merge

src/core/identification_sources/identificationpepxmlfile.cpp

+/**
+ * \file /core/identification_sources/identificationpepxmlfile.cpp
+ * \date 16/6/2018
+ * \author Olivier Langella
+ * \brief pep xml identification file handler
+ */
+
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.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/>.
+*
+******************************************************************************/
+
+#include "identificationpepxmlfile.h"
+
+#include <pappsomspp/pappsoexception.h>
+#include "../project.h"
+#include "../../input/mascot/mascotdatparser.h"
+
+IdentificationPepXmlFile::IdentificationPepXmlFile(const QFileInfo & mascot_dat_file) : IdentificationDataSource(mascot_dat_file.absoluteFilePath()), _pep_xml_file(mascot_dat_file)
+{
+    _engine = IdentificationEngine::unknown;
+}
+
+IdentificationPepXmlFile::IdentificationPepXmlFile(const IdentificationPepXmlFile& other) : IdentificationDataSource(other),_pep_xml_file (other._pep_xml_file)
+{
+    _engine = IdentificationEngine::unknown;
+}
+
+IdentificationPepXmlFile::~IdentificationPepXmlFile()
+{
+
+}
+
+bool IdentificationPepXmlFile::operator==(const IdentificationPepXmlFile& other) const
+{
+
+}
+
+pappso::SpectrumSp IdentificationPepXmlFile::getSpectrumSp(unsigned int scan_number) const {
+    pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
+    return spectrum_sp;
+}
+
+
+void IdentificationPepXmlFile::parseTo(Project* p_project) {
+    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+
+
+    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_pep_xml_file).baseName());
+    setMsRunSp(msrun_sp);
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    IdentificationGroup * identification_group_p = nullptr;
+    if (p_project->getProjectMode() == ProjectMode::combined) {
+        if (identification_list.size() == 0) {
+            identification_group_p = p_project->newIdentificationGroup();
+        }
+        else {
+            identification_group_p = identification_list[0];
+        }
+    }
+    else {
+        for (IdentificationGroup * identification_p_flist : identification_list) {
+            if (identification_p_flist->containSample(msrun_sp.get()->getSampleName())) {
+                identification_group_p = identification_p_flist;
+                break;
+            }
+        }
+        if (identification_group_p == nullptr) {
+            identification_group_p = p_project->newIdentificationGroup();
+        }
+    }
+
+    identification_group_p->addIdentificationDataSourceP(this);
+    MascotDatParser mascot_parser(p_project, identification_group_p, this);
+
+    QFile qfile(_pep_xml_file.absoluteFilePath());
+    mascot_parser.parse(&qfile);
+    
+    qfile.close();
+
+    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}

src/core/identification_sources/identificationpepxmlfile.h

+/**
+ * \file /core/identification_sources/identificationpepxmlfile.h
+ * \date 16/6/2018
+ * \author Olivier Langella
+ * \brief pep xml identification file handler
+ */
+
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.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/>.
+*
+******************************************************************************/
+
+#ifndef IDENTIFICATIONPEPXMLFILE_H
+#define IDENTIFICATIONPEPXMLFILE_H
+
+#include "identificationdatasource.h"
+#include <QFileInfo>
+
+class IdentificationPepXmlFile: public IdentificationDataSource
+{
+public:
+    IdentificationPepXmlFile(const QFileInfo & mascot_dat_file);
+    IdentificationPepXmlFile(const IdentificationPepXmlFile& other);
+    ~IdentificationPepXmlFile();
+    bool operator==(const IdentificationPepXmlFile& other) const;
+
+    virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
+    virtual void parseTo(Project* p_project) override;
+
+    //virtual const bool isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const override;
+
+private:
+    const QFileInfo _pep_xml_file;
+};
+
+#endif // IDENTIFICATIONPEPXMLFILE_H

src/core/identification_sources/identificationpwizfile.cpp

@@ -5,7 +5,6 @@
  * \brief read identification files with proteowizard library
  */
 
-
 /*******************************************************************************
 * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
 *
@@ -25,77 +24,75 @@
 *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
-*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+*implementation
 ******************************************************************************/
 
+#include "../../input/identificationpwizreader.h"
+#include "../project.h"
 #include "identificationpwizfile.h"
 #include <pappsomspp/pappsoexception.h>
-#include "../project.h"
-#include "../../input/identificationpwizreader.h"
-
-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)
-{
-    _engine = other._engine;
+IdentificationPwizFile::IdentificationPwizFile(const QFileInfo &ident_file)
+    : IdentificationDataSource(ident_file.absoluteFilePath()),
+      _ident_file(ident_file) {
+  //_engine = IdentificationEngine::XTandem;
+  _engine = IdentificationEngine::peptider;
 }
 
-IdentificationPwizFile::~IdentificationPwizFile()
-{
-
+IdentificationPwizFile::IdentificationPwizFile(
+    const IdentificationPwizFile &other)
+    : IdentificationDataSource(other), _ident_file(other._ident_file) {
+  _engine = other._engine;
 }
 
-bool IdentificationPwizFile::operator==(const IdentificationPwizFile& other) const
-{
+IdentificationPwizFile::~IdentificationPwizFile() {}
 
-}
+bool IdentificationPwizFile::
+operator==(const IdentificationPwizFile &other) const {}
 
-pappso::SpectrumSp IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const {
-    pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
-    return spectrum_sp;
+pappso::SpectrumSp
+IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const {
+  pappso::SpectrumSp spectrum_sp =
+      IdentificationDataSource::getSpectrumSp(scan_number);
+  return spectrum_sp;
 }
 
+void IdentificationPwizFile::parseTo(Project *p_project) {
+  qDebug() << "IdentificationPwizFile::parseTo begin";
 
-void IdentificationPwizFile::parseTo(Project* p_project) {
-    qDebug() << "IdentificationPwizFile::parseTo begin";
+  IdentificationPwizReader pwiz_reader(_ident_file);
 
-    IdentificationPwizReader pwiz_reader(_ident_file);
+  MsRunSp msrun_sp =
+      p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
 
-    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
-    
-    _engine = pwiz_reader.getIdentificationEngine();
-    setMsRunSp(msrun_sp);
-    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
-    IdentificationGroup * identification_group_p = nullptr;
-    if (p_project->getProjectMode() == ProjectMode::combined) {
-        if (identification_list.size() == 0) {
-            identification_group_p = p_project->newIdentificationGroup();
-        }
-        else {
-            identification_group_p = identification_list[0];
-        }
+  _engine = pwiz_reader.getIdentificationEngine();
+  setMsRunSp(msrun_sp);
+  std::vector<IdentificationGroup *> identification_list =
+      p_project->getIdentificationGroupList();
+  IdentificationGroup *identification_group_p = nullptr;
+  if (p_project->getProjectMode() == ProjectMode::combined) {
+    if (identification_list.size() == 0) {
+      identification_group_p = p_project->newIdentificationGroup();
+    } else {
+      identification_group_p = identification_list[0];
     }
-    else {
-        for (IdentificationGroup * identification_p_flist : identification_list) {
-            if (identification_p_flist->containSample(msrun_sp.get()->getSampleName())) {
-                identification_group_p = identification_p_flist;
-                break;
-            }
-        }
-        if (identification_group_p == nullptr) {
-            identification_group_p = p_project->newIdentificationGroup();
-        }
+  } else {
+    for (IdentificationGroup *identification_p_flist : identification_list) {
+      if (identification_p_flist->containSample(
+              msrun_sp.get()->getSampleName())) {
+        identification_group_p = identification_p_flist;
+        break;
+      }
     }
-        identification_group_p->addIdentificationDataSourceP(this);
-    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()));
-    
+    if (identification_group_p == nullptr) {
+      identification_group_p = p_project->newIdentificationGroup();
+    }
+  }
+  identification_group_p->addIdentificationDataSourceP(this);
+  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()));
 }

src/gui/xic_view/xicworkerthread.cpp

@@ -45,23 +45,19 @@ void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list
 
         if (p_msrun.get()->findMsRunFile()) {
             pappso::MsRunId msrun_id = * (p_msrun.get());
-            qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << msrun_id.getFilename() << " " << msrun_id.getXmlId();
+            qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << msrun_id.getFilename();
             auto it = std::find_if(_extractor_list.begin(), _extractor_list.end(), [msrun_id](const pappso::MsRunXicExtractorSp & extractor_sp) {
-                qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << extractor_sp.get()->getMsRunId().getXmlId();
                 return extractor_sp.get()->getMsRunId().getXmlId() == msrun_id.getXmlId();
             });
 
             pappso::MsRunXicExtractorSp extractor;
             if (it == _extractor_list.end()) {
-                qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " NOT FOUND " << msrun_id.getXmlId() << " " << _extractor_list.size();
 
                 pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
                 extractor =  pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorDiskBufferSp(msrun_id);
-               qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " NOT FOUND " << extractor.get()->getMsRunId().getXmlId();         _extractor_list.push_back(extractor);
-               qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " NOT FOUND " << _extractor_list.size();
+                _extractor_list.push_back(extractor);
             }
             else {
-                qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " FOUND " << msrun_id.getXmlId();
                 extractor = *it;
             }
             qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;