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Commit b62b91cf authored by Langella Olivier's avatar Langella Olivier
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indentation and really make sure that we look for MSrun in the right place

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src/core/identification_sources/identificationdatasource.cpp
+ 185
− 102
View file @ b62b91cf
/******************************************************************************* /*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>. * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
* *
* This file is part of XTPcpp. * This file is part of XTPcpp.
* *
* XTPcpp is free software: you can redistribute it and/or modify * XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by * it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or * the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version. * (at your option) any later version.
* *
* XTPcpp is distributed in the hope that it will be useful, * XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of * but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details. * GNU General Public License for more details.
* *
* You should have received a copy of the GNU General Public License * You should have received a copy of the GNU General Public License
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>. * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
* *
* Contributors: * Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
******************************************************************************/ *implementation
******************************************************************************/
#include "identificationdatasource.h" #include "identificationdatasource.h"
#include "identificationxtandemfile.h" #include "identificationxtandemfile.h"
...@@ -30,144 +31,226 @@ ...@@ -30,144 +31,226 @@
IdentificationDataSource::IdentificationDataSource(const QString resource_name) IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{ {
_resource_name = resource_name; _resource_name = resource_name;
} }
IdentificationDataSource::IdentificationDataSource(const IdentificationDataSource& other) IdentificationDataSource::IdentificationDataSource(
const IdentificationDataSource &other)
{ {
_ms_run_sp = other._ms_run_sp; _ms_run_sp = other._ms_run_sp;
_resource_name = other._resource_name; _resource_name = other._resource_name;
_xml_id = other._xml_id; _xml_id = other._xml_id;
_version = other._version; _version = other._version;
_params = other._params; _params = other._params;
_param_stats = other._param_stats; _param_stats = other._param_stats;
_fastafile_list = other._fastafile_list; _fastafile_list = other._fastafile_list;
//PeptideEvidenceStore _peptide_evidence_store; // PeptideEvidenceStore _peptide_evidence_store;
} }
IdentificationDataSource::~IdentificationDataSource() IdentificationDataSource::~IdentificationDataSource()
{ {
} }
const std::map<IdentificationEngineStatistics, QVariant> & IdentificationDataSource::getIdentificationEngineStatisticsMap() const { const std::map<IdentificationEngineStatistics, QVariant> &
return _param_stats; IdentificationDataSource::getIdentificationEngineStatisticsMap() const
{
return _param_stats;
} }
const std::map<IdentificationEngineParam, QVariant> & IdentificationDataSource::getIdentificationEngineParamMap() const { const std::map<IdentificationEngineParam, QVariant> &
return _params; IdentificationDataSource::getIdentificationEngineParamMap() const
{
return _params;
} }
const PeptideEvidenceStore & IdentificationDataSource::getPeptideEvidenceStore() const { const PeptideEvidenceStore &
return _peptide_evidence_store; IdentificationDataSource::getPeptideEvidenceStore() const
{
return _peptide_evidence_store;
} }
PeptideEvidenceStore & IdentificationDataSource::getPeptideEvidenceStore() { PeptideEvidenceStore &
return _peptide_evidence_store; IdentificationDataSource::getPeptideEvidenceStore()
{
return _peptide_evidence_store;
} }
void IdentificationDataSource::setXmlId(const QString xmlid) { void
_xml_id = xmlid; IdentificationDataSource::setXmlId(const QString xmlid)
{
_xml_id = xmlid;
} }
const QString & IdentificationDataSource::getXmlId() const { const QString &
return _xml_id; IdentificationDataSource::getXmlId() const
{
return _xml_id;
} }
bool IdentificationDataSource::operator==(const IdentificationDataSource& other) const bool
IdentificationDataSource::
operator==(const IdentificationDataSource &other) const
{ {
} }
const QString & IdentificationDataSource::getResourceName () const { const QString &
return _resource_name; IdentificationDataSource::getResourceName() const
{
return _resource_name;
} }
const QString IdentificationDataSource::getSampleName () const { const QString
return _ms_run_sp.get()->getSampleName(); IdentificationDataSource::getSampleName() const
{
return _ms_run_sp.get()->getSampleName();
} }
void IdentificationDataSource::setMsRunSp (MsRunSp ms_run_sp) { void
_ms_run_sp = ms_run_sp; IdentificationDataSource::setMsRunSp(MsRunSp ms_run_sp)
{
_ms_run_sp = ms_run_sp;
} }
MsRunSp IdentificationDataSource::getMsRunSp () const { MsRunSp
return (_ms_run_sp); IdentificationDataSource::getMsRunSp() const
{
return (_ms_run_sp);
} }
void IdentificationDataSource::setIdentificationEngine(IdentificationEngine engine) { void
_engine = engine; IdentificationDataSource::setIdentificationEngine(IdentificationEngine engine)
{
_engine = engine;
} }
IdentificationEngine IdentificationDataSource::getIdentificationEngine() const { IdentificationEngine
return _engine; IdentificationDataSource::getIdentificationEngine() const
{
return _engine;
} }
const QString IdentificationDataSource::getIdentificationEngineName() const { const QString
QString name = "unknown"; IdentificationDataSource::getIdentificationEngineName() const
switch (_engine) { {
case IdentificationEngine::XTandem : QString name = "unknown";
switch(_engine)
{
case IdentificationEngine::XTandem:
name = "X!Tandem"; name = "X!Tandem";
break; break;
case IdentificationEngine::peptider : case IdentificationEngine::peptider:
name = "peptider"; name = "peptider";
break; break;
} }
return name; return name;
} }
const QString& IdentificationDataSource::getIdentificationEngineVersion() const { const QString &
return _version; IdentificationDataSource::getIdentificationEngineVersion() const
{
return _version;
} }
void IdentificationDataSource::setIdentificationEngineVersion(const QString& version) { void
_version = version; IdentificationDataSource::setIdentificationEngineVersion(const QString &version)
{
_version = version;
} }
void IdentificationDataSource::setIdentificationEngineParam(IdentificationEngineParam param, const QVariant& value) { void
_params.insert(std::pair<IdentificationEngineParam, QVariant>(param, value)); IdentificationDataSource::setIdentificationEngineParam(
IdentificationEngineParam param, const QVariant &value)
{
_params.insert(std::pair<IdentificationEngineParam, QVariant>(param, value));
} }
const QVariant IdentificationDataSource::getIdentificationEngineParam(IdentificationEngineParam param) const { const QVariant
try { IdentificationDataSource::getIdentificationEngineParam(
return _params.at(param); IdentificationEngineParam param) const
{
try
{
return _params.at(param);
} }
catch (std::out_of_range) { catch(std::out_of_range)
return QVariant(); {
return QVariant();
} }
} }
void IdentificationDataSource::setIdentificationEngineStatistics(IdentificationEngineStatistics param, const QVariant& value) { void
_param_stats.insert(std::pair<IdentificationEngineStatistics, QVariant>(param, value)); IdentificationDataSource::setIdentificationEngineStatistics(
IdentificationEngineStatistics param, const QVariant &value)
{
_param_stats.insert(
std::pair<IdentificationEngineStatistics, QVariant>(param, value));
} }
const QVariant IdentificationDataSource::getIdentificationEngineStatistics(IdentificationEngineStatistics param) const { const QVariant
try { IdentificationDataSource::getIdentificationEngineStatistics(
return _param_stats.at(param); IdentificationEngineStatistics param) const
{
try
{
return _param_stats.at(param);
} }
catch (std::out_of_range) { catch(std::out_of_range)
return QVariant(); {
return QVariant();
} }
} }
pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const { pappso::SpectrumSp
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ; IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const
if (_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF) { {
scan_number = scan_number-1;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF)
{
scan_number = scan_number - 1;
} }
if (_ms_run_sp.get()->findMsRunFile() == false) { pappso::MsRunReaderSp msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSp();
throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(_ms_run_sp.get()->getFilename()));
if(msrun_reader_sp == nullptr)
{
if(_ms_run_sp.get()->findMsRunFile() == false)
{
throw pappso::ExceptionNotFound(
QObject::tr("mz data \"%1\" file not found")
.arg(_ms_run_sp.get()->getFilename()));
}
} }
msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSp();
//qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize(); if(msrun_reader_sp == nullptr)
pappso::SpectrumSp spectrum_sp = _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumSp(scan_number); {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ; throw pappso::ExceptionNotFound(
return spectrum_sp; QObject::tr("mz data \"%1\" file not found")
.arg(_ms_run_sp.get()->getFilename()));
}
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ <<
// _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
pappso::SpectrumSp spectrum_sp =
msrun_reader_sp.get()->getSpectrumSp(scan_number);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
return spectrum_sp;
} }
void IdentificationDataSource::addFastaFile (FastaFileSp file) { void
_fastafile_list.push_back(file); IdentificationDataSource::addFastaFile(FastaFileSp file)
{
_fastafile_list.push_back(file);
} }
const std::vector<FastaFileSp> & IdentificationDataSource::getFastaFileList() const { const std::vector<FastaFileSp> &
qDebug()<< "IdentificationDataSource::getFastaFileList begin" << _fastafile_list.size(); IdentificationDataSource::getFastaFileList() const
return _fastafile_list; {
qDebug() << "IdentificationDataSource::getFastaFileList begin"
<< _fastafile_list.size();
return _fastafile_list;
} }
const bool IdentificationDataSource::isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const { const bool
IdentificationDataSource::isValid(
if (p_peptide_evidence->getEvalue() <= automatic_filter_parameters.getFilterPeptideEvalue()) { const PeptideEvidence *p_peptide_evidence,
return true; const AutomaticFilterParameters &automatic_filter_parameters) const
{
if(p_peptide_evidence->getEvalue() <=
automatic_filter_parameters.getFilterPeptideEvalue())
{
return true;
} }
return false; return false;
} }
src/core/identificationgroup.cpp
+ 360
− 216
View file @ b62b91cf
This diff is collapsed.
src/core/msrun.cpp
+ 17
− 0
View file @ b62b91cf
...@@ -56,6 +56,21 @@ MsRun::~MsRun() ...@@ -56,6 +56,21 @@ MsRun::~MsRun()
pappso::MsRunReaderSp & pappso::MsRunReaderSp &
MsRun::getMsRunReaderSp() MsRun::getMsRunReaderSp()
{ {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " filename=" << getFilename();
if(_msrun_reader_sp == nullptr)
{
try
{
_msrun_reader_sp =
pappso::MsRunReaderFactory::getInstance().buildPwizMsRunReaderSp(
*this);
}
catch(pappso::PappsoException &error)
{
_msrun_reader_sp = nullptr;
}
}
return _msrun_reader_sp; return _msrun_reader_sp;
} }
...@@ -87,6 +102,8 @@ MsRun::getMsRunStatistics(MsRunStatistics param) const ...@@ -87,6 +102,8 @@ MsRun::getMsRunStatistics(MsRunStatistics param) const
bool bool
MsRun::findMsRunFile() MsRun::findMsRunFile()
{ {
// first look at the file path :)
_msrun_reader_sp = getMsRunReaderSp();
if(_msrun_reader_sp != nullptr) if(_msrun_reader_sp != nullptr)
return true; return true;
QFileInfo file_original(this->getFilename()); QFileInfo file_original(this->getFilename());
......
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