grab mascot parameters

src/input/mascot/mascotdatparser.cpp

@@ -38,7 +38,8 @@
 #include "../../core/peptideevidence.h"
 
 MascotDatParser::MascotDatParser(
-  Project *p_project, IdentificationGroup *p_identification_group,
+  Project *p_project,
+  IdentificationGroup *p_identification_group,
   IdentificationDataSource *p_identification_data_source)
 {
   _p_project                    = p_project;
@@ -71,6 +72,14 @@ MascotDatParser::parse(QIODevice *in_stream)
               parseProteinLine(mime_parser.getCurrentTextStream().readLine());
             }
         }
+      else if(mime_parser.getCurrentFileName() == "parameters")
+        {
+          while(!mime_parser.getCurrentTextStream().atEnd())
+            {
+              parseParametersLine(
+                mime_parser.getCurrentTextStream().readLine());
+            }
+        }
       else if(mime_parser.getCurrentFileName() == "header")
         {
           while(!mime_parser.getCurrentTextStream().atEnd())
@@ -321,6 +330,103 @@ MascotDatParser::parseHeaderLine(const QString &header_line)
     }
 }
 
+void
+MascotDatParser::parseParametersLine(const QString &header_line)
+{
+  if(_regexp_header_line.exactMatch(header_line))
+    {
+      QStringList header_list = _regexp_header_line.capturedTexts();
+      /*
+       * LICENSE=licence du logiciel
+MP=
+NM=
+COM=WP4 Batch4 inj2 paramSTR QEKAC160601_02.raw.mgf
+IATOL=
+IA2TOL=
+IASTOL=
+IBTOL=
+IB2TOL=
+IBSTOL=
+IYTOL=
+IY2TOL=
+IYSTOL=
+SEG=
+SEGT=
+SEGTU=
+LTOL=
+TOL=5
+TOLU=ppm
+ITH=
+ITOL=70
+ITOLU=mmu
+PFA=1
+DB=Contaminants_WP4_D
+DB2=S_cerevisiae_D
+DB3=UPS1UPS2_D
+MODS=Carbamidomethyl (C)
+MASS=Monoisotopic
+CLE=Trypsin/P
+FILE=F:\MSData\Batch4 Qex+TOUL Injection2\QEKAC160601_02.raw.mgf
+PEAK=
+QUE=
+TWO=
+SEARCH=MIS
+USERNAME=AMH
+USEREMAIL=
+CHARGE=2+ and 3+
+INTERMEDIATE=
+REPORT= AUTO
+OVERVIEW=
+FORMAT=Mascot generic
+FORMVER=1.01
+FRAG=
+IT_MODS=Acetyl (Protein N-term),Oxidation (M)
+USER00=
+USER01=
+USER02=
+USER03=
+USER04=
+USER05=
+USER06=
+USER07=
+USER08=
+USER09=
+USER10=
+USER11=
+USER12=
+PRECURSOR=
+TAXONOMY=All entries
+ACCESSION=
+REPTYPE=
+SUBCLUSTER=
+ICAT=
+INSTRUMENT=ESI FTMS HCD
+ERRORTOLERANT=
+FRAMES=
+CUTOUT=
+USERID=0
+QUANTITATION=
+DECOY=
+PEP_ISOTOPE_ERROR=
+MULTI_SITE_MODS=
+DATAURL=
+RULES=1,2,4,5,6,7,8,9,10,13,14,15,17,18
+INTERNALS=0.0,700.0
+*/
+      if(header_list[1] == "FILE")
+        {
+          // FILE=F:\MSData\Batch4 Qex+TOUL Injection2\QEKAC160601_02.raw.mgf
+          /* not finished
+        QFileInfo fileinfo(header_list[2]);
+        _p_identification_data_source->getMsRunSp().get()->setSampleName(
+          fileinfo.baseName());
+          */
+          _p_identification_data_source->getMsRunSp().get()->setFilename(
+            header_list[2]);
+        }
+    }
+}
+
 void
 MascotDatParser::parsePeptidesLine(const QString &peptide_line)
 {
@@ -415,8 +521,9 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
 
   catch(pappso::PappsoException exception_pappso)
     {
-      _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine "
-                               "%1, PAPPSO exception:\n%2")
+      _error_str = QObject::tr(
+                     "ERROR in MascotDatParser::parsePeptidesLine "
+                     "%1, PAPPSO exception:\n%2")
                      .arg(peptide_line)
                      .arg(exception_pappso.qwhat());
       qDebug() << _error_str;
@@ -424,11 +531,11 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
     }
   catch(std::exception exception_std)
     {
-      _error_str =
-        QObject::tr(
-          "ERROR in MascotDatParser::parsePeptidesLine %1, std exception:\n%2")
-          .arg(peptide_line)
-          .arg(exception_std.what());
+      _error_str = QObject::tr(
+                     "ERROR in MascotDatParser::parsePeptidesLine %1, std "
+                     "exception:\n%2")
+                     .arg(peptide_line)
+                     .arg(exception_std.what());
       qDebug() << _error_str;
       throw pappso::PappsoException(_error_str);
     }
@@ -482,11 +589,11 @@ MascotDatParser::parseQueryLine(const QString &query_line)
 
   catch(pappso::PappsoException exception_pappso)
     {
-      _error_str =
-        QObject::tr(
-          "ERROR in MascotDatParser::parseQueryLine %1, PAPPSO exception:\n%2")
-          .arg(query_line)
-          .arg(exception_pappso.qwhat());
+      _error_str = QObject::tr(
+                     "ERROR in MascotDatParser::parseQueryLine %1, PAPPSO "
+                     "exception:\n%2")
+                     .arg(query_line)
+                     .arg(exception_pappso.qwhat());
       qDebug() << _error_str;
       throw pappso::PappsoException(_error_str);
     }
@@ -633,9 +740,10 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
 
       if(is_decoy)
         {
-          peptide_evidence.setEvalue(getEvalue(
-            ion_score, _decoy_summary_list.at(_current_query.query_index - 1),
-            0.05));
+          peptide_evidence.setEvalue(
+            getEvalue(ion_score,
+                      _decoy_summary_list.at(_current_query.query_index - 1),
+                      0.05));
         }
       else
         {
@@ -767,7 +875,8 @@ MascotDatParser::getEvalue(pappso::pappso_double ion_score,
 
 pappso::pappso_double
 MascotDatParser::getEvalueExperimental(
-  pappso::pappso_double ion_score, SummaryLine &summary_line,
+  pappso::pappso_double ion_score,
+  SummaryLine &summary_line,
   pappso::pappso_double confidence_interval) const
 {
   // Evalue experimental  Homology threshold (QPlughole value from .dat file).

src/input/mascot/mascotdatparser.h

@@ -43,6 +43,7 @@ class MascotDatParser
   void parse(QIODevice *in_stream);
 
   private:
+  void parseParametersLine(const QString &parameters_line);
   void parseProteinLine(const QString &protein_line);
   void parseHeaderLine(const QString &protein_line);
   void parsePeptidesLine(const QString &peptide_line);