diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 1f0a2ad7ab6b225bf3dfdf6142049e93eae7a504..01f925f22d16bff66280bd86794e92e1e3ca7670 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -90,6 +90,30 @@ PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match)
_engine_columns_to_display.insert(
PeptideListColumn::mascot_expectation_value);
}
+ else if(engine == IdentificationEngine::OMSSA)
+ {
+ _engine_columns_to_display.insert(PeptideListColumn::omssa_evalue);
+ _engine_columns_to_display.insert(PeptideListColumn::omssa_pvalue);
+ }
+ else if(engine == IdentificationEngine::MSGFplus)
+ {
+ _engine_columns_to_display.insert(PeptideListColumn::msgfplus_raw);
+ _engine_columns_to_display.insert(PeptideListColumn::msgfplus_denovo);
+ _engine_columns_to_display.insert(PeptideListColumn::msgfplus_energy);
+ _engine_columns_to_display.insert(
+ PeptideListColumn::msgfplus_SpecEValue);
+ _engine_columns_to_display.insert(PeptideListColumn::msgfplus_EValue);
+ }
+ else if(engine == IdentificationEngine::Comet)
+ {
+ _engine_columns_to_display.insert(PeptideListColumn::comet_deltacn);
+ _engine_columns_to_display.insert(PeptideListColumn::comet_deltacnstar);
+ _engine_columns_to_display.insert(PeptideListColumn::comet_expectation_value);
+ _engine_columns_to_display.insert(
+ PeptideListColumn::comet_sprank);
+ _engine_columns_to_display.insert(PeptideListColumn::comet_spscore);
+ _engine_columns_to_display.insert(PeptideListColumn::comet_xcorr);
+ }
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
@@ -121,7 +145,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent) const
int
PeptideTableModel::columnCount(const QModelIndex &parent) const
{
- return 33;
+ return 39;
}
QVariant
PeptideTableModel::headerData(int section, Qt::Orientation orientation,
@@ -387,6 +411,85 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
->getParam(
PeptideEvidenceParam::peptide_inter_prophet_probability);
break;
+ case(std::int8_t)PeptideListColumn::omssa_evalue:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::omssa_evalue);
+ break;
+ case(std::int8_t)PeptideListColumn::omssa_pvalue:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::omssa_pvalue);
+ break;
+ case(std::int8_t)PeptideListColumn::msgfplus_denovo:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::msgfplus_denovo);
+ break;
+ case(std::int8_t)PeptideListColumn::msgfplus_energy:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::msgfplus_energy);
+ break;
+ case(std::int8_t)PeptideListColumn::msgfplus_EValue:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::msgfplus_EValue);
+ break;
+ case(std::int8_t)PeptideListColumn::msgfplus_raw:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::msgfplus_raw);
+ break;
+ case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::msgfplus_SpecEValue);
+ break;
+
+ case(std::int8_t)PeptideListColumn::comet_xcorr:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::comet_xcorr);
+ break;
+ case(std::int8_t)PeptideListColumn::comet_deltacn:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::comet_deltacn);
+ break;
+ case(std::int8_t)PeptideListColumn::comet_deltacnstar:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::comet_deltacnstar);
+ break;
+ case(std::int8_t)PeptideListColumn::comet_spscore:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::comet_spscore);
+ break;
+ case(std::int8_t)PeptideListColumn::comet_sprank:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::comet_sprank);
+ break;
+ case(std::int8_t)PeptideListColumn::comet_expectation_value:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::comet_expectation_value);
+ break;
}
}
return QString();
@@ -503,6 +606,34 @@ PeptideTableModel::getTitle(std::int8_t column)
return "Prophet probability";
case(std::int8_t)PeptideListColumn::peptide_inter_prophet_probability:
return "Inter prophet probability";
+ case(std::int8_t)PeptideListColumn::omssa_evalue:
+ return "OMSSA E-value";
+ case(std::int8_t)PeptideListColumn::omssa_pvalue:
+ return "OMSSA p-value";
+ case(std::int8_t)PeptideListColumn::msgfplus_denovo:
+ return "MS-GF de novo";
+ case(std::int8_t)PeptideListColumn::msgfplus_energy:
+ return "MS-GF energy";
+ case(std::int8_t)PeptideListColumn::msgfplus_EValue:
+ return "MS-GF E-value";
+ case(std::int8_t)PeptideListColumn::msgfplus_raw:
+ return "MS-GF raw score";
+ case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue:
+ return "MS-GF spectral E-value";
+
+ case(std::int8_t)PeptideListColumn::comet_xcorr:
+ return "Comet XCorr";
+
+ case(std::int8_t)PeptideListColumn::comet_deltacn:
+ return "Comet DeltaCn";
+ case(std::int8_t)PeptideListColumn::comet_deltacnstar:
+ return "Comet DeltaCnStar";
+ case(std::int8_t)PeptideListColumn::comet_spscore:
+ return "Comet SpScore";
+ case(std::int8_t)PeptideListColumn::comet_sprank:
+ return "Comet SpRank";
+ case(std::int8_t)PeptideListColumn::comet_expectation_value:
+ return "Comet E-value";
}
return "";
}
@@ -590,6 +721,32 @@ PeptideTableModel::getDescription(std::int8_t column)
return "Peptide prophet probability";
case(std::int8_t)PeptideListColumn::peptide_inter_prophet_probability:
return "Peptide inter prophet probability";
+ case(std::int8_t)PeptideListColumn::omssa_evalue:
+ return "OMSSA E-value";
+ case(std::int8_t)PeptideListColumn::omssa_pvalue:
+ return "OMSSA p-value";
+ case(std::int8_t)PeptideListColumn::msgfplus_denovo:
+ return "MS-GF de novo";
+ case(std::int8_t)PeptideListColumn::msgfplus_energy:
+ return "MS-GF energy";
+ case(std::int8_t)PeptideListColumn::msgfplus_EValue:
+ return "MS-GF E-value";
+ case(std::int8_t)PeptideListColumn::msgfplus_raw:
+ return "MS-GF raw score";
+ case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue:
+ return "MS-GF spectral E-value";
+ case(std::int8_t)PeptideListColumn::comet_xcorr:
+ return "The Comet result 'XCorr'";
+ case(std::int8_t)PeptideListColumn::comet_deltacn:
+ return "The Comet result 'DeltaCn'";
+ case(std::int8_t)PeptideListColumn::comet_deltacnstar:
+ return "The Comet result 'DeltaCnStar'";
+ case(std::int8_t)PeptideListColumn::comet_spscore:
+ return "The Comet result 'SpScore'";
+ case(std::int8_t)PeptideListColumn::comet_sprank:
+ return "The Comet result 'SpRank'";
+ case(std::int8_t)PeptideListColumn::comet_expectation_value:
+ return "The Comet result 'Expectation value'";
}
return "";
}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index ed865d621924396970dd52a6dfabb09e750c20d5..dea80398aff58e8a186ab425745849fe84dbdc7d 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -68,6 +68,14 @@ enum class PeptideListColumn : std::int8_t
msgfplus_energy = 30, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
msgfplus_SpecEValue = 31, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
msgfplus_EValue = 32, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
+ comet_xcorr = 33, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI]
+ comet_deltacn = 34, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI]
+ comet_deltacnstar =
+ 35, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI]
+ comet_spscore = 36, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI]
+ comet_sprank = 37, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI]
+ comet_expectation_value =
+ 38, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI]
};
class PeptideListWindow;
@@ -105,7 +113,7 @@ class PeptideTableModel : public QAbstractTableModel
private:
ProteinMatch *_p_protein_match = nullptr;
PeptideListWindow *_p_peptide_list_window = nullptr;
- //contains columns to display (present in this peptide match)
+ // contains columns to display (present in this peptide match)
std::set<PeptideListColumn> _engine_columns_to_display;
};
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index 3823fe2e48ae217b736115428167f91f3cfc9f27..c17896a42929e0c8cdcb9dc532b1a2120bbd67e8 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -326,7 +326,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
@@ -542,6 +542,46 @@ PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
QVariant(valueStr.simplified().toDouble()));
}
}
+ else if(identification_engine == IdentificationEngine::Comet)
+ {
+ if(name == "xcorr")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::comet_xcorr,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ else if(name == "deltacn")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::comet_deltacn,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ else if(name == "deltacnstar")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::comet_deltacnstar,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ else if(name == "spscore")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::comet_spscore,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ else if(name == "sprank")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::comet_sprank,
+ QVariant(valueStr.simplified().toInt()));
+ }
+ else if(name == "expect")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::comet_expectation_value,
+ QVariant(valueStr.simplified().toDouble()));
+ _p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
+ }
+ }
else if(identification_engine == IdentificationEngine::MSGFplus)
{
if(name == "raw")
@@ -561,6 +601,7 @@ PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
_p_peptide_evidence->setParam(
PeptideEvidenceParam::msgfplus_EValue,
QVariant(valueStr.simplified().toDouble()));
+ _p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
}
}
}
diff --git a/src/utils/types.h b/src/utils/types.h
index df9423e49c30412be224aff7c0b17ce0786bf60e..ed75f68914921012be195f19f44325782dedae3d 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -80,6 +80,12 @@ enum class PeptideEvidenceParam : std::int8_t
msgfplus_energy = 10, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
msgfplus_SpecEValue = 11, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
msgfplus_EValue = 12, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
+ comet_xcorr = 13, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI]
+ comet_deltacn = 14, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI]
+ comet_deltacnstar = 15, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI]
+ comet_spscore = 16, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI]
+ comet_sprank = 17, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI]
+ comet_expectation_value = 18, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI]
};