new identification engine statistics

src/core/identification_sources/identificationdatasource.cpp

@@ -97,6 +97,19 @@ const QVariant IdentificationDataSource::getIdentificationEngineParam(Identifica
         return QVariant();
     }
 }
+
+void IdentificationDataSource::setIdentificationEngineStatistics(IdentificationEngineStatistics param, const QVariant& value) {
+    _param_stats.insert(std::pair<IdentificationEngineStatistics, QVariant>(param, value));
+}
+const QVariant IdentificationDataSource::getIdentificationEngineStatistics(IdentificationEngineStatistics param) const {
+    try {
+        return _param_stats.at(param);
+    }
+    catch (std::out_of_range) {
+        return QVariant();
+    }
+}
+
 pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
     pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp, scan_number);
     return spectrum_sp;

src/core/identification_sources/identificationdatasource.h

@@ -85,7 +85,18 @@ public:
     /** \brief get specific identification engine parameter value
      */
     virtual const QVariant getIdentificationEngineParam(IdentificationEngineParam param) const;
+
+       
+    /** \brief set identification engine statistics
+     * any statistics on this identification run that can be told by the identification engine
+     */
+    virtual void setIdentificationEngineStatistics(IdentificationEngineStatistics param, const QVariant& value);
+    
     
+    /** \brief get specific identification engine statistics value
+     */
+    virtual const QVariant getIdentificationEngineStatistics(IdentificationEngineStatistics param) const;
+
     /** \brief add Fastafile used by the identification engine
      */
     void addFastaFile (FastaFileSp file);
@@ -100,6 +111,7 @@ private :
     QString _version;
     MsRunSp _ms_run_sp = nullptr;
     std::map<IdentificationEngineParam, QVariant> _params;
+    std::map<IdentificationEngineStatistics, QVariant> _param_stats;
     std::vector<FastaFileSp> _fastafile_list;
 };
 

src/gui/tandem_run_dialog/tandem_run_dialog.ui

@@ -253,22 +253,6 @@
  </widget>
  <resources/>
  <connections>
-  <connection>
-   <sender>add_files_button</sender>
-   <signal>clicked()</signal>
-   <receiver>TandemRunDialog</receiver>
-   <slot>chooseFiles()</slot>
-   <hints>
-    <hint type="sourcelabel">
-     <x>550</x>
-     <y>310</y>
-    </hint>
-    <hint type="destinationlabel">
-     <x>550</x>
-     <y>264</y>
-    </hint>
-   </hints>
-  </connection>
   <connection>
    <sender>pushButton_2</sender>
    <signal>clicked()</signal>
@@ -305,7 +289,7 @@
    <sender>clear_list_button</sender>
    <signal>clicked()</signal>
    <receiver>TandemRunDialog</receiver>
-   <slot>clearFileList()</slot>
+   <slot>clearFastaFiles()</slot>
    <hints>
     <hint type="sourcelabel">
      <x>464</x>
@@ -402,6 +386,7 @@
   <slot>reject()</slot>
   <slot>accept()</slot>
   <slot>selectFastaFiles()</slot>
+  <slot>clearFastaFiles()</slot>
   <slot>selectMzFiles()</slot>
   <slot>selectOutputDirectory()</slot>
   <slot>setPresetName(QString)</slot>

src/gui/tandem_run_dialog/tandemrundialog.cpp

@@ -159,6 +159,10 @@ void TandemRunDialog::selectOutputDirectory() {
     }
 }
 
+void TandemRunDialog::clearFastaFiles() {
+    _p_fasta_file_list->removeRows( 0, _p_fasta_file_list->rowCount() );
+}
+
 void TandemRunDialog::selectFastaFiles() {
     try {
         QSettings settings;

src/gui/tandem_run_dialog/tandemrundialog.h

@@ -51,6 +51,7 @@ public:
     void reset();
 public slots:
     void selectFastaFiles();
+    void clearFastaFiles();
     void selectMzFiles();
     void selectOutputDirectory();
     void selectPresetDirectory();

src/input/xtandemsaxhandler.cpp

@@ -295,7 +295,7 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
     _p_peptide_match->setExperimentalMass(exp_mass);
     _p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
     _p_peptide_match->setCharge(_charge);
-    
+
     _p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore,  QVariant( attributes.value("hyperscore").toDouble()));
 
     _p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
@@ -336,11 +336,11 @@ bool XtandemSaxHandler::endElement_note() {
     bool is_ok = true;
     if (_is_protein_description) {
         //_p_protein_match->getProteinXtpSp().get()->setDescription(_current_text.section(" ",1));
-	_p_protein_match->getProteinXtpSp().get()->setCompleteDescription(_current_text);
-	if (!_p_protein_match->getProteinXtpSp().get()->getAccession().endsWith(":reversed") && _p_protein_match->getProteinXtpSp().get()->getDescription().endsWith(":reversed")) {
-	  //to fit most cases, just check that the :reversed chars added by X!Tandem are not in the description. if so, then add it too in the accession
-	  _p_protein_match->getProteinXtpSp().get()->setAccession(QString("%1%2").arg(_p_protein_match->getProteinXtpSp().get()->getAccession()).arg(":reversed"));
-	}
+        _p_protein_match->getProteinXtpSp().get()->setCompleteDescription(_current_text);
+        if (!_p_protein_match->getProteinXtpSp().get()->getAccession().endsWith(":reversed") && _p_protein_match->getProteinXtpSp().get()->getDescription().endsWith(":reversed")) {
+            //to fit most cases, just check that the :reversed chars added by X!Tandem are not in the description. if so, then add it too in the accession
+            _p_protein_match->getProteinXtpSp().get()->setAccession(QString("%1%2").arg(_p_protein_match->getProteinXtpSp().get()->getAccession()).arg(":reversed"));
+        }
     }
     else {
 
@@ -470,13 +470,30 @@ bool XtandemSaxHandler::endElement_note() {
         <note label="modelling, estimated false positives">18</note>
         <note label="modelling, reversed sequence false positives">20</note>
         <note label="modelling, spectrum noise suppression ratio">0.00</note>
-        <note label="modelling, total peptides used">96618641</note>
-        <note label="modelling, total proteins used">273656</note>
-        <note label="modelling, total spectra assigned">7464</note>
-        <note label="modelling, total spectra used">12199</note>
-        <note label="modelling, total unique assigned">6260</note>
-        <note label="process, start time">2013:12:20:16:47:19</note>
         */
+        //<note label="modelling, total peptides used">96618641</note>
+        if (_current_note_label == "modelling, total peptides used") {
+            _p_identification_data_source->setIdentificationEngineStatistics(IdentificationEngineStatistics::total_peptide_used, _current_text.toUInt());
+        }
+
+        //<note label="modelling, total proteins used">273656</note>
+        if (_current_note_label == "modelling, total proteins used") {
+            _p_identification_data_source->setIdentificationEngineStatistics(IdentificationEngineStatistics::total_proteins_used, _current_text.toUInt());
+        }
+        //<note label="modelling, total spectra assigned">7464</note>
+        if (_current_note_label == "modelling, total spectra assigned") {
+            _p_identification_data_source->setIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned, _current_text.toUInt());
+        }
+        //<note label="modelling, total spectra used">12199</note>
+        if (_current_note_label == "modelling, total spectra used") {
+            _p_identification_data_source->setIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used, _current_text.toUInt());
+        }
+        //<note label="modelling, total unique assigned">6260</note>
+        if (_current_note_label == "modelling, total unique assigned") {
+            _p_identification_data_source->setIdentificationEngineStatistics(IdentificationEngineStatistics::total_unique_assigned, _current_text.toUInt());
+        }
+        //<note label="process, start time">2013:12:20:16:47:19</note>
+        
         //<note label="process, version">X! Tandem Sledgehammer (2013.09.01.1)</note>
         if (_current_note_label == "process, version") {
             QRegExp rx("\\((.*)\\)");

src/output/ods/samplesheet.cpp

@@ -60,6 +60,29 @@ void SampleSheet::writeHeaders()  {
     _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");
+
+
+    _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_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
+
+    */
 
 }
 
@@ -79,5 +102,14 @@ void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ide
     _p_writer->writeCell(fasta_files.join(" "));
 
     _p_writer->writeCell(p_ident_data_source->getIdentificationEngineParam(IdentificationEngineParam::tandem_param).toString());
+    _p_writer->writeCell(p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned).toString());
+
+    _p_writer->writeCell(p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used).toString());
+
+    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());
+    }
+
+    _p_writer->writeCell(p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_unique_assigned).toString());
 
 }

src/utils/types.h

@@ -64,6 +64,19 @@ enum class IdentificationEngineParam {
     tandem_param ///< X!Tandem xml parameters file
 };
 
+
+/** \def IdentificationEngineStatistics identification engine statistics
+ *
+ */
+enum class IdentificationEngineStatistics: std::int8_t {
+    total_spectra_assigned=1, ///< total_spectra_assigned in one identification file (one sample)
+    total_spectra_used=2,///< total_spectra_used in one identification file (one sample)
+    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
+    total_unique_assigned=5,///< total number unique peptide sequence assigned
+    
+};
+
 /** \def GroupingType list of available grouping algoritms
  *
  */