readig mzIdentML

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;

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) {

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;

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) {

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);

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
 };