new object TandemRunBatch to handle all informations needed to run X\!Tandem

src/core/tandem_run/tandemrunbatch.cpp

+/**
+ * \file /core/tandem_run/tandem_run_batch.cpp
+ * \date 2/9/2017
+ * \author Olivier Langella
+ * \brief all data needed to run a Tandem batch
+ */
+
+/*******************************************************************************
+* 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 "tandemrunbatch.h"

src/core/tandem_run/tandemrunbatch.h

+/**
+ * \file /core/tandem_run/tandem_run_batch.h
+ * \date 2/9/2017
+ * \author Olivier Langella
+ * \brief all data needed to run a Tandem batch
+ */
+
+/*******************************************************************************
+* 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 TANDEMRUNBATCH_H
+#define TANDEMRUNBATCH_H
+
+#include <QStringList>
+struct TandemRunBatch
+{
+    QString _tandem_bin_path;
+    QStringList _mz_file_list;
+    QString _preset_file;
+    QStringList _fasta_file_list;
+    QString _output_directory;
+};
+
+#endif // TANDEMRUNBATCH_H

src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp

@@ -40,7 +40,7 @@ void PtmSequenceDelegate::paint(QPainter *painter, const QStyleOptionViewItem &o
                          const QModelIndex &index) const
 {
     if (index.data().canConvert<PtmSampleScan *>()) {
-        PtmSampleScan * p_ptm_sample_scan = qvariant_cast<PtmSampleScan *>(index.data());
+        PtmSampleScan * p_ptm_sample_scan = index.data().value<PtmSampleScan *>();
 
        // if (option.state & QStyle::State_Selected)
         //    painter->fillRect(option.rect, option.palette.highlight());

src/gui/tandem_run_dialog/tandemrundialog.cpp

@@ -35,6 +35,7 @@
 #include <QMessageBox>
 #include <pappsomspp/pappsoexception.h>
 
+Q_DECLARE_METATYPE(QFileInfo)
 
 TandemRunDialog::TandemRunDialog(QWidget * parent):
     QDialog(parent),
@@ -172,3 +173,14 @@ void TandemRunDialog::selectMzFiles() {
         //                  tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
     }
 }
+
+TandemRunBatch TandemRunDialog::getTandemRunBatch() const {
+    TandemRunBatch tandem_run_batch;
+    tandem_run_batch._tandem_bin_path = ui->tandem_bin_label->text();
+    tandem_run_batch._mz_file_list = _p_mz_file_list->stringList();
+    tandem_run_batch._fasta_file_list = _p_fasta_file_list->stringList();
+    //tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
+    tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
+    tandem_run_batch._output_directory = ui->output_directory_label->text();
+    return tandem_run_batch;
+}

src/gui/tandem_run_dialog/tandemrundialog.h

@@ -32,6 +32,8 @@
 
 #include <QDialog>
 #include <QStringListModel>
+#include "../../core/tandem_run/tandemrunbatch.h"
+
 namespace Ui {
 class TandemRunDialog;
 }
@@ -45,6 +47,7 @@ public:
     explicit TandemRunDialog(QWidget * parent);
     ~TandemRunDialog();
 
+    TandemRunBatch getTandemRunBatch() const;
     void reset();
 public slots:
     void selectFastaFiles();