diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp index 6ca588d3b25109367f51f2580d4fb598bd2bc2ce..efe5c63f6cea2e3a0d61bef8cd983edf3e4993e0 100644 --- a/src/gui/peptide_list_view/peptidetablemodel.cpp +++ b/src/gui/peptide_list_view/peptidetablemodel.cpp @@ -651,7 +651,7 @@ PeptideTableModel::getTitle(std::int8_t column) return "MS-GF spectral E-value"; break; case(std::int8_t)PeptideListColumn::msgfplus_isotope_error: - return "MS-GF istotope error"; + return "MS-GF isotope error"; break; case(std::int8_t)PeptideListColumn::comet_xcorr: @@ -788,7 +788,7 @@ PeptideTableModel::getDescription(std::int8_t column) return "MS-GF spectral E-value"; break; case(std::int8_t)PeptideListColumn::msgfplus_isotope_error: - return "MS-GF istotope error"; + return "MS-GF isotope error"; break; case(std::int8_t)PeptideListColumn::comet_xcorr: return "The Comet result 'XCorr'"; diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp index 0666dc90974fe1b6fcb04859719848f441a46ada..f8ef38faa3f993a29ca76829feb0af298f94ca97 100644 --- a/src/input/identificationpwizreader.cpp +++ b/src/input/identificationpwizreader.cpp @@ -200,6 +200,11 @@ IdentificationPwizReader::getIdentificationEngine( { identification_engine = IdentificationEngine::mascot; } + else if(analysis_software_p.get()->softwareName.hasCVParam( + pwiz::cv::MS_MS_GF_)) + { + identification_engine = IdentificationEngine::MSGFplus; + } else { return IdentificationEngine::unknown; @@ -521,6 +526,62 @@ IdentificationPwizReader::read( } + //<cvParam cvRef="PSI-MS" accession="MS:1002049" + // name="MS-GF:RawScore" value="164"/> + QVariant MSGFplus_rawscore = getQVariantDoubleParam( + spid_item.get(), pwiz::cv::MS_MS_GF_RawScore); + if(!MSGFplus_rawscore.isNull()) + { + p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_raw, MSGFplus_rawscore); + } + //<cvParam cvRef = "PSI-MS" accession = "MS:1002050" name + //="MS-GF:DeNovoScore" value = "170" /> + + QVariant MSGFplus_denovoscore = getQVariantDoubleParam( + spid_item.get(), pwiz::cv::MS_MS_GF_DeNovoScore); + if(!MSGFplus_denovoscore.isNull()) + { + p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_denovo, + MSGFplus_denovoscore); + } + + //<cvParam cvRef = "PSI-MS" accession = "MS:1002052" name + //="MS-GF:SpecEValue" value = "5.4876387E-19"/> + + QVariant MSGFplus_specevalue = getQVariantDoubleParam( + spid_item.get(), pwiz::cv::MS_MS_GF_SpecEValue); + if(!MSGFplus_specevalue.isNull()) + { + p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_SpecEValue, + MSGFplus_specevalue); + } + //<cvParam cvRef = "PSI-MS" accession = "MS:1002053" name = + //"MS-GF:EValue" value = "1.0822937E-11" /> + + QVariant MSGFplus_evalue = getQVariantDoubleParam( + spid_item.get(), pwiz::cv::MS_MS_GF_EValue); + if(!MSGFplus_evalue.isNull()) + { + p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_EValue, MSGFplus_evalue); + p_peptide_evidence->setEvalue(MSGFplus_evalue.toDouble()); + } + + //<userParam name="IsotopeError" value="0"/> + QVariant isotope_error = + QVariant(QString::fromStdString( + spid_item.get()->userParam("IsotopeError").value) + .toInt()); + if(!isotope_error.isNull()) + { + p_peptide_evidence->setParam( + PeptideEvidenceParam::msgfplus_isotope_error, + isotope_error); + } + for(pwiz::identdata::PeptideEvidencePtr peptide_evidence_sp : spid_item.get()->peptideEvidencePtr) {