diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp index edc002009e76ac0708f7be6cc9c6d0cc241399a8..991729a019d1816be422aba00c91eff93cfa6045 100644 --- a/src/gui/peptide_list_view/peptidetablemodel.cpp +++ b/src/gui/peptide_list_view/peptidetablemodel.cpp @@ -104,6 +104,8 @@ PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match) _engine_columns_to_display.insert( PeptideListColumn::msgfplus_SpecEValue); _engine_columns_to_display.insert(PeptideListColumn::msgfplus_EValue); + _engine_columns_to_display.insert( + PeptideListColumn::msgfplus_isotope_error); } else if(engine == IdentificationEngine::Comet) { @@ -147,7 +149,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent) const int PeptideTableModel::columnCount(const QModelIndex &parent) const { - return 39; + return 40; } QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, @@ -456,6 +458,12 @@ PeptideTableModel::data(const QModelIndex &index, int role) const ->getParam(PeptideEvidenceParam::msgfplus_SpecEValue); break; + case(std::int8_t)PeptideListColumn::msgfplus_isotope_error: + return _p_protein_match->getPeptideMatchList() + .at(row) + .getPeptideEvidence() + ->getParam(PeptideEvidenceParam::msgfplus_isotope_error); + break; case(std::int8_t)PeptideListColumn::comet_xcorr: return _p_protein_match->getPeptideMatchList() .at(row) @@ -635,6 +643,9 @@ PeptideTableModel::getTitle(std::int8_t column) case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue: return "MS-GF spectral E-value"; break; + case(std::int8_t)PeptideListColumn::msgfplus_isotope_error: + return "MS-GF istotope error"; + break; case(std::int8_t)PeptideListColumn::comet_xcorr: return "Comet XCorr"; @@ -769,6 +780,9 @@ PeptideTableModel::getDescription(std::int8_t column) case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue: return "MS-GF spectral E-value"; break; + case(std::int8_t)PeptideListColumn::msgfplus_isotope_error: + return "MS-GF istotope error"; + break; case(std::int8_t)PeptideListColumn::comet_xcorr: return "The Comet result 'XCorr'"; break; diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h index dea80398aff58e8a186ab425745849fe84dbdc7d..aa2bea21b3fb15621b2e04ef6d2918dc9d52a8da 100644 --- a/src/gui/peptide_list_view/peptidetablemodel.h +++ b/src/gui/peptide_list_view/peptidetablemodel.h @@ -68,14 +68,15 @@ 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] + msgfplus_isotope_error = 33, ///< MS:1002053 "MS-GF E-value." [PSI:PI] + comet_xcorr = 34, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI] + comet_deltacn = 35, ///< 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] + 36, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI] + comet_spscore = 37, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI] + comet_sprank = 38, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI] comet_expectation_value = - 38, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI] + 39, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI] }; class PeptideListWindow; diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp index c17896a42929e0c8cdcb9dc532b1a2120bbd67e8..a51e5f6078ea6318d298c082c0bafa2c76fe63e5 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 @@ -603,6 +603,19 @@ PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes) QVariant(valueStr.simplified().toDouble())); _p_peptide_evidence->setEvalue(valueStr.simplified().toDouble()); } + + else if(name == "denovo") + { + _p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_denovo, + QVariant(valueStr.simplified().toDouble())); + } + else if(name == "IsotopeError") + { + _p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_isotope_error, + QVariant(valueStr.simplified().toInt())); + } } } return is_ok; diff --git a/src/utils/types.h b/src/utils/types.h index ed75f68914921012be195f19f44325782dedae3d..a7b2cd5366578fe3c971b4f03d01dfd242610a63 100644 --- a/src/utils/types.h +++ b/src/utils/types.h @@ -80,12 +80,13 @@ 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] + msgfplus_isotope_error = 13, ///< MS-GF isotope error + comet_xcorr = 14, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI] + comet_deltacn = 15, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI] + comet_deltacnstar = 16, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI] + comet_spscore = 17, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI] + comet_sprank = 18, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI] + comet_expectation_value = 19, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI] };