write TIC in ODS file

src/core/msrun.cpp

@@ -157,11 +157,11 @@ MsRun::checkMsRunStatistics()
           setMsRunStatistics(MsRunStatistics::total_spectra_ms3,
                              (unsigned int)stats.getMsLevelCount(3));
           setMsRunStatistics(MsRunStatistics::tic_spectra_ms1,
-                             (unsigned int)stats.getMsLevelTic(1));
+                             stats.getMsLevelTic(1));
           setMsRunStatistics(MsRunStatistics::tic_spectra_ms2,
-                             (unsigned int)stats.getMsLevelTic(2));
+                             stats.getMsLevelTic(2));
           setMsRunStatistics(MsRunStatistics::tic_spectra_ms3,
-                             (unsigned int)stats.getMsLevelTic(3));
+                             stats.getMsLevelTic(3));
         }
       catch(pappso::ExceptionNotFound &error)
         {

src/output/ods/samplesheet.cpp

@@ -6,183 +6,304 @@
  */
 
 /*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-*     XTPcpp 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.
-*
-*     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp 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.
+ *
+ *     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
 
 #include "samplesheet.h"
 
-SampleSheet::SampleSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
-    _p_writer = p_writer;
-    _p_ods_export = p_ods_export;
-    p_writer->writeSheet("samples");
-    
-    OdsTableSettings table_settings;
-    table_settings.setVerticalSplit(1);
-    _p_writer->setCurrentOdsTableSettings(table_settings);
+SampleSheet::SampleSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+                         const Project *p_project)
+  : _p_project(p_project)
+{
+  _p_writer     = p_writer;
+  _p_ods_export = p_ods_export;
+  p_writer->writeSheet("samples");
 
-    writeHeaders();
+  OdsTableSettings table_settings;
+  table_settings.setVerticalSplit(1);
+  _p_writer->setCurrentOdsTableSettings(table_settings);
 
-    std::vector<IdentificationDataSourceSp> idrun_list = _p_project->getIdentificationDataSourceStore().getIdentificationDataSourceList();
+  writeHeaders();
 
-    for (IdentificationDataSourceSp idrun_sp: idrun_list) {
-        writeIdentificationDataSource(idrun_sp.get());
+  std::vector<IdentificationDataSourceSp> idrun_list =
+    _p_project->getIdentificationDataSourceStore()
+      .getIdentificationDataSourceList();
+
+  for(IdentificationDataSourceSp idrun_sp : idrun_list)
+    {
+      writeIdentificationDataSource(idrun_sp.get());
     }
 }
 
-void SampleSheet::writeHeaders()  {
-    // MS sample name	X!tandem xml result file name	X!Tandem version
-    //X!tandem xml model file name	total spectra used	total spectra assigned	assigned/used percent
-    //total unique assigned	database file names	MS/MS data source file name	MS/MS data source file path
-    //MS level 1	MS level 2	TIC mean in MS 1	TIC mean in MS 2	rt min	rt max
+void
+SampleSheet::writeHeaders()
+{
+  // MS sample name	X!tandem xml result file name	X!Tandem version
+  // X!tandem xml model file name	total spectra used	total spectra assigned
+  // assigned/used percent total unique assigned	database file names	MS/MS data
+  // source file name	MS/MS data source file path MS level 1	MS level 2	TIC
+  // mean in MS 1	TIC mean in MS 2	rt min	rt max
 
 
-    _p_writer->writeLine();
-    _p_writer->writeCell("sample ID");
-    _p_writer->writeCell("sample");
-    _p_writer->writeCell("MS run file");
-    _p_writer->writeCell("Identification engine");
-    _p_writer->writeCell("Identification engine version");
-    _p_writer->writeCell("Identification result file");
-    _p_writer->writeCell("Identification fasta files");
-    _p_writer->writeCell("X!Tandem parameters");
+  _p_writer->writeLine();
+  _p_writer->writeCell("sample ID");
+  _p_writer->writeCell("sample");
+  _p_writer->writeCell("MS run file");
+  _p_writer->writeCell("Identification engine");
+  _p_writer->writeCell("Identification engine version");
+  _p_writer->writeCell("Identification result file");
+  _p_writer->writeCell("Identification fasta files");
+  _p_writer->writeCell("X!Tandem parameters");
 
-    //   total_spectra_assigned=1, ///< total_spectra_assigned in one identification file (one sample)
-    _p_writer->setCellAnnotation("total spectra assigned in one identification file (one mzdata sample) given by the identification engine");
-    _p_writer->writeCell("Total spectra assigned");
-    //
-    //total_spectra_used=2,///< total_spectra_used in one identification file (one sample)
-    _p_writer->setCellAnnotation("total spectra used in one identification file (one mzdata sample) given by the identification engine");
-    _p_writer->writeCell("Total spectra used");
+  //   total_spectra_assigned=1, ///< total_spectra_assigned in one
+  //   identification file (one sample)
+  _p_writer->setCellAnnotation(
+    "total spectra assigned in one identification file (one mzdata sample) "
+    "given by the identification engine");
+  _p_writer->writeCell("Total spectra assigned");
+  //
+  // total_spectra_used=2,///< total_spectra_used in one identification file
+  // (one sample)
+  _p_writer->setCellAnnotation(
+    "total spectra used in one identification file (one mzdata sample) given "
+    "by the identification engine");
+  _p_writer->writeCell("Total spectra used");
 
 
-    _p_writer->setCellAnnotation("Percentage of spectra assignment (spectra assigned / spectra used");
-    _p_writer->writeCell("Assignment percentage");
+  _p_writer->setCellAnnotation(
+    "Percentage of spectra assignment (spectra assigned / spectra used");
+  _p_writer->writeCell("Assignment percentage");
 
-    //total_unique_assigned=5,///< total number unique peptide sequence assigned
-    _p_writer->setCellAnnotation("total unique peptide sequence assigned in one identification file (one mzdata sample) given by the identification engine");
-    _p_writer->writeCell("Total unique assigned");
+  // total_unique_assigned=5,///< total number unique peptide sequence assigned
+  _p_writer->setCellAnnotation(
+    "total unique peptide sequence assigned in one identification file (one "
+    "mzdata sample) given by the identification engine");
+  _p_writer->writeCell("Total unique assigned");
 
 
-    if (_msrun_statistics) {
-        _p_writer->setCellAnnotation("total number of scans during the MS run (from mz file)");
-        _p_writer->writeCell("Total scans");
+  if(_msrun_statistics)
+    {
+      _p_writer->setCellAnnotation(
+        "total number of scans during the MS run (from mz file)");
+      _p_writer->writeCell("Total scans");
 
-        _p_writer->setCellAnnotation("total number of MS level 1 during the MS run (from mz file)");
-        _p_writer->writeCell("Total MS1");
+      _p_writer->setCellAnnotation(
+        "total number of MS level 1 during the MS run (from mz file)");
+      _p_writer->writeCell("Total MS1");
 
-        _p_writer->setCellAnnotation("total number of MS level 2 during the MS run (from mz file)");
-        _p_writer->writeCell("Total MS2");
+      _p_writer->setCellAnnotation(
+        "total number of MS level 2 during the MS run (from mz file)");
+      _p_writer->writeCell("Total MS2");
 
-        _p_writer->setCellAnnotation("total number of MS level 3 during the MS run (from mz file)");
-        _p_writer->writeCell("Total MS3");
+      _p_writer->setCellAnnotation(
+        "total number of MS level 3 during the MS run (from mz file)");
+      _p_writer->writeCell("Total MS3");
 
-    }
+      _p_writer->setCellAnnotation("total ion current in MS level 1 spectra "
+                                   "during the MS run (from mz file)");
+      _p_writer->writeCell("TIC MS1");
 
-    /*
-    total_peptide_used=3,///< total number of peptides generated and used in identification
-    total_proteins_used=4,///< total number of proteins generated and used in identification
+      _p_writer->setCellAnnotation("total ion current in MS level 2 spectra "
+                                   "during the MS run (from mz file)");
+      _p_writer->writeCell("TIC MS2");
 
-    */
+      _p_writer->setCellAnnotation("total ion current in MS level 3 spectra "
+                                   "during the MS run (from mz file)");
+      _p_writer->writeCell("TIC MS3");
+    }
 
+  /*
+  total_peptide_used=3,///< total number of peptides generated and used in
+  identification total_proteins_used=4,///< total number of proteins generated
+  and used in identification
+
+  */
 }
 
-void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ident_data_source) {
-    _p_writer->writeLine();
-    MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
-    if (_msrun_statistics) {
-        if (msrun_sp->findMsRunFile()) msrun_sp->checkMsRunStatistics();
+void
+SampleSheet::writeIdentificationDataSource(
+  IdentificationDataSource *p_ident_data_source)
+{
+  _p_writer->writeLine();
+  MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
+  if(_msrun_statistics)
+    {
+      if(msrun_sp->findMsRunFile())
+        msrun_sp->checkMsRunStatistics();
     }
 
-    _p_writer->writeCell(msrun_sp.get()->getXmlId());
-    _p_writer->writeCell(msrun_sp.get()->getSampleName());
-    _p_writer->writeCell(msrun_sp.get()->getFilename());
-    _p_writer->writeCell(p_ident_data_source->getIdentificationEngineName());
-    _p_writer->writeCell(p_ident_data_source->getIdentificationEngineVersion());
-    _p_writer->writeCell(p_ident_data_source->getResourceName());
+  _p_writer->writeCell(msrun_sp.get()->getXmlId());
+  _p_writer->writeCell(msrun_sp.get()->getSampleName());
+  _p_writer->writeCell(msrun_sp.get()->getFilename());
+  _p_writer->writeCell(p_ident_data_source->getIdentificationEngineName());
+  _p_writer->writeCell(p_ident_data_source->getIdentificationEngineVersion());
+  _p_writer->writeCell(p_ident_data_source->getResourceName());
 
-    QStringList fasta_files;
-    for (FastaFileSp fasta_file:p_ident_data_source->getFastaFileList()) {
-        fasta_files << fasta_file.get()->getAbsoluteFilePath();
+  QStringList fasta_files;
+  for(FastaFileSp fasta_file : p_ident_data_source->getFastaFileList())
+    {
+      fasta_files << fasta_file.get()->getAbsoluteFilePath();
     }
-    _p_writer->writeCell(fasta_files.join(" "));
+  _p_writer->writeCell(fasta_files.join(" "));
 
-    QVariant var_sample = p_ident_data_source->getIdentificationEngineParam(IdentificationEngineParam::tandem_param);
-    if (var_sample.isNull()) {
-        _p_writer->writeEmptyCell();
-    } else {
-        _p_writer->writeCell(var_sample.toString());
+  QVariant var_sample = p_ident_data_source->getIdentificationEngineParam(
+    IdentificationEngineParam::tandem_param);
+  if(var_sample.isNull())
+    {
+      _p_writer->writeEmptyCell();
+    }
+  else
+    {
+      _p_writer->writeCell(var_sample.toString());
     }
-    var_sample = p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned);
-    if (var_sample.isNull()) {
-        _p_writer->writeEmptyCell();
-    } else {
-        _p_writer->writeCell(var_sample.toInt());
+  var_sample = p_ident_data_source->getIdentificationEngineStatistics(
+    IdentificationEngineStatistics::total_spectra_assigned);
+  if(var_sample.isNull())
+    {
+      _p_writer->writeEmptyCell();
     }
-    var_sample = p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used);
-    if (var_sample.isNull()) {
-        _p_writer->writeEmptyCell();
-    } else {
-        _p_writer->writeCell(var_sample.toInt());
+  else
+    {
+      _p_writer->writeCell(var_sample.toInt());
+    }
+  var_sample = p_ident_data_source->getIdentificationEngineStatistics(
+    IdentificationEngineStatistics::total_spectra_used);
+  if(var_sample.isNull())
+    {
+      _p_writer->writeEmptyCell();
+    }
+  else
+    {
+      _p_writer->writeCell(var_sample.toInt());
     }
 
-    if (!p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned).isNull() && !p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used).isNull()) {
-        _p_writer->writeCellPercentage(p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned).toDouble() / p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used).toDouble());
+  if(!p_ident_data_source
+        ->getIdentificationEngineStatistics(
+          IdentificationEngineStatistics::total_spectra_assigned)
+        .isNull() &&
+     !p_ident_data_source
+        ->getIdentificationEngineStatistics(
+          IdentificationEngineStatistics::total_spectra_used)
+        .isNull())
+    {
+      _p_writer->writeCellPercentage(
+        p_ident_data_source
+          ->getIdentificationEngineStatistics(
+            IdentificationEngineStatistics::total_spectra_assigned)
+          .toDouble() /
+        p_ident_data_source
+          ->getIdentificationEngineStatistics(
+            IdentificationEngineStatistics::total_spectra_used)
+          .toDouble());
     }
-    else {
-        _p_writer->writeEmptyCell();
+  else
+    {
+      _p_writer->writeEmptyCell();
     }
 
 
-    var_sample = p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_unique_assigned);
-    if (var_sample.isNull()) {
-        _p_writer->writeEmptyCell();
-    } else {
-        _p_writer->writeCell(var_sample.toInt());
+  var_sample = p_ident_data_source->getIdentificationEngineStatistics(
+    IdentificationEngineStatistics::total_unique_assigned);
+  if(var_sample.isNull())
+    {
+      _p_writer->writeEmptyCell();
+    }
+  else
+    {
+      _p_writer->writeCell(var_sample.toInt());
     }
 
-    if (_msrun_statistics) {
-        var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
-        if (var_sample.isNull()) {
-            _p_writer->writeEmptyCell();
-        } else {
-            _p_writer->writeCell(var_sample.toInt());
+  if(_msrun_statistics)
+    {
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
+        }
+      else
+        {
+          _p_writer->writeCell(var_sample.toInt());
+        }
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms1);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
         }
-        var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms1);
-        if (var_sample.isNull()) {
-            _p_writer->writeEmptyCell();
-        } else {
-            _p_writer->writeCell(var_sample.toInt());
+      else
+        {
+          _p_writer->writeCell(var_sample.toInt());
         }
-        var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms2);
-        if (var_sample.isNull()) {
-            _p_writer->writeEmptyCell();
-        } else {
-            _p_writer->writeCell(var_sample.toInt());
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms2);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
         }
-        var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms3);
-        if (var_sample.isNull()) {
-            _p_writer->writeEmptyCell();
-        } else {
-            _p_writer->writeCell(var_sample.toInt());
+      else
+        {
+          _p_writer->writeCell(var_sample.toInt());
+        }
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms3);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
+        }
+      else
+        {
+          _p_writer->writeCell(var_sample.toInt());
+        }
+        
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms1);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
+        }
+      else
+        {
+          _p_writer->writeCell(var_sample.toDouble());
+        }
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms2);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
+        }
+      else
+        {
+          _p_writer->writeCell(var_sample.toDouble());
+        }
+      var_sample =
+        msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms3);
+      if(var_sample.isNull())
+        {
+          _p_writer->writeEmptyCell();
+        }
+      else
+        {
+          _p_writer->writeCell(var_sample.toDouble());
         }
     }
-
 }

src/utils/msrunstatisticshandler.cpp

@@ -28,6 +28,7 @@
 
 #include "msrunstatisticshandler.h"
 #include <pappsomspp/msrun/msrunreader.h>
+#include <QDebug>
 
 
 bool
@@ -44,8 +45,8 @@ MsRunStatisticsHandler::setQualifiedSpectrum(
     return;
   if(ms_level > _count_ms_level_spectrum.size())
     {
-      _count_ms_level_spectrum.resize(ms_level);
-      _tic_ms_level_spectrum.resize(ms_level);
+      _count_ms_level_spectrum.resize(ms_level, 0);
+      _tic_ms_level_spectrum.resize(ms_level, 0);
     }
   _count_ms_level_spectrum[ms_level - 1]++;
 
@@ -77,6 +78,7 @@ MsRunStatisticsHandler::getMsLevelTic(unsigned int ms_level) const
     return 0;
   if(ms_level > _tic_ms_level_spectrum.size())
     return 0;
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << _tic_ms_level_spectrum[ms_level - 1];
   return (_tic_ms_level_spectrum[ms_level - 1]);
 }