introducing MsRunStatistics

src/core/msrun.cpp

@@ -82,6 +82,18 @@ MzFormat MsRun::getMzFormat() const {
     return _mz_format;
 }
 
+void MsRun::setMsRunStatistics(MsRunStatistics param, const QVariant& value) {
+    _param_stats.insert(std::pair<MsRunStatistics, QVariant>(param, value));
+}
+const QVariant MsRun::getMsRunStatistics(MsRunStatistics param) const {
+    try {
+        return _param_stats.at(param);
+    }
+    catch (std::out_of_range) {
+        return QVariant();
+    }
+}
+
 /*
 void MsRun::setMzFormat(MzFormat mz_format) {
     _mz_format = mz_format;

src/core/msrun.h

@@ -34,6 +34,7 @@
 
 #include <memory>
 #include <QString>
+#include <QVariant>
 #include "../utils/types.h"
 
 class MsRun;
@@ -55,11 +56,24 @@ public:
     
     MzFormat getMzFormat() const;
     //void setMzFormat(MzFormat mz_format);
+    
+           
+    /** \brief set MS run statistics
+     * any statistics on this MS run file
+     */
+    virtual void setMsRunStatistics(MsRunStatistics param, const QVariant& value);
+    
+    
+    /** \brief get MS run statistics
+     */
+    virtual const QVariant getMsRunStatistics(MsRunStatistics param) const;
+
 private :
     QString _xml_id;
     QString _location;
     QString _name;
     MzFormat _mz_format=MzFormat::mzXML;
+    std::map<MsRunStatistics, QVariant> _param_stats;
 };
 
 #endif // MSRUN_H

src/output/ods/samplesheet.cpp

@@ -28,6 +28,7 @@
 ******************************************************************************/
 
 #include "samplesheet.h"
+#include "../../utils/readspectrum.h"
 
 SampleSheet::SampleSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
     _p_writer = p_writer;
@@ -88,9 +89,12 @@ void SampleSheet::writeHeaders()  {
 
 void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ident_data_source) {
     _p_writer->writeLine();
-    _p_writer->writeCell(p_ident_data_source->getMsRunSp().get()->getXmlId());
-    _p_writer->writeCell(p_ident_data_source->getMsRunSp().get()->getSampleName());
-    _p_writer->writeCell(p_ident_data_source->getMsRunSp().get()->getFilename());
+    MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
+    SpectrumStore::checkMsRunStatistics(msrun_sp);
+    
+    _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());
@@ -101,15 +105,40 @@ 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());
+    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_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());
     }
+    else {
+        _p_writer->writeEmptyCell();
+    }
+
 
-    _p_writer->writeCell(p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_unique_assigned).toString());
+    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());
+    }
+    
+    
 
 }

src/utils/readspectrum.cpp

@@ -258,8 +258,20 @@ const QString SpectrumStore::findMzFile(const QString &filename) {
     return QString();
 }
 
-pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num) {
-    pappso::QualifiedSpectrum spectrum;
+void SpectrumStore::checkMsRunStatistics(MsRunSp msrun) {
+    QVariant msrun_var = msrun.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
+    if (msrun_var.isNull()) {
+        try {
+            pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
+            msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) p_msdatafile->run.spectrumListPtr.get()->size());
+        }
+        catch (pappso::ExceptionNotFound& error) {
+            //no file found, no statistics
+        }
+    }
+}
+
+pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(MsRunSp msrun) {
     pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
     std::map<MsRunSp, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(msrun);
     if (it_msdata == _map_msrun_msdatafile.end()) {
@@ -279,6 +291,13 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsign
     else {
         p_msdatafile =it_msdata->second;
     }
+    return p_msdatafile;
+}
+
+pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num) {
+    pappso::QualifiedSpectrum spectrum;
+    pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
+    
     if (p_msdatafile == nullptr) {
         return spectrum.getOriginalSpectrumSp();
     }

src/utils/readspectrum.h

@@ -42,8 +42,12 @@ class MSDataFile;
 class SpectrumStore {
 public:
     static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num);
+    /** @brief try to find MS run statistics
+     */
+    static void checkMsRunStatistics(MsRunSp msrun);
 private:
     static const QString findMzFile(const QString &filename);
+    static pwiz::msdata::MSDataFile * findPwizMSDataFile(MsRunSp msrun) ;
 private:
     static std::map<MsRunSp, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
 };

src/utils/types.h

@@ -74,9 +74,20 @@ enum class IdentificationEngineStatistics: std::int8_t {
     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 MsRunStatistics MS run statistics
+ *
+ */
+enum class MsRunStatistics: std::int8_t {
+    total_spectra=1, ///< total number of spectra
+    total_spectra_ms1=2,///< total number of MS1 spectra
+    total_spectra_ms2=3,///< total number of MS2 spectra
+    total_spectra_ms3=4,///< total number of MS3 spectra
+};
+
+
+
 /** \def GroupingType list of available grouping algoritms
  *
  */