diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 2f50e84cdb323f196be95a17902409143d639b42..c5f99aea3d34e314e5fade52285978c26431e183 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -187,7 +187,7 @@ void ProteinXtp::parseAccession2dbxref() {
for (unsigned int i=0; i < access_list.size(); i++) {
accession = access_list.at(i);
- qDebug() << "ProteinXtp::parseAccession2dbxref accession " << accession;
+ //qDebug() << "ProteinXtp::parseAccession2dbxref accession " << accession;
if (atg.indexIn(accession, 0) != -1) {
QStringList temp = accession.split(".");
_dbxref_list.push_back(DbXref(ExternalDatabase::AGI_LocusCode, temp.at(0)));
@@ -195,13 +195,13 @@ void ProteinXtp::parseAccession2dbxref() {
}
if (swiss_prot.indexIn(accession, 0) != -1) {
- qDebug() << "ProteinXtp::parseAccession2dbxref accession SwissProt " << accession;
+ //qDebug() << "ProteinXtp::parseAccession2dbxref accession SwissProt " << accession;
_dbxref_list.push_back(DbXref(ExternalDatabase::SwissProt, accession));
continue;
}
if (trembl.indexIn(accession, 0) != -1) {
- qDebug() << "ProteinXtp::parseAccession2dbxref accession TrEMBL " << accession;
+ //qDebug() << "ProteinXtp::parseAccession2dbxref accession TrEMBL " << accession;
_dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
continue;
}
@@ -236,7 +236,7 @@ void ProteinXtp::parseAccession2dbxref() {
}
- qDebug() << "ProteinXtp::parseAccession2dbxref end" ;
+ //qDebug() << "ProteinXtp::parseAccession2dbxref end" ;
}
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index d6d4209e53d85a5a957fc5da55cf2639d558efec..51d69a9efd512961a6b8f0c50a5039dab9783e97 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -65,6 +65,12 @@ void MascotDatParser::parse(QIODevice * in_stream) {
parseHeaderLine( mime_parser.getCurrentTextStream().readLine());
}
}
+ else if (mime_parser.getCurrentFileName() == "masses") {
+ while(!mime_parser.getCurrentTextStream().atEnd()) {
+ parseMassesLine( mime_parser.getCurrentTextStream().readLine());
+ }
+
+ }
else if (mime_parser.getCurrentFileName() == "summary") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseSummaryLine( mime_parser.getCurrentTextStream().readLine());
@@ -99,11 +105,39 @@ void MascotDatParser::parse(QIODevice * in_stream) {
}
saveQuery();
}
+
}
mime_parser.close();
qDebug() << "MascotDatParser::parse end";
}
+
+void MascotDatParser::parseMassesLine(const QString & masses_line) {
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << masses_line;
+ if (_regexp_header_line.exactMatch(masses_line)) {
+ QStringList header_list = _regexp_header_line.capturedTexts();
+// C_term=17.002740
+//N_term=1.007825
+//delta1=15.994915,Oxidation (M)
+ if (header_list[1].startsWith("delta")) {
+ QStringList delta_mod_list = header_list[2].split(",");
+ pappso::pappso_double mass = delta_mod_list[0].toDouble();
+ //_number_of_residues = header_list[5].toUInt();
+ }
+
+//NeutralLoss1=0.000000
+//NeutralLoss1_master=63.998285
+//FixedMod1=57.021464,Carbamidomethyl (C)
+ if (header_list[1].startsWith("FixedMod")) {
+ QStringList fixed_mod_list = header_list[2].split(",");
+ pappso::pappso_double mass = fixed_mod_list[0].toDouble();
+ //_number_of_residues = header_list[2].toUInt();
+ }
+
+//FixedModResidues1=C
+ }
+}
+
void MascotDatParser::parseProteinLine(const QString & protein_line) {
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << protein_line;
ProteinXtpSp sp_xtp_protein;
@@ -224,14 +258,14 @@ void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
//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;
+ //qDebug() << "peptide_string=" << peptide_string;
_current_peptide.peptide_string_list = peptide_string.split(",");
QString protein_string = value.mid(position+2);
- qDebug() << "protein_string=" << protein_string;
+ //qDebug() << "protein_string=" << protein_string;
//"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
_current_peptide.protein_string_list = protein_string.split(",\"");
}
@@ -266,6 +300,7 @@ void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
q856_p9_terms=-,L:-,V
q856_p9_subst=1,X,W
*/
+
}
}
@@ -415,6 +450,20 @@ void MascotDatParser::savePeptideList(std::vector< PeptideLine> & peptide_list,
//parse and save
for(PeptideLine & peptide_line:peptide_list) {
+ /*
+ *
+ 0 setMissedCleavages(Integer.parseInt(st.nextToken()));
+ 1 setPeptideMr(Double.parseDouble(st.nextToken()));
+ 2 setDeltaMass(Double.parseDouble(st.nextToken()));
+ 3 setNumberOfIonsMatched(Integer.parseInt(st.nextToken()));
+ 4 setSequence(st.nextToken());
+ 5 setPeaksUsedFromIons1(Integer.parseInt(st.nextToken()));
+ 6 setVariableModificationsArray(st.nextToken());
+ 7 setIonsScore(Double.parseDouble(st.nextToken()));
+ 8 parseIonSeries(st.nextToken());
+ 9 setPeaksUsedFromIons2(Integer.parseInt(st.nextToken()));
+ 10 setPeaksUsedFromIons3(Integer.parseInt(st.nextToken()));
+ */
pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
@@ -439,6 +488,9 @@ void MascotDatParser::savePeptideList(std::vector< PeptideLine> & peptide_list,
PeptideXtpSp peptide_sp;
peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
+ //variable modifications :
+ setVariableModifications(peptide_sp, peptide_line.peptide_string_list.at(6));
+
peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
@@ -456,7 +508,7 @@ void MascotDatParser::savePeptideList(std::vector< PeptideLine> & peptide_list,
if (is_decoy) {
accession = QString("%1|reversed").arg(accession);
}
- qDebug() << "accession=" << accession;
+ //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));
@@ -501,3 +553,6 @@ pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_doub
pappso::pappso_double eval = (ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
eval = confidence_interval / pow((pappso::pappso_double)10, eval);
}
+
+void MascotDatParser::setVariableModifications(PeptideXtpSp & peptide_sp, QString variable_modifications_string) {
+}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index 42bf445d3c5029918237adf659df95381fd9fcac..592727de0f14231103fdd8fe3063032738a7496b 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -45,8 +45,10 @@ private:
void parsePeptidesLine(const QString & peptide_line);
void parseQueryLine(const QString & query_line);
void parseSummaryLine(const QString & summary_line);
+ void parseMassesLine(const QString & masses_line);
void saveQuery();
void saveAndClearPeptide();
+ void setVariableModifications(PeptideXtpSp & peptide_sp, QString variable_modifications_string);