diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 2367b510127f1a7954ee1f956715eb8cf7308546..e91c08516e6aa48c2ae4deea7de8179ac099497e 100644
--- a/src/CMakeLists.txt
+++ b/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
diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index 556212006967ea22e288770057f161d25ee7dd6e..2b79687d9005eb4b1a1b3fa9ea956fdc4f9e597f 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/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()));
+
}
diff --git a/src/core/identification_sources/identificationpwizfile.h b/src/core/identification_sources/identificationpwizfile.h
index 3e15f074f369e55cb1ff419ad8911d544dea3aa8..01da96a8c9f8369255d34688982f161a88f0b421 100644
--- a/src/core/identification_sources/identificationpwizfile.h
+++ b/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
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 2dd6449edae4f1c1feb100483387b6253de4c686..52adda2e121a0dcbbe881692e32efe6f6239b504 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/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;
+ }
diff --git a/src/input/identificationpwizreader.h b/src/input/identificationpwizreader.h
index a658dd273b4be10f19d404b16dcb05ad30478e6d..66317aaa11e774013aa149ec5052d6990c3f6d43 100644
--- a/src/input/identificationpwizreader.h
+++ b/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