WIP mascot parser

src/input/mascot/mascotdatparser.cpp

@@ -58,6 +58,11 @@ void MascotDatParser::parse(QIODevice * in_stream) {
                 parseHeaderLine( mime_parser.getCurrentTextStream().readLine());
             }
         }
+        else if (mime_parser.getCurrentFileName() == "peptides") {
+            while(!mime_parser.getCurrentTextStream().atEnd()) {
+                parsePeptidesLine( mime_parser.getCurrentTextStream().readLine());
+            }
+        }
     }
 
     mime_parser.close();
@@ -130,3 +135,48 @@ void MascotDatParser::parseHeaderLine(const QString & header_line) {
 //taskid=151758718701
     }
 }
+
+void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
+    QRegExp   regexp_header_line("^([a-z,0-9,_]+)=(.*)$");
+    if (regexp_header_line.exactMatch(peptide_line)) {
+        QStringList header_list = regexp_header_line.capturedTexts();
+        QString index = header_list[1];
+        QString value = header_list[2];
+        QStringList index_list = index.split("_");
+        if (index_list.size() == 3) {
+            if (index_list[2] == "db") {
+                _peptides_fasta_file_list.clear();
+                while(value.size() > 0) {
+                    _peptides_fasta_file_list.push_back( _fasta_file_list[value.left(2).toInt()-1]);
+                    value = value.mid(2);
+                }
+            }
+        }
+        else if (index_list.size() == 2) {
+
+            QString query = index_list[0];
+            QString peptide = index_list[1];
+
+        }
+        /*
+        q1_p1_db=02
+        q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
+        q1_p1_terms=K,L
+        q1_p2_db=02
+        q1_p2=1,598.296219,0.003987,2,KEEPP,11,0000000,1.32,0002000000000000000,0,0;"tr|E9PNM8|E9PNM8_HUMAN":0:134:138:1
+        q1_p2_terms=R,-
+        q2_p1_db=02
+        q2_p1=1,598.380234,-0.000316,3,KAGVPK,13,00000000,17.13,0002011000000000000,0,0;"tr|H7C1P9|H7C1P9_HUMAN":0:945:950:2
+        q2_p1_terms=K,K
+        q2_p2_db=0202
+        q2_p2=1,598.380234,-0.000316,2,KQPVK,9,0000000,9.54,0002011000000000000,0,0;"sp|P33527|MRP1_HUMAN":0:270:274:1,"tr|I3L4X2|I3L4X2_HUMAN":0:169:173:1
+        q2_p2_terms=R,V:R,V
+        q2_p3_db=02
+        q2_p3=1,598.380234,-0.000316,2,KAVPGK,13,00000000,7.03,0002001000000000000,0,0;"sp|Q13061|TRDN_HUMAN":0:440:445:2
+        q2_p3_terms=K,K
+        q2_p4_db=0202
+        q2_p4=1,598.380234,-0.000316,2,IPGGKK,14,00000000,1.26,0002001000000000000,0,0;"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
+        q2_p4_terms=K,F:K,F
+        */
+    }
+}

src/input/mascot/mascotdatparser.h

@@ -42,6 +42,7 @@ public:
 private:
     void parseProteinLine(const QString & protein_line);
     void parseHeaderLine(const QString & protein_line);
+    void parsePeptidesLine(const QString & peptide_line);
 private:
     Project * _p_project;
     IdentificationGroup * _p_identification_group;
@@ -50,6 +51,8 @@ private:
     
     ProteinXtp _current_protein;
     std::vector<FastaFileSp> _fasta_file_list;
+    
+    std::vector<FastaFileSp> _peptides_fasta_file_list;
 };
 
 #endif // MASCOTDATPARSER_H