indentation and really make sure that we look for MSrun in the right place

src/core/identification_sources/identificationdatasource.cpp

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

src/core/msrun.cpp

@@ -56,6 +56,21 @@ MsRun::~MsRun()
 pappso::MsRunReaderSp &
 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;
 }
 
@@ -87,6 +102,8 @@ MsRun::getMsRunStatistics(MsRunStatistics param) const
 bool
 MsRun::findMsRunFile()
 {
+  // first look at the file path :)
+  _msrun_reader_sp = getMsRunReaderSp();
   if(_msrun_reader_sp != nullptr)
     return true;
   QFileInfo file_original(this->getFilename());