diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index 962c36c5b7b62b1ca015893590fb326e22fa2e17..d6d4209e53d85a5a957fc5da55cf2639d558efec 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -395,90 +395,109 @@ void MascotDatParser::saveQuery() {
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
if (_current_query.query_index > 0) {
std::vector< PeptideLine> peptide_list = _query_peptide_results[_current_query.query_index-1];
+ savePeptideList(peptide_list, false);
+ peptide_list = _decoy_query_peptide_results[_current_query.query_index-1];
+ savePeptideList(peptide_list, true);
+ }
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+}
+
+void MascotDatParser::savePeptideList(std::vector< PeptideLine> & peptide_list, bool is_decoy) {
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- PeptideEvidence peptide_evidence(_p_identification_data_source->getMsRunSp().get(),_current_query.query_index);
- peptide_evidence.setCharge(_current_query.charge);
- peptide_evidence.setChecked(true);
- peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
- peptide_evidence.setRetentionTime(_current_query.rt);
+ PeptideEvidence peptide_evidence(_p_identification_data_source->getMsRunSp().get(),_current_query.query_index);
+ peptide_evidence.setCharge(_current_query.charge);
+ peptide_evidence.setChecked(true);
+ peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
+ peptide_evidence.setRetentionTime(_current_query.rt);
- peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
- //parse and save
- for(PeptideLine & peptide_line:peptide_list) {
+ peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
+ //parse and save
+ for(PeptideLine & peptide_line:peptide_list) {
- pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
- peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
+ pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
+ peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
- peptide_evidence.setEvalue(getEvalue(ion_score, _current_query.query_index, 0.05));
+ if (is_decoy) {
+ peptide_evidence.setEvalue(getEvalue(ion_score, _decoy_summary_list.at(_current_query.query_index-1), 0.05));
+ }
+ else {
+ peptide_evidence.setEvalue(getEvalue(ion_score, _summary_list.at(_current_query.query_index-1), 0.05));
+ }
- peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value, QVariant(peptide_evidence.getEvalue()));
+ peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value, QVariant(peptide_evidence.getEvalue()));
- QString peptide_str =peptide_line.peptide_string_list.at(4);
- if (!peptide_line.subst.isEmpty()) {
- //q856_p9_subst=1,X,W
- //q24379_p2_subst=1,B,D,8,B,D
- QStringList subst_list = peptide_line.subst.split(",");
- for (unsigned int i=0; i < subst_list.size(); i+=3) {
- peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
- }
+ QString peptide_str =peptide_line.peptide_string_list.at(4);
+ if (!peptide_line.subst.isEmpty()) {
+ //q856_p9_subst=1,X,W
+ //q24379_p2_subst=1,B,D,8,B,D
+ QStringList subst_list = peptide_line.subst.split(",");
+ for (unsigned int i=0; i < subst_list.size(); i+=3) {
+ peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
}
- PeptideXtpSp peptide_sp;
- peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
+ }
+ PeptideXtpSp peptide_sp;
+ peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
+
+ peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
- peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
+ //qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" << peptide_str << " evalue=" << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" << peptide_str << " evalue=" << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
+ if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
+ throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
+ }
- if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
- throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
+ unsigned int i=0;
+ foreach (const QString &str, peptide_line.protein_string_list) {
+ //sp|O95006|OR2F2_HUMAN":0:299:303:1
+ int position = str.indexOf("\"", 0);
+ QString accession = str.mid(0, position);
+ if (is_decoy) {
+ accession = QString("%1|reversed").arg(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));
+ }
+ unsigned int start = position_list.at(1).toUInt()-1;
+ unsigned int stop = position_list.at(2).toUInt()-1;
+ //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ ProteinXtp protein;
+ protein.setAccession(accession);
+ protein.setFastaFileP(peptide_line.fasta_file_list[i].get());
+ if (is_decoy) {
+ protein.setIsDecoy(true);
}
- unsigned int i=0;
- foreach (const QString &str, peptide_line.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()-1;
- unsigned int stop = position_list.at(2).toUInt()-1;
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- ProteinXtp protein;
- protein.setAccession(accession);
- protein.setFastaFileP(peptide_line.fasta_file_list[i].get());
-
- ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(accession);
- if (p_protein_match == nullptr) {
- throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
- }
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
- p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
- p_protein_match->setChecked(true);
+ ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(accession);
+ if (p_protein_match == nullptr) {
+ throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
+ }
+ //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
+ p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
+ p_protein_match->setChecked(true);
- PeptideMatch peptide_match;
- peptide_match.setStart(start);
- peptide_match.setPeptideEvidenceSp(_p_identification_data_source->getPeptideEvidenceStore().getInstance(&peptide_evidence));
+ PeptideMatch peptide_match;
+ peptide_match.setStart(start);
+ peptide_match.setPeptideEvidenceSp(_p_identification_data_source->getPeptideEvidenceStore().getInstance(&peptide_evidence));
- p_protein_match->addPeptideMatch(peptide_match);
- i++;
- }
+ p_protein_match->addPeptideMatch(peptide_match);
+ i++;
}
}
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
}
-pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval) const {
- pappso::pappso_double identity_threshold = (pappso::pappso_double)10.0 * std::log(_summary_list.at(query_index-1).match / (confidence_interval * (pappso::pappso_double)20.0)) / log((pappso::pappso_double)10);;
+pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval) const {
+ pappso::pappso_double identity_threshold = (pappso::pappso_double)10.0 * std::log(summary_line.match / (confidence_interval * (pappso::pappso_double)20.0)) / log((pappso::pappso_double)10);;
return (confidence_interval * pow((pappso::pappso_double)10, ((identity_threshold - ion_score) / (pappso::pappso_double)10)));
}
-pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval) const {
+pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval) const {
// Evalue experimental Homology threshold (QPlughole value from .dat file).
- pappso::pappso_double eval = (ion_score - _summary_list.at(query_index-1).plug_hole) / (pappso::pappso_double)10;
+ pappso::pappso_double eval = (ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
eval = confidence_interval / pow((pappso::pappso_double)10, eval);
}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index b1233770fc879434e3a75df997434586cc37cb50..42bf445d3c5029918237adf659df95381fd9fcac 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -49,8 +49,6 @@ private:
void saveAndClearPeptide();
- pappso::pappso_double getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
- pappso::pappso_double getEvalueExperimental(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
@@ -74,6 +72,10 @@ private:
pappso::pappso_double exp_mass=0;
pappso::pappso_double plug_hole=0; //qplughole, homology threshold
};
+ void savePeptideList(std::vector< PeptideLine> & peptide_list, bool is_decoy);
+ pappso::pappso_double getEvalue(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval = 0.05) const;
+ pappso::pappso_double getEvalueExperimental(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval = 0.05) const;
+
private:
Project * _p_project;
IdentificationGroup * _p_identification_group;