better mascot parser

src/input/mascot/mascotdatparser.cpp

@@ -53,24 +53,80 @@ void MascotDatParser::parse(QIODevice * in_stream) {
                 parseProteinLine( mime_parser.getCurrentTextStream().readLine());
             }
         }
+        else if (mime_parser.getCurrentFileName() == "header") {
+            while(!mime_parser.getCurrentTextStream().atEnd()) {
+                parseHeaderLine( mime_parser.getCurrentTextStream().readLine());
+            }
+        }
     }
 
     mime_parser.close();
     qDebug() << "MascotDatParser::parse end";
 }
 void MascotDatParser::parseProteinLine(const QString & protein_line) {
+    ProteinXtpSp sp_xtp_protein;
     //02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4 SV=1"
     QRegExp   regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
     if (regexp_protein.exactMatch(protein_line)) {
         QStringList protein_list = regexp_protein.capturedTexts();
+        _current_protein.setAccession(protein_list[2]);
+        _current_protein.setDescription(protein_list[4]);
+
+        sp_xtp_protein = _current_protein.makeProteinXtpSp();
+        sp_xtp_protein = _p_project->getProteinStore().getInstance(sp_xtp_protein);
     }
     else {
         QRegExp   regexp_proteinb("^\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
         if (regexp_proteinb.exactMatch(protein_line)) {
             QStringList protein_list = regexp_proteinb.capturedTexts();
+
+            _current_protein.setAccession(protein_list[1]);
+            _current_protein.setDescription(protein_list[3]);
+
+            sp_xtp_protein = _current_protein.makeProteinXtpSp();
+            sp_xtp_protein = _p_project->getProteinStore().getInstance(sp_xtp_protein);
         }
         else {
             qDebug() << "MascotDatParser::parseProteinLine error " << protein_line;
         }
     }
 }
+void MascotDatParser::parseHeaderLine(const QString & header_line) {
+    QRegExp   regexp_header_line("^([a-z,0-9,_]+)=(.*)$");
+    if (regexp_header_line.exactMatch(header_line)) {
+        QStringList header_list = regexp_header_line.capturedTexts();
+//sequences=73998
+//sequences_after_tax=73998
+//residues=24900901
+//distribution=64847,0,1,576,2254,1934,1417,984,683,419,238,192,113,89,74,46,23,32,28,21,11,3,2,3,3,2,1,1,0,0,0,0,0,0,1
+//decoy_type=1
+//distribution_decoy=65162,0,1,552,2259,1891,1422,957,601,376,192,159,126,73,56,64,26,27,22,14,6,4,1,1,3,2,1
+//exec_time=484
+//date=1517587671
+//time=17:07:51
+//queries=54084
+//min_peaks_for_homology=6
+//max_hits=50
+//version=2.5.0
+        if (header_list[1] == "version") {
+            _p_identification_data_source->setIdentificationEngineVersion(header_list[2]);
+        }
+//fastafile=C:/inetpub/mascot/sequence/ECOLI_INRA/current/ECOLI_INRA_1.fasta
+        else if (header_list[1].startsWith("fastafile")) {
+            qDebug() << "fastafile=" <<  header_list[2];
+            _fasta_file_list.push_back( _p_project->getFastaFileStore().getInstance(FastaFile(header_list[2])));
+
+            _p_identification_data_source->addFastaFile(_fasta_file_list.back());
+        }
+//release=ECOLI_INRA_1.fasta
+//sequences1=4305
+//sequences_after_tax1=4305
+//residues1=1356026
+//fastafile2=C:/inetpub/mascot/sequence/HUMAN_INRA/current/HUMAN_INRA_1.fasta
+//release2=HUMAN_INRA_1.fasta
+//sequences2=69693
+//sequences_after_tax2=69693
+//residues2=23544875
+//taskid=151758718701
+    }
+}

src/input/mascot/mascotdatparser.h

@@ -41,10 +41,15 @@ public:
     void parse(QIODevice * in_stream);
 private:
     void parseProteinLine(const QString & protein_line);
+    void parseHeaderLine(const QString & protein_line);
 private:
     Project * _p_project;
     IdentificationGroup * _p_identification_group;
     IdentificationDataSource * _p_identification_data_source;
+    
+    
+    ProteinXtp _current_protein;
+    std::vector<FastaFileSp> _fasta_file_list;
 };
 
 #endif // MASCOTDATPARSER_H