diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index 3502835d87158b8de89bcdf77dcf0d4561bd6253..2fb6f1506674c6c233c242ca7d062f5efe5c3ba8 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/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;
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 23eebfb3e05a4317cb4c674aebdce26978a6e42f..6b332d4e5b0b976074462ae975f5aca0bad9435a 100644
--- a/src/core/identificationgroup.cpp
+++ b/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;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 8a03691f71654a48bdcbcca1cd7a84cbf85f2a4a..023c091235555831bfea48cd45cff6bb19741704 100644
--- a/src/gui/mainwindow.cpp
+++ b/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";
}
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 8e7b258b143004f204a6d008029b0391ba243f0f..0f63fe248c26f15e5478e558b0349c1d15547b56 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/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>
diff --git a/src/input/xtandemsaxhandler.h b/src/input/xtandemsaxhandler.h
index f129e5c30d53b0777e1de5c6ef60b95e50a1604b..85babb2ec2f4403022bb734769cbf4f16da8209f 100644
--- a/src/input/xtandemsaxhandler.h
+++ b/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;