
+  qDebug();
+  return spectrum_sp;
+}
+
+
 void
 IdentificationDataSource::addFastaFile(FastaFileSp file)
 {

src/core/identification_sources/identificationdatasource.h

@@ -63,8 +63,16 @@ class IdentificationDataSource
    * */
   virtual pappso::MassSpectrumCstSPtr
   getMassSpectrumCstSPtr(unsigned int scan_number) const;
-
-
+  /** @brief get the spectrum from MGF values such as precursor mz, precursor
+   * charge, RT and K0
+   * */
+  pappso::MassSpectrumCstSPtr
+  getMassSpectrumCstSPtrMgfToTdf(unsigned int scan_number,
+                                 QString tdf_file,
+                                 int charge,
+                                 double mz_val,
+                                 double rt_sec,
+                                 double k0) const;
   /** \brief read source content to store it in project
    */
   virtual void parseTo(Project *p_project) = 0;

src/core/msrun.cpp

@@ -69,77 +69,94 @@ MsRun::getMsRunReaderSPtr()
   // qDebug() << " filename=" << getFileName();
   if(_msrun_reader_sp == nullptr)
     {
-      qDebug() << " runid=" << getRunId() << " xmlid=" << getXmlId();
-      pappso::MsFileAccessor *p_accessor = nullptr;
+      setMsRunReaderSp(getFileName());
+    }
+
+  return _msrun_reader_sp;
+}
+
+pappso::MsRunReaderSPtr &
+MsRun::getMsRunReaderSPtrMgfToTdf(QString tdf_file)
+{
+  qDebug() << " filename=" << getFileName();
+  qDebug() << "filenameTDF = " << tdf_file;
+
+  if(_msrun_reader_sp == nullptr)
+    {
+      setMsRunReaderSp(tdf_file);
+    }
+
+  return _msrun_reader_sp;
+}
+
+void
+MsRun::setMsRunReaderSp(QString ms_run_file)
+{
+  qDebug() << " runid=" << getRunId() << " xmlid=" << getXmlId();
+  pappso::MsFileAccessor *p_accessor = nullptr;
+
+  try
+    {
+
+      p_accessor = new pappso::MsFileAccessor(ms_run_file, "runa1");
 
+      p_accessor->setPreferedFileReaderType(pappso::MzFormat::brukerTims,
+                                            pappso::FileReaderType::tims_ms2);
+    }
+  catch(pappso::ExceptionNotFound &error)
+    {
+      qDebug() << "not found";
+      _msrun_reader_sp = nullptr;
+      /// p_accessor       = nullptr;
+      // throw error;
+      // file not found, don't throw exception, we'll try another location
+    }
+  if(p_accessor != nullptr)
+    {
       try
         {
+          _msrun_reader_sp =
+            p_accessor->getMsRunReaderSPtrByRunId(getRunId(), getXmlId());
+          delete p_accessor;
+          p_accessor = nullptr;
 
-          // pappso::MsFileAccessor accessor(getFileName(), "");
-          p_accessor = new pappso::MsFileAccessor(getFileName(), "runa1");
-          p_accessor->setPreferedFileReaderType(
-            pappso::MzFormat::brukerTims, pappso::FileReaderType::tims_ms2);
-        }
-      catch(pappso::ExceptionNotFound &error)
-        {
-          qDebug() << "not found";
-          _msrun_reader_sp = nullptr;
-          /// p_accessor       = nullptr;
-          // throw error;
-          // file not found, don't throw exception, we'll try another location
-        }
-      if(p_accessor != nullptr)
-        {
-          try
+          qDebug() << m_centroidOptions;
+          if(!m_centroidOptions.isEmpty())
             {
-              _msrun_reader_sp =
-                p_accessor->getMsRunReaderSPtrByRunId(getRunId(), getXmlId());
-              delete p_accessor;
-              p_accessor = nullptr;
-
-              //qDebug() << m_centroidOptions;
-              if(!m_centroidOptions.isEmpty())
+              pappso::TimsMsRunReaderMs2 *tims2_reader =
+                dynamic_cast<pappso::TimsMsRunReaderMs2 *>(
+                  _msrun_reader_sp.get());
+              if(tims2_reader != nullptr)
                 {
-                  pappso::TimsMsRunReaderMs2 *tims2_reader =
-                    dynamic_cast<pappso::TimsMsRunReaderMs2 *>(
-                      _msrun_reader_sp.get());
-                  if(tims2_reader != nullptr)
-                    {
-                      qDebug() << m_centroidOptions;
-                      QStringList option_list = m_centroidOptions.split(" ");
-                      std::shared_ptr<pappso::FilterPseudoCentroid> ms2filter =
-                        std::make_shared<pappso::FilterPseudoCentroid>(
-                          option_list.at(0).toDouble(),
-                          option_list.at(1).toDouble(),
-                          option_list.at(2).toDouble(),
-                          option_list.at(3).toDouble());
-
-                      tims2_reader->setMs2FilterCstSPtr(ms2filter);
-                      qDebug() << m_centroidOptions;
-                    }
+                  qDebug() << m_centroidOptions;
+                  QStringList option_list = m_centroidOptions.split(" ");
+                  std::shared_ptr<pappso::FilterPseudoCentroid> ms2filter =
+                    std::make_shared<pappso::FilterPseudoCentroid>(
+                      option_list.at(0).toDouble(),
+                      option_list.at(1).toDouble(),
+                      option_list.at(2).toDouble(),
+                      option_list.at(3).toDouble());
+
+                  tims2_reader->setMs2FilterCstSPtr(ms2filter);
+                  qDebug() << m_centroidOptions;
                 }
             }
+        }
 
-          catch(pappso::PappsoException &error2)
+      catch(pappso::PappsoException &error2)
+        {
+          _msrun_reader_sp = nullptr;
+          if(p_accessor != nullptr)
             {
-              _msrun_reader_sp = nullptr;
-              if(p_accessor != nullptr)
-                {
-                  delete p_accessor;
-                  p_accessor = nullptr;
-                }
-              throw error2;
+              delete p_accessor;
+              p_accessor = nullptr;
             }
+          throw error2;
         }
     }
-  else
-    {
-      // qDebug();
-    }
-
-  return _msrun_reader_sp;
 }
 
+
 void
 MsRun::freeMsRunReaderSp()
 {

src/core/msrun.h

@@ -78,6 +78,8 @@ class MsRun : public pappso::MsRunId
   pappso::MsRunReaderSPtr findMsRunFile();
 
   pappso::MsRunReaderSPtr &getMsRunReaderSPtr();
+  pappso::MsRunReaderSPtr &getMsRunReaderSPtrMgfToTdf(QString tdf_file);
+  void setMsRunReaderSp(QString ms_run_file);
 
   /** @brief release shared pointer on MSrun reader
    */

src/gui/edit/edit_settings/edit_settings.ui

@@ -14,7 +14,7 @@
    </rect>
   </property>
   <property name="windowTitle">
-   <string>About</string>
+   <string>Settings</string>
   </property>
   <property name="sizeGripEnabled">
    <bool>false</bool>
@@ -161,6 +161,44 @@
         </item>
        </layout>
       </item>
+      <item>
+       <widget class="QLabel" name="label_4">
+        <property name="text">
+         <string>Raw data used in spectrum(MGF file)</string>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_5">
+        <item>
+         <widget class="QRadioButton" name="mgf_button">
+          <property name="text">
+           <string>&amp;MGF</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QRadioButton" name="tdf_button">
+          <property name="text">
+           <string>&amp;TDF</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </item>
      </layout>
     </widget>
    </item>

src/gui/edit/edit_settings/editsettings.cpp

@@ -37,11 +37,14 @@
 #include <QProcess>
 #include <pappsomspp/exception/exceptionnotfound.h>
 #include <QMessageBox>
+#include "gui/mainwindow.h"
 
-EditSettings::EditSettings(QWidget *parent)
+EditSettings::EditSettings(MainWindow *parent)
   : QDialog(parent), ui(new Ui::EditSettingsDialog)
 {
   ui->setupUi(this);
+  mp_mainWindow = parent;
+
   QSettings settings;
   QString xic_extraction_method =
     settings.value("global/xic_extractor", "pwiz").toString();
@@ -54,9 +57,20 @@ EditSettings::EditSettings(QWidget *parent)
   QString tandemwrapper_path =
     settings.value("timstof/tandemwrapper_path", "").toString();
   QString tmp_dir_path = settings.value("timstof/tmp_dir_path", "").toString();
+  QString spectrum_load_method =
+    settings.value("timstof/spectrum_load_method", "mgf").toString();
 
   ui->tandemwrapper_path_line->setText(tandemwrapper_path);
   ui->tmp_dir_line->setText(tmp_dir_path);
+  ui->tdf_button->setChecked(true);
+  if(spectrum_load_method == "mgf")
+    {
+      ui->mgf_button->setChecked(true);
+    }
+  connect(this,
+          &EditSettings::operateFreeAllMsRunReaders,
+          mp_mainWindow,
+          &MainWindow::doFreeAllMsRunReaders);
 }
 
 
@@ -106,6 +120,14 @@ EditSettings::done(int r)
           settings.setValue("timstof/tmp_dir_path", tmp_dir_path);
         }
 
+      QString spectrum_load_method = "mgf";
+      if(ui->tdf_button->isChecked())
+        {
+          spectrum_load_method = "tdf";
+        }
+      settings.setValue("timstof/spectrum_load_method", spectrum_load_method);
+      emit operateFreeAllMsRunReaders();
+
       QDialog::done(r);
       return;
     }

src/gui/edit/edit_settings/editsettings.h

@@ -33,6 +33,8 @@
 #include <QDialog>
 #include <QFileInfo>
 
+class MainWindow;
+
 namespace Ui
 {
 class EditSettingsDialog;
@@ -43,7 +45,7 @@ class EditSettings : public QDialog
   Q_OBJECT
 
   public:
-  explicit EditSettings(QWidget *parent = 0);
+  explicit EditSettings(MainWindow *parent = 0);
   ~EditSettings();
 
   protected:
@@ -54,6 +56,10 @@ class EditSettings : public QDialog
   void selectTandemWrapperPath();
   void selectTmpDirPath();
 
+  signals:
+  void operateFreeAllMsRunReaders();
+
   private:
   Ui::EditSettingsDialog *ui;
+  MainWindow *mp_mainWindow = nullptr;
 };

src/gui/mainwindow.cpp

@@ -84,6 +84,11 @@ MainWindow::MainWindow(QWidget *parent) : QMainWindow(parent), ui(new Ui::Main)
           &HttpVersion::httpVersionReady,
           this,
           &MainWindow::doCheckNewVersion);
+  connect(this,
+          &MainWindow::operateFreeAllMsRunReaders,
+          _project_window,
+          &ProjectWindow::doCleanMsRunReaders);
+
 #else
 #endif
 }
@@ -893,3 +898,9 @@ MainWindow::getWorkerThread()
 {
   return mp_worker;
 }
+
+void
+MainWindow::doFreeAllMsRunReaders()
+{
+  emit operateFreeAllMsRunReaders();
+}

src/gui/mainwindow.h

@@ -101,6 +101,7 @@ class MainWindow : public QMainWindow
   void doGroupingFinished();
   void doActionSpectralCountingMcq();
   void doCheckNewVersion();
+  void doFreeAllMsRunReaders();
   // void peptideEdited(QString peptideStr);
   // void setColor(const QColor &color);
   // void setShape(Shape shape);
@@ -126,6 +127,7 @@ class MainWindow : public QMainWindow
   void operateGrouping(ProjectSp project_sp);
   void operateRunningXtandem(TandemRunBatch tandem_run_batch);
   void projectNameChanged(QString project_name);
+  void operateFreeAllMsRunReaders();
 
   protected:
   void closeEvent(QCloseEvent *event) override;

src/gui/peptide_detail_view/peptidewindow.cpp

@@ -42,11 +42,53 @@ SpectrumSpLoaderThread::doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence)
 {
   qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp begin";
   pappso::MassSpectrumCstSPtr spectrum;
+  QSettings settings;
+  QString spectrum_load_method =
+    settings.value("timstof/spectrum_load_method", "mgf").toString();
   try
     {
-      spectrum =
-        p_peptide_evidence->getIdentificationDataSource()
-          ->getMassSpectrumCstSPtr(p_peptide_evidence->getScanNumber());
+      QString tdf_file =
+        QFileInfo(p_peptide_evidence->getIdentificationDataSource()
+                    ->getMsRunSp()
+                    ->getFileName())
+          .absoluteDir()
+          .absolutePath() +
+        "/analysis.tdf";
+
+      if(QFileInfo(tdf_file).exists())
+        {
+          if(spectrum_load_method == "mgf")
+            {
+              spectrum =
+                p_peptide_evidence->getIdentificationDataSource()
+                  ->getMassSpectrumCstSPtr(p_peptide_evidence->getScanNumber());
+            }
+          else
+            {
+              QString tdf_file =
+                QFileInfo(p_peptide_evidence->getIdentificationDataSource()
+                            ->getMsRunSp()
+                            ->getFileName())
+                  .absoluteDir()
+                  .absolutePath() +
+                "/analysis.tdf";
+              spectrum = p_peptide_evidence->getIdentificationDataSource()
+                           ->getMassSpectrumCstSPtrMgfToTdf(
+                             p_peptide_evidence->getScanNumber(),
+                             tdf_file,
+                             p_peptide_evidence->getCharge(),
+                             p_peptide_evidence->getExperimentalMz(),
+                             p_peptide_evidence->getRetentionTime(),
+                             0.99); // TODO add the K0 param
+            }
+        }
+      else
+        {
+          spectrum =
+            p_peptide_evidence->getIdentificationDataSource()
+              ->getMassSpectrumCstSPtr(p_peptide_evidence->getScanNumber());
+        }
+
       emit spectrumSpReady(spectrum, QString(""), QString(""));
     }
 

src/gui/project_view/projectwindow.cpp

@@ -1124,3 +1124,16 @@ ProjectWindow::getPtmMode()
 
   return ptm_mode;
 }
+
+void
+ProjectWindow::doCleanMsRunReaders()
+{
+  if(_project_sp.get() != nullptr)
+    {
+      for(MsRunSp ms_run_sp : _project_sp.get()->getMsRunStore().getMsRunList())
+        {
+          qDebug() << "free reader of " << ms_run_sp.get()->getFileName();
+          ms_run_sp.get()->freeMsRunReaderSp();
+        }
+    }
+}

src/gui/project_view/projectwindow.h

@@ -92,9 +92,11 @@ class ProjectWindow : public QMainWindow
   void doProjectStatusChanged();
   void doFindBestMsRunInAlignmentGroup(MsRunAlignmentGroupSp);
   void doBestMsRunForAlignmentFinished(MsRunSp msrun_sp);
+  void doCleanMsRunReaders();
   // void setColor(const QColor &color);
   // void setShape(Shape shape);
 
+
   signals:
   void identificationGroupGrouped(IdentificationGroup *p_identification_group);
   void