From 64644804d99a36400ad1490cd84da9d32d5837f8 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 2 Sep 2017 16:29:29 +0200
Subject: [PATCH] new object TandemRunBatch to handle all informations needed
to run X\!Tandem
---
src/core/tandem_run/tandemrunbatch.cpp | 30 +++++++++++++
src/core/tandem_run/tandemrunbatch.h | 43 +++++++++++++++++++
.../ptmsequencedelegate.cpp | 2 +-
src/gui/tandem_run_dialog/tandemrundialog.cpp | 12 ++++++
src/gui/tandem_run_dialog/tandemrundialog.h | 3 ++
5 files changed, 89 insertions(+), 1 deletion(-)
create mode 100644 src/core/tandem_run/tandemrunbatch.cpp
create mode 100644 src/core/tandem_run/tandemrunbatch.h
diff --git a/src/core/tandem_run/tandemrunbatch.cpp b/src/core/tandem_run/tandemrunbatch.cpp
new file mode 100644
index 00000000..c617687b
--- /dev/null
+++ b/src/core/tandem_run/tandemrunbatch.cpp
@@ -0,0 +1,30 @@
+/**
+ * \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"
diff --git a/src/core/tandem_run/tandemrunbatch.h b/src/core/tandem_run/tandemrunbatch.h
new file mode 100644
index 00000000..dc80f51a
--- /dev/null
+++ b/src/core/tandem_run/tandemrunbatch.h
@@ -0,0 +1,43 @@
+/**
+ * \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
diff --git a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp
index d3832ff9..57a2c504 100644
--- a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp
+++ b/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());
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index c00b0d52..664686ed 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/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;
+}
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.h b/src/gui/tandem_run_dialog/tandemrundialog.h
index 199854b2..a45df02a 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.h
+++ b/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();
--
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