diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index ca1dfdb3f783a67b4118c5dcd0073c30f2ea5f65..c7302963a2cad2a1259003509567e5bc53a2f255 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/src/core/identification_sources/identificationpwizfile.cpp
@@ -36,7 +36,7 @@
IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & ident_file) : IdentificationDataSource(ident_file.absoluteFilePath()), _ident_file(ident_file)
{
//_engine = IdentificationEngine::XTandem;
- _engine = IdentificationEngine::peptider;
+ _engine = IdentificationEngine::peptider;
}
IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_ident_file (other._ident_file)
@@ -66,6 +66,8 @@ void IdentificationPwizFile::parseTo(Project* p_project) {
IdentificationPwizReader pwiz_reader(_ident_file);
MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
+
+ _engine = pwiz_reader.getIdentificationEngine();
setMsRunSp(msrun_sp);
std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
IdentificationGroup * identification_group_p = nullptr;
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 3004435f2807ed111d526696eddd6a266a18c45a..ab3a9377b13ec4e4d985d7a167aa937e1f3a85a3 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -46,6 +46,7 @@ PeptideMatch::PeptideMatch(const PeptideMatch & other): PeptideMatch(other._msru
_params = other._params;
_checked = other._checked;
_proxy_valid = other._proxy_valid;
+
}
void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 29b290a3949db2b6c8d4a991a6c3a576f1d6a54f..0c5ccf6a04c9f51acc75d919e83e46d16ff1e824 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -124,7 +124,7 @@ private :
pappso::GrpPeptideSp _sp_grp_peptide;
PeptideXtpSp _peptide_sp;
pappso::pappso_double _rt;
- pappso::pappso_double _evalue;
+ pappso::pappso_double _evalue=0;
pappso::pappso_double _exp_mass;
unsigned int _start=0;
unsigned int _charge;
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 3bc43897b9e6951da69b38a8e1793b8a0db73d6a..484df0d3f48ebde4af7eb03c7e3d98912b9c7eec 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -37,6 +37,7 @@
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/exception/exceptionoutofrange.h>
+#include <pwiz/data/common/ParamTypes.hpp>
#include <pwiz/data/identdata/IdentData.hpp>
#include <pwiz/data/identdata/IdentDataFile.hpp>
#include "../core/peptidematch.h"
@@ -87,6 +88,43 @@ const QString IdentificationPwizReader::getMsrunName() const {
return QString::fromStdString(pwiz_msrun->name);
}
+
+IdentificationEngine IdentificationPwizReader::getIdentificationEngine() const {
+
+ /*
+ <AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+ <AnalysisSoftware version="X!Tandem Vengeance (2015.12.15.2)" name="X!Tandem" id="as1">
+ <SoftwareName>
+ <cvParam accession="MS:1001476" cvRef="PSI-MS" name="X!Tandem"/>
+ </SoftwareName>
+ </AnalysisSoftware>
+ </AnalysisSoftwareList>
+ */
+ IdentificationEngine identification_engine = IdentificationEngine::peptider;
+ for (pwiz::identdata::AnalysisSoftwarePtr software_ptr :_pwiz_ident_data_file->analysisSoftwareList) {
+ // qDebug() << "IdentificationPwizReader::getIdentificationEngine " << QString::fromStdString(software_ptr.get()->cvParam(param).name);
+ if (software_ptr.get()->softwareName.hasCVParam(pwiz::cv::MS_X_Tandem))
+ {
+ identification_engine = IdentificationEngine::XTandem;
+ }
+ if (software_ptr.get()->softwareName.hasCVParam(pwiz::cv::MS_Mascot_DAT_format))
+ {
+ identification_engine = IdentificationEngine::mascot;
+ }
+ }
+ return identification_engine;
+}
+
+QVariant getQVariantDoubleParam(pwiz::data::ParamContainer * item, pwiz::cv::CVID param) {
+ if (item->hasCVParam(param))
+ {
+ return QVariant (QString::fromStdString(item->cvParam(param).value).toDouble());
+ }
+ else {
+ return QVariant();
+ }
+}
+
void IdentificationPwizReader::read(
IdentificationDataSource * p_identification_data_source, Project * p_project, IdentificationGroup * p_identification_group) {
qDebug() << "IdentificationPwizReader::read begin";
@@ -114,7 +152,7 @@ void IdentificationPwizReader::read(
ProteinMatch * protein_match_p = _p_identification_group->getProteinMatchInstance(protein_sp.get()->getAccession());
protein_match_p->setProteinXtpSp(protein_sp);
- protein_match_p->setChecked(true);
+ protein_match_p->setChecked(true);
map_id2protein.insert(std::pair<QString, ProteinMatch *>(QString::fromStdString( sequence_pwiz->id), protein_match_p));
@@ -146,14 +184,9 @@ void IdentificationPwizReader::read(
}
//<cvParam accession="MS:1001115" cvRef="PSI-MS" value="4925" name="scan number(s)"/>
- double rt=0;
-
- if (spectrum_ptr.get()->hasCVParam(pwiz::cv::MS_retention_time))
+ QVariant rt = getQVariantDoubleParam(spectrum_ptr.get(), pwiz::cv::MS_retention_time);
+ if (rt.isNull())
{
- rt =
- std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_retention_time).value);
- }
- else {
//throw pappso::PappsoException(QObject::tr("Scan number not found"));
}
@@ -167,20 +200,22 @@ void IdentificationPwizReader::read(
// </SpectrumIdentificationItem>
for ( pwiz::identdata::SpectrumIdentificationItemPtr spid_item : spectrum_ptr.get()->spectrumIdentificationItem) {
PeptideMatch * p_peptide_match = new PeptideMatch(_sp_msrun.get(), scan);
- p_peptide_match->setRetentionTime(rt);
+ p_peptide_match->setRetentionTime(rt.toDouble());
p_peptide_match->setCharge(spid_item->chargeState);
pappso::pappso_double exp_mass = spid_item->experimentalMassToCharge * ((double) spid_item->chargeState) - (((double) spid_item->chargeState) * pappso::MHPLUS);
p_peptide_match->setExperimentalMass(exp_mass);
p_peptide_match->setIdentificationDataSource( p_identification_data_source);
p_peptide_match->setChecked(true);
- if (spectrum_ptr.get()->hasCVParam(pwiz::cv::MS_X_Tandem_expect))
+ QVariant evalue = getQVariantDoubleParam(spid_item.get(), pwiz::cv::MS_X_Tandem_expect);
+ if (!evalue.isNull())
{
- p_peptide_match->setEvalue(std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_X_Tandem_expect).value));
+ p_peptide_match->setEvalue(evalue.toDouble());
}
- if (spectrum_ptr.get()->hasCVParam(pwiz::cv::MS_X_Tandem_hyperscore))
+ QVariant hyperscore = getQVariantDoubleParam(spid_item.get(), pwiz::cv::MS_X_Tandem_hyperscore);
+ if (!hyperscore.isNull())
{
- p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, QVariant(std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_X_Tandem_hyperscore).value)));
+ p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, hyperscore);
}
for ( pwiz::identdata::PeptideEvidencePtr peptide_evidence_sp : spid_item.get()->peptideEvidencePtr) {
diff --git a/src/input/identificationpwizreader.h b/src/input/identificationpwizreader.h
index a4999a71f9b572a1f38981a85b60d420d7230469..6a069c868e4273d9d925bceec48fccf7e5a95a23 100644
--- a/src/input/identificationpwizreader.h
+++ b/src/input/identificationpwizreader.h
@@ -35,6 +35,7 @@
#include "../core/identification_sources/identificationdatasource.h"
#include "../core/project.h"
#include "../core/identificationgroup.h"
+#include "../utils/types.h"
namespace pwiz {
@@ -49,6 +50,7 @@ public:
IdentificationPwizReader(const QFileInfo & filename);
virtual ~IdentificationPwizReader();
const QString getMsrunName() const;
+ IdentificationEngine getIdentificationEngine() const;
void read(
IdentificationDataSource * p_identification_data_source, Project * p_project, IdentificationGroup * p_identification_group);
diff --git a/src/utils/types.h b/src/utils/types.h
index 2226518680c97846ad43edf1d50bbc52bea7576f..b18293cd2c5ca123726ec252ae4b6ff429b79761 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -46,6 +46,7 @@ enum class ExternalDatabase: std::int8_t {
enum class IdentificationEngine {
unknown, ///< X!Tandem
XTandem, ///< X!Tandem
+ mascot, ///< Mascot
peptider ///< peptider
};