new files to read pwiz identifications

src/core/identification_sources/identificationpwizfile.cpp

+/**
+ * \filed core/identification_sources/identificationpwizfile.cpp
+ * \date 17/6/2017
+ * \author Olivier Langella
+ * \brief read identification files with proteowizard 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 "identificationpwizfile.h"
+#include <pappsomspp/pappsoexception.h>
+#include "../project.h"
+#include "../../input/xtandemsaxhandler.h"
+
+IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & xtandem_file) : IdentificationDataSource(xtandem_file.absoluteFilePath()), _xtandem_file(xtandem_file)
+{
+    _engine = IdentificationEngine::XTandem;
+}
+
+IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_xtandem_file (other._xtandem_file)
+{
+    _engine = IdentificationEngine::XTandem;
+}
+
+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;
+}
+
+
+void IdentificationPwizFile::parseTo(Project* p_project) {
+    qDebug() << "Project::readXpipFile begin";
+
+    qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
+
+    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
+    setMsRunSp(msrun_sp);
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    IdentificationGroup * identification_group_p = nullptr;
+    if (p_project->isCombineMode()) {
+        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->contains(msrun_sp.get())) {
+                identification_group_p = identification_p_flist;
+                break;
+            }
+        }
+        if (identification_group_p == nullptr) {
+            identification_group_p = p_project->newIdentificationGroup();
+        }
+    }
+    
+    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()));
+    }
+
+}

src/core/identification_sources/identificationpwizfile.h

+/**
+ * \filed core/identification_sources/identificationpwizfile.h
+ * \date 17/6/2017
+ * \author Olivier Langella
+ * \brief read identification files with proteowizard 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
+******************************************************************************/
+
+#ifndef IDENTIFICATIONPWIZFILE_H
+#define IDENTIFICATIONPWIZFILE_H
+
+#include "identificationdatasource.h"
+#include <QFileInfo>
+
+class IdentificationPwizFile: public IdentificationDataSource
+{
+public:
+    IdentificationPwizFile(const QFileInfo & xtandem_file);
+    IdentificationPwizFile(const IdentificationPwizFile& other);
+    ~IdentificationPwizFile();
+    bool operator==(const IdentificationPwizFile& other) const;
+
+    virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
+    virtual void parseTo(Project* p_project) override;
+    
+private:
+    const QFileInfo _xtandem_file;
+};
+
+#endif // IDENTIFICATIONPWIZFILE_H

src/input/identificationpwizreader.cpp

+/**
+ * \file input/identificationpwizreader.cpp
+ * \date 17/6/2017
+ * \author Olivier Langella
+ * \brief read identification files using pwiz library
+ */
+
+#include "identificationpwizreader.h"

src/input/identificationpwizreader.h

+/**
+ * \file input/identificationpwizreader.h
+ * \date 17/6/2017
+ * \author Olivier Langella
+ * \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
+******************************************************************************/
+
+#ifndef IDENTIFICATIONPWIZREADER_H
+#define IDENTIFICATIONPWIZREADER_H
+
+class IdentificationPwizReader
+{
+};
+
+#endif // IDENTIFICATIONPWIZREADER_H