diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index c05a5855e25fd834814abe0242838f417833a460..ca1dfdb3f783a67b4118c5dcd0073c30f2ea5f65 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/src/core/identification_sources/identificationpwizfile.cpp
@@ -36,6 +36,7 @@
IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & ident_file) : IdentificationDataSource(ident_file.absoluteFilePath()), _ident_file(ident_file)
{
//_engine = IdentificationEngine::XTandem;
+ _engine = IdentificationEngine::peptider;
}
IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_ident_file (other._ident_file)
@@ -60,7 +61,7 @@ pappso::SpectrumSp IdentificationPwizFile::getSpectrumSp(unsigned int scan_numbe
void IdentificationPwizFile::parseTo(Project* p_project) {
- qDebug() << "Project::readXpipFile begin";
+ qDebug() << "IdentificationPwizFile::parseTo begin";
IdentificationPwizReader pwiz_reader(_ident_file);
@@ -91,6 +92,7 @@ void IdentificationPwizFile::parseTo(Project* p_project) {
pwiz_reader.read(this, p_project, identification_group_p);
+ qDebug() << "IdentificationPwizFile::parseTo end";
// throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index 1555984d040d2ef607b4576f1aa0954a40978342..aa5bcdb29efd9e1d7e43fb22fee1c150f2250f85 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -52,7 +52,7 @@ pappso::SpectrumSp IdentificationXtandemFile::getSpectrumSp(unsigned int scan_nu
void IdentificationXtandemFile::parseTo(Project* p_project) {
- qDebug() << "Project::readXpipFile begin";
+ qDebug() << "IdentificationXtandemFile::parseTo begin";
qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
@@ -104,4 +104,5 @@ void IdentificationXtandemFile::parseTo(Project* p_project) {
throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
}
+ qDebug() << "IdentificationXtandemFile::parseTo end";
}
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index d2e718d733c1ab58c66cb402186c0bc90c088e0b..712b9e2f88c8f5806c7fa413ef61821032a5633d 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -32,6 +32,21 @@ PeptideMatch::PeptideMatch(MsRun * msrunid_sp, unsigned int scan) {
_hash_sample_scan = PeptideMatch::_hash_fn (QString("%1 %2").arg(msrunid_sp->getXmlId()).arg(_scan).toStdString());
}
+PeptideMatch::PeptideMatch(const PeptideMatch & other): PeptideMatch(other._msrunid_sp, other._scan) {
+ _hash_sample_scan = other._hash_sample_scan;
+ _sp_grp_peptide = other._sp_grp_peptide;
+ _peptide_sp = other._peptide_sp;
+ _rt = other._rt;
+ _evalue = other._evalue;
+ _exp_mass = other._exp_mass;
+ _start=other._start;
+ _charge= other._charge;
+ _p_identification_source = other._p_identification_source;
+ _params = other._params;
+ _checked = other._checked;
+ _proxy_valid = other._proxy_valid;
+}
+
void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
_proxy_valid = false;
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 93b6d92ececb2b0e8908c602f02a462836297ec1..29b290a3949db2b6c8d4a991a6c3a576f1d6a54f 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -35,6 +35,7 @@ class PeptideMatch
{
public :
PeptideMatch(MsRun * msrunid_sp, unsigned int scan);
+ PeptideMatch(const PeptideMatch & other);
std::size_t getHashSampleScan() const;
std::size_t getHashPeptideMassSample() const;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index cb5d7b6a730c0f1cdd46a638a3bf66a104cedfc9..07eea92fbcd354f31241c40d3df26b5e388bde0f 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -24,6 +24,7 @@
#include "../input/xpipsaxhandler.h"
#include "peptidematch.h"
#include "proteinmatch.h"
+#include <QDebug>
Project::Project()
{
@@ -46,6 +47,7 @@ void Project::readResultFile(QString filename) {
IdentificationDataSourceSp ident_source = _identification_data_source_store.getInstance(filename);
ident_source.get()->parseTo(this);
+ qDebug() << "Project::readResultFile end";
}
bool Project::isCombineMode() const {
@@ -92,11 +94,14 @@ const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const
return _automatic_filter_parameters;
}
void Project::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+
+ qDebug() << "Project::updateAutomaticFilters begin";
_automatic_filter_parameters = automatic_filter_parameters;
for (auto & p_id_group : _identification_goup_list) {
p_id_group->updateAutomaticFilters(_automatic_filter_parameters);
}
+ qDebug() << "Project::updateAutomaticFilters end";
}
ProjectSp Project::makeProjectSp() const {
return std::make_shared<Project>(*this);
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 3ff811aa1ff7d93f8349385196c64ec692e6d6bd..7bc526d66cd13f88c5408e9b59617007cce10704 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -41,7 +41,7 @@
WorkerThread::WorkerThread(MainWindow * p_main_window)
{
qDebug() << "WorkerThread::WorkerThread begin MainWindow";
-
+
_p_work_monitor = new WorkMonitor();
#if QT_VERSION >= 0x050000
@@ -53,7 +53,7 @@ WorkerThread::WorkerThread(MainWindow * p_main_window)
*/
#else
// Qt4 code
- //worker message
+ //worker message
connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_main_window,SLOT(doDisplayLoadingMessage(QString)));
connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_main_window,SLOT(doDisplayLoadingMessage(QString, int)));
@@ -87,7 +87,7 @@ WorkerThread::WorkerThread(MainWindow * p_main_window)
WorkerThread::WorkerThread(ProjectWindow * p_project_window)
{
qDebug() << "WorkerThread::WorkerThread begin ProjectWindow";
-
+
_p_work_monitor = new WorkMonitor();
#if QT_VERSION >= 0x050000
@@ -95,8 +95,8 @@ WorkerThread::WorkerThread(ProjectWindow * p_project_window)
#else
// Qt4 code
qDebug() << "WorkerThread::WorkerThread Qt4 code";
-
- //worker message
+
+ //worker message
connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_project_window,SLOT(doDisplayLoadingMessage(QString)));
connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_project_window,SLOT(doDisplayLoadingMessage(QString, int)));
@@ -104,16 +104,16 @@ WorkerThread::WorkerThread(ProjectWindow * p_project_window)
//grouping
connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,SLOT(doGrouping(ProjectSp)));
connect(this, SIGNAL(groupingFinished()), p_project_window,SLOT(doGroupingFinished()));
-
-
- //PTM grouping on IdentificationGroup
+
+
+ //PTM grouping on IdentificationGroup
connect(p_project_window, SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)), this,SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
connect(this, SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)), p_project_window,SLOT(refreshPtmGroup(IdentificationGroup *)));
//grouping on IdentificationGroup
connect(p_project_window, SIGNAL(operateGroupingOnIdentification(IdentificationGroup *, GroupingType)), this,SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)), p_project_window,SLOT(refreshGroup(IdentificationGroup *)));
-
+
connect(this, SIGNAL(operationFailed(QString)), p_project_window,SLOT(doOperationFailed(QString)));
connect(this, SIGNAL(operationFinished()), p_project_window,SLOT(doOperationFinished()));
@@ -277,6 +277,7 @@ void WorkerThread::doLoadingResults(bool is_individual, AutomaticFilterParameter
emit loadingMessage(tr("filtering proteins"));
project_sp.get()->updateAutomaticFilters(param);
+ qDebug() << "WorkerThread::doLoadingResults emit projectReady(project_sp) ";
emit projectReady(project_sp);
}
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index f39039bbbb8f430807c6840dd4f44f89ea3f8faf..171cd7abfd97925a22c201b3026a495ec0e9629f 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -35,6 +35,7 @@
#include <QDir>
#include <QString>
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/exception/exceptionoutofrange.h>
#include <pwiz/data/identdata/IdentData.hpp>
#include <pwiz/data/identdata/IdentDataFile.hpp>
@@ -98,7 +99,7 @@ void IdentificationPwizReader::read(
try {
ProteinStore & protein_store = _p_project->getProteinStore();
PeptideStore & peptide_store = _p_project->getPeptideStore();
- std::map<QString, ProteinXtpSp> map_id2protein;
+ std::map<QString, ProteinMatch *> map_id2protein;
std::map<QString, PeptideXtpSp> map_id2peptide;
for (pwiz::identdata::DBSequencePtr seq_ptr :_pwiz_ident_data_file->sequenceCollection.dbSequences) {
@@ -109,7 +110,15 @@ void IdentificationPwizReader::read(
protein.setSequence(QString::fromStdString( sequence_pwiz->seq));
ProteinXtpSp protein_sp(protein.makeProteinXtpSp());
protein_sp = protein_store.getInstance(protein_sp);
- map_id2protein.insert(std::pair<QString, ProteinXtpSp>(QString::fromStdString( sequence_pwiz->id), protein_sp));
+
+
+ ProteinMatch * protein_match_p = _p_identification_group->getProteinMatchInstance(protein_sp.get()->getAccession());
+ protein_match_p->setProteinXtpSp(protein_sp);
+ protein_match_p->setChecked(true);
+
+
+ map_id2protein.insert(std::pair<QString, ProteinMatch *>(QString::fromStdString( sequence_pwiz->id), protein_match_p));
+
}
for (pwiz::identdata::PeptidePtr seq_ptr :_pwiz_ident_data_file->sequenceCollection.peptides) {
@@ -136,7 +145,6 @@ void IdentificationPwizReader::read(
throw pappso::PappsoException(QObject::tr("Scan number not found"));
}
//<cvParam accession="MS:1001115" cvRef="PSI-MS" value="4925" name="scan number(s)"/>
- PeptideMatch * p_peptide_match = new PeptideMatch(_sp_msrun.get(), scan);
double rt=0;
@@ -144,30 +152,61 @@ void IdentificationPwizReader::read(
{
rt =
std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_retention_time).value);
- p_peptide_match->setRetentionTime(rt);
}
else {
//throw pappso::PappsoException(QObject::tr("Scan number not found"));
}
- /*
- 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::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->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hyperscore").toDouble()));
-
- p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
- p_peptide_match->setChecked(true);
- _p_protein_match->addPeptideMatch(p_peptide_match);
- */
+ //<SpectrumIdentificationItem passThreshold="true" rank="1"
+ //experimentalMassToCharge="388.2189331" id="sii2" chargeState="2" calculatedMassToCharge="388.2161235">
+
+ // <PeptideEvidenceRef peptideEvidence_ref="dbseq821_pep947_414"/>
+ // <PeptideEvidenceRef peptideEvidence_ref="dbseq821_pep947_414"/>
+ // <cvParam accession="MS:1001330" cvRef="PSI-MS" value="0.000452757388" name="X!Tandem:expect"/>
+ //<cvParam accession="MS:1001331" cvRef="PSI-MS" value="24.275219" name="X!Tandem:hyperscore"/>
+ // </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->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))
+ {
+ p_peptide_match->setEvalue(std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_X_Tandem_expect).value));
+ }
+ if (spectrum_ptr.get()->hasCVParam(pwiz::cv::MS_X_Tandem_hyperscore))
+ {
+ p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, QVariant(std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_X_Tandem_hyperscore).value)));
+ }
+
+ for ( pwiz::identdata::PeptideEvidencePtr peptide_evidence_sp : spid_item.get()->peptideEvidencePtr) {
+ PeptideMatch * p_peptide_match_from_evidence = new PeptideMatch(*p_peptide_match);
+ p_peptide_match_from_evidence->setStart(peptide_evidence_sp.get()->start);
+
+
+ auto it_pep = map_id2peptide.find(QString::fromStdString(peptide_evidence_sp.get()->peptidePtr.get()->id));
+ if (it_pep == map_id2peptide.end()) {
+ throw pappso::ExceptionOutOfRange(QObject::tr("key %1 not found in map_id2peptide, reading SpectrumIdentificationItem %2")
+ .arg(QString::fromStdString(peptide_evidence_sp.get()->peptidePtr.get()->id))
+ .arg(QString::fromStdString(spid_item.get()->id))
+ );
+ }
+ p_peptide_match->setPeptideXtpSp(it_pep->second);
+
+ auto it = map_id2protein.find(QString::fromStdString(peptide_evidence_sp.get()->dbSequencePtr.get()->id));
+ if (it == map_id2protein.end()) {
+ throw pappso::ExceptionOutOfRange(QObject::tr("key %1 not found in map_id2protein").arg(QString::fromStdString(peptide_evidence_sp.get()->dbSequencePtr.get()->id)));
+ }
+ ProteinMatch * protein_match_p = it->second;
+
+ protein_match_p->addPeptideMatch(p_peptide_match_from_evidence);
+ }
+ delete p_peptide_match;
+ }
}
}