first pwiz reader, not working yet

src/CMakeLists.txt

@@ -53,6 +53,7 @@ SET(CPP_FILES
   core/automaticfilterparameters.cpp
   core/identificationgroup.cpp
   core/identification_sources/identificationdatasource.cpp
+  core/identification_sources/identificationpwizfile.cpp
   core/identification_sources/identificationxtandemfile.cpp
   core/labeling/label.cpp
   core/labeling/labelingmethod.cpp
@@ -73,6 +74,7 @@ SET(CPP_FILES
   grouping/ptm/ptmislandgroup.cpp
   grouping/ptm/ptmislandsubgroup.cpp
   gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
+  input/identificationpwizreader.cpp
   input/xpipsaxhandler.cpp
   input/xtandemsaxhandler.cpp
   output/masschroqml.cpp

src/core/identification_sources/identificationpwizfile.cpp

@@ -31,16 +31,16 @@
 #include "identificationpwizfile.h"
 #include <pappsomspp/pappsoexception.h>
 #include "../project.h"
-#include "../../input/xtandemsaxhandler.h"
+#include "../../input/identificationpwizreader.h"
 
-IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & xtandem_file) : IdentificationDataSource(xtandem_file.absoluteFilePath()), _xtandem_file(xtandem_file)
+IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & ident_file) : IdentificationDataSource(ident_file.absoluteFilePath()), _ident_file(ident_file)
 {
-    _engine = IdentificationEngine::XTandem;
+    //_engine = IdentificationEngine::XTandem;
 }
 
-IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_xtandem_file (other._xtandem_file)
+IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_ident_file (other._ident_file)
 {
-    _engine = IdentificationEngine::XTandem;
+    _engine = other._engine;
 }
 
 IdentificationPwizFile::~IdentificationPwizFile()
@@ -62,9 +62,9 @@ pappso::SpectrumSp IdentificationPwizFile::getSpectrumSp(unsigned int scan_numbe
 void IdentificationPwizFile::parseTo(Project* p_project) {
     qDebug() << "Project::readXpipFile begin";
 
-    qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
+    IdentificationPwizReader pwiz_reader(_ident_file);
 
-    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
+    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunQFileInfo().baseName());
     setMsRunSp(msrun_sp);
     std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
     IdentificationGroup * identification_group_p = nullptr;
@@ -88,28 +88,8 @@ void IdentificationPwizFile::parseTo(Project* p_project) {
         }
     }
     
-    identification_group_p->addIdentificationDataSourceP(this);
-    XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p, this);
 
-    QXmlSimpleReader simplereader;
-    simplereader.setContentHandler(parser);
-    simplereader.setErrorHandler(parser);
-
-    QFile qfile(_xtandem_file.absoluteFilePath());
-    QXmlInputSource xmlInputSource(&qfile);
-
-    if (simplereader.parse(xmlInputSource)) {
-
-        qfile.close();
-    } else {
-        qDebug() << parser->errorString();
-        // throw PappsoException(
-        //    QObject::tr("error reading tandem XML result file :\n").append(
-        //         parser->errorString()));
-
-        qfile.close();
-
-        throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
-    }
+      //  throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
+    
 
 }

src/core/identification_sources/identificationpwizfile.h

@@ -37,7 +37,7 @@
 class IdentificationPwizFile: public IdentificationDataSource
 {
 public:
-    IdentificationPwizFile(const QFileInfo & xtandem_file);
+    IdentificationPwizFile(const QFileInfo & ident_file);
     IdentificationPwizFile(const IdentificationPwizFile& other);
     ~IdentificationPwizFile();
     bool operator==(const IdentificationPwizFile& other) const;
@@ -46,7 +46,7 @@ public:
     virtual void parseTo(Project* p_project) override;
     
 private:
-    const QFileInfo _xtandem_file;
+    const QFileInfo _ident_file;
 };
 
 #endif // IDENTIFICATIONPWIZFILE_H

src/input/identificationpwizreader.cpp

@@ -5,4 +5,67 @@
  * \brief read identification files using pwiz library
  */
 
+/*******************************************************************************
+* Copyright (c) 2017 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/>.
+*
+* Contributors:
+*     Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
 #include "identificationpwizreader.h"
+
+#include <QDebug>
+#include <QSettings>
+#include <QFileInfo>
+#include <QDir>
+#include <QString>
+#include <pappsomspp/exception/exceptionnotfound.h>
+
+#include <pwiz/data/identdata/IdentData.hpp>
+#include <pwiz/data/identdata/IdentDataFile.hpp>
+#include <locale>
+
+
+pwiz::identdata::IdentDataFile * getPwizIdentDataFile(const QString & filename);
+
+
+pwiz::identdata::IdentDataFile * getPwizIdentDataFile(const QString & filename) {
+    qDebug() << "getPwizIdentDataFile opening file " << filename ;
+    std::string env;
+    env=setlocale(LC_ALL,"");
+    struct lconv * lc = localeconv ();
+    qDebug() << " env=" << env.c_str() << " lc->decimal_point " << lc->decimal_point;
+    setlocale(LC_ALL,"C");
+    //lc = localeconv ();
+    //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
+    pwiz::identdata::IdentDataFile * dataFile = new pwiz::identdata::IdentDataFile(filename.toStdString());
+
+    setlocale(LC_ALL,env.c_str());
+
+    return dataFile;
+}
+
+IdentificationPwizReader::IdentificationPwizReader(const QFileInfo & filename):_identfile(filename) {
+    
+    _pwiz_ident_data_file = getPwizIdentDataFile(filename.absoluteFilePath());
+}
+
+const QFileInfo & IdentificationPwizReader::getMsrunQFileInfo() const {
+    //qDebug() << "IdentificationPwizReader::getMsrunQFileInfo begin" <<  _pwiz_ident_data_file->analysisSampleCollection.size();
+        return _identfile;
+    }

src/input/identificationpwizreader.h

@@ -31,8 +31,21 @@
 #ifndef IDENTIFICATIONPWIZREADER_H
 #define IDENTIFICATIONPWIZREADER_H
 
+#include <QFileInfo>
+
+namespace pwiz::identdata {
+class IdentDataFile;
+}
+
 class IdentificationPwizReader
 {
+public:
+    IdentificationPwizReader(const QFileInfo & filename);
+    const QFileInfo & getMsrunQFileInfo() const;
+    
+private:
+    QFileInfo _identfile;
+    pwiz::identdata::IdentDataFile * _pwiz_ident_data_file;
 };
 
 #endif // IDENTIFICATIONPWIZREADER_H