reading Xtandem files seems to work!

src/core/identification_sources/identificationxtandemfile.cpp

@@ -78,6 +78,7 @@ void IdentificationXtandemFile::parseTo(Project* p_project) {
         }
     }
     
+    identification_group_p->addMsRunSp(msrun_sp);
     XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p, this);
 
     QXmlSimpleReader simplereader;

src/core/identificationgroup.cpp

@@ -66,12 +66,20 @@ void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
     if (accession.isEmpty()) {
         throw pappso::PappsoException(QObject::tr("Error adding protein match : accession is empty"));
     }
+    bool push = true;
     for (ProteinMatch * p_protein_match : _protein_match_list) {
-        if ((p_protein_match != protein_match) && (p_protein_match->getProteinXtpSp().get()->getAccession() == accession)) {
-            throw pappso::PappsoException(QObject::tr("Error adding protein match : accession %1 already registered").arg(accession));
+        if (p_protein_match == protein_match) {
+            push = false;
         }
+        else {
+            if(p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+                throw pappso::PappsoException(QObject::tr("Error adding protein match : accession %1 already registered").arg(accession));
+            }
+        }
+    }
+    if (push) {
+        _protein_match_list.push_back(protein_match);
     }
-    _protein_match_list.push_back(protein_match);
 }
 
 bool IdentificationGroup::contains (const MsRun * p_msrun) const {
@@ -81,7 +89,10 @@ bool IdentificationGroup::contains (const MsRun * p_msrun) const {
     return false;
 }
 void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
-    _ms_run_list.push_back(ms_run_sp);
+    auto it = std::find (_ms_run_list.begin() ,_ms_run_list.end(),ms_run_sp);
+    if (it == _ms_run_list.end()) {
+        _ms_run_list.push_back(ms_run_sp);
+    }
 }
 const std::vector<MsRunSp> & IdentificationGroup::getMsRunSpList() const {
     return _ms_run_list;

src/gui/mainwindow.cpp

@@ -58,12 +58,14 @@ void XtpLoaderThread::doLoadingResults(bool is_individual, AutomaticFilterParame
     qDebug() << "XtpLoaderThread::doLoadingResults begin ";
     try {
         ProjectSp project_sp = Project().makeProjectSp();
-	project_sp.get()->setCombineMode(!is_individual);
+        project_sp.get()->setCombineMode(!is_individual);
 
         for (QString filename : file_list) {
+            emit loadingMessage(tr("loading result file %1").arg(filename));
             project_sp.get()->readResultFile(filename);
         }
 
+        emit loadingMessage(tr("filtering proteins"));
         project_sp.get()->updateAutomaticFilters(param);
         emit projectReady(project_sp);
 
@@ -114,6 +116,8 @@ MainWindow::MainWindow(QWidget *parent):
     connect(worker, SIGNAL(projectReady(ProjectSp)), this,SLOT(doProjectReady(ProjectSp)));
     connect(this, SIGNAL(operateLoadingResults(bool,AutomaticFilterParameters,QStringList)), worker,SLOT(doLoadingResults(bool,AutomaticFilterParameters,QStringList)));
     connect(_p_load_results_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedLoadResultDialog()));
+    connect(worker, SIGNAL(loadingMessage(QString)), this,SLOT(doDisplayLoadingMessage(QString)));
+    connect(worker, SIGNAL(projectNotReady(QString)), this,SLOT(doProjectNotReady(QString)));
     /*
         connect(&workerThread, SIGNAL(finished()), worker, SLOT(deleteLater()));
         connect(this, SIGNAL(operateMsDataFile(QString)), worker,SLOT(doMsDataFileLoad(QString)));
@@ -147,6 +151,7 @@ void MainWindow::viewError(QString error) {
 }
 
 void MainWindow::doDisplayLoadingMessage(QString message) {
+    qDebug() << "MainWindow::doDisplayLoadingMessage " <<  message;
     ui->statusbar->showMessage(message);
 }
 
@@ -168,13 +173,17 @@ void MainWindow::doAcceptedLoadResultDialog() {
 
 void MainWindow::doProjectReady(ProjectSp project_sp) {
 
+    qDebug() << "MainWindow::doProjectReady begin";
     try {
+        doDisplayLoadingMessage(tr("grouping proteins"));
         project_sp.get()->startGrouping();
     }
     catch (pappso::PappsoException & error) {
         viewError(tr("Error while grouping :\n%1").arg(error.qwhat()));
     }
     _project_window->setProjectSp(project_sp);
+
+    qDebug() << "MainWindow::doProjectReady end";
 }
 
 

src/input/xtandemsaxhandler.cpp

@@ -96,6 +96,9 @@ bool XtandemSaxHandler::endElement(const QString & namespaceURI, const QString &
         if (qName == "note")
         {
             is_ok = endElement_note();
+        } else if (qName == "domain")
+        {
+            is_ok = endElement_domain();
         }
 
         // end of detection_moulon
@@ -159,14 +162,15 @@ bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) {
     _current_protein.setAccession(accession);
     if (_p_protein_match == nullptr) {
         _p_protein_match = new ProteinMatch();
-	//qDebug() << "startElement_protein p_protein_match 2 " << _p_protein_match;
+        //qDebug() << "startElement_protein p_protein_match 2 " << _p_protein_match;
         _p_protein_match->setChecked(false);
 
     }
     //qDebug() << "startElement_protein p_protein_match 3 " << _p_protein_match;
     ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
     _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
-    
+    _p_protein_match->setChecked(true);
+
     _p_identification_group->addProteinMatch(_p_protein_match);
     //qDebug() << "startElement_protein end" ;
     return is_ok;
@@ -187,7 +191,7 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
 //<domain id="1976.1.1" start="620" end="629" expect="9.7e-04" mh="1120.5307" delta="-0.0012" hyperscore="29.9"
     //nextscore="10.2" y_score="10.4" y_ions="7" b_score="11.2" b_ions="3" pre="QLYR" post="RYGV"
     //seq="AQEEMAQVAK" missed_cleavages="0">
-    qDebug() << "startElement_domain ";
+    //qDebug() << "startElement_domain ";
     bool is_ok = true;
     _current_text = _current_text.simplified().replace(" ", "");
     if (!_current_text.isEmpty()) {
@@ -206,21 +210,19 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
 
     _p_peptide_match->setRetentionTime(_retention_time);
     _p_peptide_match->setEvalue(attributes.value("expect").simplified().toDouble());
+    //qDebug() << "XtandemSaxHandler::startElement_domain evalue "  << _p_peptide_match->getEvalue() << " scan " << _p_peptide_match->getScan();
 
     pappso::pappso_double xtandem_mhtheo = attributes.value("mh").simplified().toDouble();
     pappso::pappso_double xtandem_delta = attributes.value("delta").simplified().toDouble();
 
-    pappso::pappso_double exp_mass = xtandem_mhtheo - xtandem_delta;
+    pappso::pappso_double exp_mass = xtandem_mhtheo + xtandem_delta - pappso::MHPLUS;
 
     _p_peptide_match->setExperimentalMass(exp_mass);
     _p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
     _p_peptide_match->setCharge(_charge);
 
     _p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
-    _p_peptide_match->setChecked(false);
-    if (attributes.value("validate").simplified().toLower() == "true") {
-        _p_peptide_match->setChecked(true);
-    }
+    _p_peptide_match->setChecked(true);
     _p_protein_match->addPeptideMatch(_p_peptide_match);
 
 
@@ -236,14 +238,21 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
 bool XtandemSaxHandler::startElement_aa(QXmlAttributes attributes) {
 //<aa type="M" at="624" modified="15.99491" />
     bool is_ok = true;
-    qDebug() << "startElement_aa ";
+    //qDebug() << "startElement_aa ";
     pappso::AaModificationP modif = getAaModificationP(attributes.value("modified").simplified().toDouble());
     unsigned int position_in_prot = attributes.value("at").simplified().toUInt()-1;
     _current_peptide_sp.get()->addAaModification(modif, position_in_prot-_p_peptide_match->getStart());
-    qDebug() << "startElement_aa end" ;
+    //qDebug() << "startElement_aa end" ;
     return is_ok;
 }
 
+bool XtandemSaxHandler::endElement_domain() {
+   bool is_ok = true;
+    _current_peptide_sp = _p_project->getPeptideStore().getInstance(_current_peptide_sp);
+
+    _p_peptide_match->setPeptideXtpSp(_current_peptide_sp);
+    return is_ok;
+}
 bool XtandemSaxHandler::endElement_note() {
 //<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
     ////parent_gene=GRMZM2G083841</note>

src/input/xtandemsaxhandler.h

@@ -72,6 +72,7 @@ private:
     bool startElement_file(QXmlAttributes attributes);
     bool startElement_aa(QXmlAttributes attributes);
     bool startElement_domain(QXmlAttributes attributes);
+    bool endElement_domain();
     bool endElement_note();
 
     pappso::AaModificationP getAaModificationP(pappso::mz mass) const;