diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index f49bb8ac45d908cb0adc387adf52651aeb93d1c7..99254b55925b3e6a640476c0d6a8f9a4074099b3 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -147,6 +147,39 @@ void MascotDatParser::parseHeaderLine(const QString & header_line) {
}
}
+void MascotDatParser::saveAndClearPeptide() {
+ qDebug() << "MascotDatParser::saveAndClearPeptide begin";
+ if (_current_peptide.query_index > 0) {
+ //parse and save
+
+ pappso::Peptide peptide(_current_peptide.peptide_string_list.at(4));
+
+ if (_current_peptide.protein_string_list.size() != _current_peptide.fasta_file_list.size()) {
+ throw pappso::PappsoException(QObject::tr("ERROR (_current_peptide.protein_string_list.size() != _current_peptide.fasta_file_list.size()) %1").arg(_current_peptide.protein_string_list.join(",\"")));
+ }
+
+ foreach (const QString &str, _current_peptide.protein_string_list) {
+ //sp|O95006|OR2F2_HUMAN":0:299:303:1
+ int position = str.indexOf("\"", 0);
+ QString accession = str.mid(0, position);
+ qDebug() << "accession=" << accession;
+ QStringList position_list = str.mid(position+2).split(":");
+ if (position_list.size() != 4) {
+ throw pappso::PappsoException(QObject::tr("ERROR position_list.size() != 4 %1").arg(str));
+ }
+ unsigned int start = position_list.at(1).toUInt();
+ unsigned int stop = position_list.at(2).toUInt();
+ }
+ }
+
+ //new peptide query clear
+ _current_peptide.peptide_string_list.clear();
+ _current_peptide.fasta_file_list.clear();
+ _current_peptide.query_index = 0;
+ _current_peptide.subst = "";
+ qDebug() << "MascotDatParser::saveAndClearPeptide end";
+}
+
void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
try {
if (_regexp_header_line.exactMatch(peptide_line)) {
@@ -156,14 +189,18 @@ void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
QStringList index_list = index.split("_");
if (index_list.size() == 3) {
if (index_list[2] == "db") {
+ saveAndClearPeptide();
//q1_p1_db=02
- _peptides_fasta_file_list.clear();
while (value.size() > 0) {
QString fasta_str = value.mid(0,2);
- _peptides_fasta_file_list.push_back(_fasta_file_list.at(fasta_str.toInt()-1));
+ _current_peptide.fasta_file_list.push_back(_fasta_file_list.at(fasta_str.toInt()-1));
value = value.mid(2);
}
}
+ //q856_p9_subst=1,X,W
+ else if (index_list[2] == "subst") {
+ _current_peptide.subst = value;
+ }
}
else if (index_list.size() == 2) {
if (value == "-1") {
@@ -172,37 +209,22 @@ void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
else {
QString query_index = index_list[0];
+ _current_peptide.query_index = query_index.mid(1).toUInt();
QString peptide_index = index_list[1];
+ _current_peptide.peptide_index = peptide_index.mid(1).toUInt();
//q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
int position = value.indexOf(";\"", 0);
QString peptide_string = value.mid(0, position);
qDebug() << "peptide_string=" << peptide_string;
- QStringList peptide_string_list = peptide_string.split(",");
- pappso::Peptide peptide(peptide_string_list.at(4));
+ _current_peptide.peptide_string_list = peptide_string.split(",");
QString protein_string = value.mid(position+2);
qDebug() << "protein_string=" << protein_string;
//"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
- QStringList protein_string_list = protein_string.split(",\"");
- if (protein_string_list.size() != _peptides_fasta_file_list.size()) {
- throw pappso::PappsoException(QObject::tr("ERROR (protein_string_list.size() != _peptides_fasta_file_list.size()) %1").arg(value));
- }
-
- foreach (const QString &str, protein_string_list) {
- //sp|O95006|OR2F2_HUMAN":0:299:303:1
- int position = str.indexOf("\"", 0);
- QString accession = str.mid(0, position);
- qDebug() << "accession=" << accession;
- QStringList position_list = str.mid(position+2).split(":");
- if (position_list.size() != 4) {
- throw pappso::PappsoException(QObject::tr("ERROR position_list.size() != 4 %1").arg(value));
- }
- unsigned int start = position_list.at(1).toUInt();
- unsigned int stop = position_list.at(2).toUInt();
- }
+ _current_peptide.protein_string_list = protein_string.split(",\"");
}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index f15aa1ff5382385c11d44f57ae716cc4510d6f6d..c349ff68c94b8fdfd27f7da9065709cc18bc2772 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -43,6 +43,16 @@ private:
void parseProteinLine(const QString & protein_line);
void parseHeaderLine(const QString & protein_line);
void parsePeptidesLine(const QString & peptide_line);
+ void saveAndClearPeptide();
+
+ struct PeptideLine {
+ unsigned int query_index=0;
+ unsigned int peptide_index=0;
+ QString subst;
+ QStringList peptide_string_list;
+ QStringList protein_string_list;
+ std::vector<FastaFileSp> fasta_file_list;
+ };
private:
Project * _p_project;
IdentificationGroup * _p_identification_group;
@@ -52,13 +62,16 @@ private:
ProteinXtp _current_protein;
std::vector<FastaFileSp> _fasta_file_list;
- std::vector<FastaFileSp> _peptides_fasta_file_list;
+
QRegExp _regexp_header_line;
unsigned int _number_of_queries=0;
unsigned int _number_of_residues=0;
QString _error_str;
+ PeptideLine _current_peptide;
+
+
};
#endif // MASCOTDATPARSER_H