From 2b1c074a268fabcf86b6a2464ada822e316e303c Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 25 Jan 2019 16:25:05 +0100
Subject: [PATCH] new masschroqfile parameters structure to handle mcq file
parameters
---
src/CMakeLists.txt | 1 +
.../exportmasschroqdialog.cpp | 44 +++++++++++
.../exportmasschroqdialog.h | 13 ++--
.../masschroqfileparameters.cpp | 78 +++++++++++++++++++
.../masschroqfileparameters.h | 50 ++++++++++++
src/gui/mainwindow.cpp | 26 +++----
src/gui/mainwindow.h | 2 +-
src/gui/workerthread.cpp | 4 +-
src/gui/workerthread.h | 3 +-
src/main.cpp | 1 +
src/output/masschroqml.cpp | 54 +++++++++----
src/output/masschroqml.h | 5 +-
src/utils/types.h | 10 +++
13 files changed, 253 insertions(+), 38 deletions(-)
create mode 100644 src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
create mode 100644 src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 681bbd3e0..963b3c076 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -174,6 +174,7 @@ SET(XTPCPP_SRCS
./gui/edit_modifications/editmodifications.cpp
./gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
./gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+ ./gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
./gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
./gui/load_results_dialog/loadresultsdialog.cpp
./gui/mainwindow.cpp
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index 1d9d24108..f5172e1f0 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -57,3 +57,47 @@ ExportMasschroqDialog::~ExportMasschroqDialog()
{
delete ui;
}
+
+void
+ExportMasschroqDialog::setMasschroqFileParameters(
+ const MasschroqFileParameters ¶ms)
+{
+ ui->outputFileEdit->setText(params.result_file_name);
+ ui->outputFileFormatComboBox->setCurrentText("ODS");
+ if(params.result_file_format == TableFileFormat::tsv)
+ {
+ ui->outputFileFormatComboBox->setCurrentText("TSV");
+ }
+
+ ui->comparFileGroupBox->setChecked(params.export_compar_file);
+
+ ui->comparFileEdit->setText(params.compar_file_name);
+ ui->comparFileFormatComboBox->setCurrentText("ODS");
+ if(params.compar_file_format == TableFileFormat::tsv)
+ {
+ ui->comparFileFormatComboBox->setCurrentText("TSV");
+ }
+}
+
+
+MasschroqFileParameters
+ExportMasschroqDialog::getMasschroqFileParameters() const
+{
+ MasschroqFileParameters params;
+
+ params.result_file_name = ui->outputFileEdit->text();
+ params.result_file_format = TableFileFormat::ods;
+ if(ui->outputFileFormatComboBox->currentText() == "TSV")
+ {
+ params.result_file_format = TableFileFormat::tsv;
+ }
+
+ params.export_compar_file = ui->comparFileGroupBox->isChecked();
+ params.compar_file_name = ui->comparFileEdit->text();
+ params.compar_file_format = TableFileFormat::ods;
+ if(ui->comparFileFormatComboBox->currentText() == "TSV")
+ {
+ params.compar_file_format = TableFileFormat::tsv;
+ }
+ return params;
+}
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
index 79f4b4625..cc5ef264c 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
@@ -31,25 +31,28 @@
#pragma once
#include <QDialog>
-
+#include "masschroqfileparameters.h"
namespace Ui
{
- class ExportMasschroqDialog;
+class ExportMasschroqDialog;
}
class ExportMasschroqDialog : public QDialog
{
Q_OBJECT
+ private:
+ Ui::ExportMasschroqDialog *ui;
+
public:
explicit ExportMasschroqDialog(QWidget *parent);
~ExportMasschroqDialog();
+ void setMasschroqFileParameters(const MasschroqFileParameters ¶ms);
+ MasschroqFileParameters getMasschroqFileParameters() const;
+
public slots:
signals:
-
- private:
- Ui::ExportMasschroqDialog *ui;
};
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
new file mode 100644
index 000000000..bdd715819
--- /dev/null
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
@@ -0,0 +1,78 @@
+/**
+ * \file gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
+ * \date 25/01/2019
+ * \author Olivier Langella
+ * \brief all needed informations to write a MassChroqML file
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2019 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 "masschroqfileparameters.h"
+#include <QSettings>
+
+void
+MasschroqFileParameters::save() const
+{
+ QSettings settings;
+ settings.setValue("export_masschroqml/result_file_name",
+ QString("%1").arg(result_file_name));
+ settings.setValue("export_masschroqml/result_file_format",
+ (std::uint8_t)result_file_format);
+
+
+ settings.setValue("export_masschroqml/export_compar_file",
+ QString("%1").arg(export_compar_file));
+ settings.setValue("export_masschroqml/compar_file_name",
+ QString("%1").arg(compar_file_name));
+ settings.setValue("export_masschroqml/compar_file_format",
+ (std::uint8_t)compar_file_format);
+}
+void
+MasschroqFileParameters::load()
+{
+ QSettings settings;
+ result_file_name =
+ settings.value("export_masschroqml/result_file_name", QString("results"))
+ .toString();
+ result_file_format =
+ (TableFileFormat)settings
+ .value("export_masschroqml/result_file_format",
+ QString("%1").arg((std::uint8_t)TableFileFormat::ods))
+ .toUInt();
+
+
+ export_compar_file =
+ settings
+ .value("export_masschroqml/compar_file_name", QString("%1").arg(true))
+ .toBool();
+ compar_file_name =
+ settings
+ .value("export_masschroqml/compar_file_name", QString("compar_results"))
+ .toString();
+ compar_file_format =
+ (TableFileFormat)settings
+ .value("export_masschroqml/compar_file_format",
+ QString("%1").arg((std::uint8_t)TableFileFormat::ods))
+ .toUInt();
+}
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
new file mode 100644
index 000000000..ac115eabe
--- /dev/null
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
@@ -0,0 +1,50 @@
+/**
+ * \file gui/export/export_masschroq_dialog/masschroqfileparameters.h
+ * \date 25/01/2019
+ * \author Olivier Langella
+ * \brief all needed informations to write a MassChroqML file
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2019 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
+ ******************************************************************************/
+
+#pragma once
+
+#include "../../../utils/types.h"
+#include <QString>
+
+struct MasschroqFileParameters
+{
+ void save() const;
+ void load();
+
+ /** @brief quantification result output file name*/
+ QString result_file_name;
+
+ /** @brief quantification result output file type*/
+ TableFileFormat result_file_format = TableFileFormat::ods;
+
+ bool export_compar_file = false;
+ QString compar_file_name;
+ TableFileFormat compar_file_format = TableFileFormat::ods;
+};
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 8e38874ea..141abd8dd 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -35,6 +35,7 @@
#include "../utils/utils.h"
#include "workerthread.h"
#include "output/xpip.h"
+#include "export/export_masschroq_dialog/masschroqfileparameters.h"
MainWindow::MainWindow(QWidget *parent) : QMainWindow(parent), ui(new Ui::Main)
{
@@ -118,6 +119,10 @@ MainWindow::~MainWindow()
delete _p_load_results_dialog;
delete _p_export_spreadsheet_dialog;
delete _p_waiting_message_dialog;
+ if(_p_export_masschroq_dialog != nullptr)
+ {
+ delete _p_export_masschroq_dialog;
+ }
qDebug() << "MainWindow::~MainWindow end";
}
@@ -574,6 +579,7 @@ MainWindow::doActionMassChroQ()
try
{
+ _project_sp.get()->checkPsimodCompliance();
if(_p_export_masschroq_dialog == nullptr)
{
_p_export_masschroq_dialog = new ExportMasschroqDialog(this);
@@ -583,9 +589,11 @@ MainWindow::doActionMassChroQ()
&MainWindow::doAcceptedExportMasschroqDialog);
}
+ MasschroqFileParameters params;
+ params.load();
if(_project_sp.get() != nullptr)
{
- //_p_export_masschroq_dialog->setProject(_project_sp.get());
+ _p_export_masschroq_dialog->setMasschroqFileParameters(params);
}
_p_export_masschroq_dialog->show();
_p_export_masschroq_dialog->raise();
@@ -595,17 +603,6 @@ MainWindow::doActionMassChroQ()
{
viewError(tr("Error doActionMassChroQ :\n%1").arg(error.qwhat()));
}
- try
- {
- _project_sp.get()->checkPsimodCompliance();
-
- // emit operateXpipFile(filename);
- }
- catch(pappso::PappsoException &error)
- {
- viewError(
- tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
- }
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
@@ -617,6 +614,9 @@ MainWindow::doAcceptedExportMasschroqDialog()
try
{
+ MasschroqFileParameters params =
+ _p_export_masschroq_dialog->getMasschroqFileParameters();
+ params.save();
QSettings settings;
QString default_location = settings.value("path/mcqfile", "").toString();
@@ -635,7 +635,7 @@ MainWindow::doAcceptedExportMasschroqDialog()
showWaitingMessage(
tr("Writing %1 MassChroqML file").arg(QFileInfo(filename).fileName()));
- emit operateWritingMassChroqFile(filename, _project_sp);
+ emit operateWritingMassChroqFile(filename, _project_sp, params);
}
catch(pappso::PappsoException &error)
{
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index f3cc9cf84..c93a4cc32 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -108,7 +108,7 @@ class MainWindow : public QMainWindow
void operateWritingXpipFile(QString filename, ProjectSp project_sp);
void
operateWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
- void operateWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void operateWritingMassChroqFile(QString filename, ProjectSp project_sp, MasschroqFileParameters params);
void operateWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void operateWritingProticFile(QString filename, ProjectSp project_sp);
void operateWritingMcqrSpectralCountFile(QString filename,
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index add639e0d..be10ce490 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -547,7 +547,7 @@ WorkerThread::doWritingOdsFile(QString filename,
void
-WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp)
+WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp, MasschroqFileParameters params)
{
try
@@ -555,7 +555,7 @@ WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp)
emit loadingMessage(tr("writing MassChroqML file, please wait"));
project_sp.get()->checkPsimodCompliance();
- MassChroQml output(filename);
+ MassChroQml output(filename, params);
output.write(project_sp);
output.close();
emit operationFinished();
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 6bb87eaec..686485d74 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -37,6 +37,7 @@
#include "../core/project.h"
#include "../utils/workmonitor.h"
#include "../core/tandem_run/tandemrunbatch.h"
+#include "../gui/export/export_masschroq_dialog/masschroqfileparameters.h"
class MainWindow;
class ProjectWindow;
@@ -60,7 +61,7 @@ class WorkerThread : public QObject
QStringList file_list);
void doWritingXpipFile(QString filename, ProjectSp project_sp);
void doWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
- void doWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void doWritingMassChroqFile(QString filename, ProjectSp project_sp, MasschroqFileParameters params);
void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void doWritingProticFile(QString filename, ProjectSp project_sp);
void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
diff --git a/src/main.cpp b/src/main.cpp
index 8cf6312fc..46c12fc9b 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -49,6 +49,7 @@ main(int argc, char *argv[])
qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
"std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
qRegisterMetaType<ExportFastaType>("ExportFastaType");
+ qRegisterMetaType<MasschroqFileParameters>("MasschroqFileParameters");
try
{
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 5c7fa74c5..bf70e81c5 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -66,7 +66,9 @@ struct McqPsimod
QString accession;
};
-MassChroQml::MassChroQml(const QString &out_filename)
+MassChroQml::MassChroQml(const QString &out_filename,
+ const MasschroqFileParameters ¶ms)
+ : m_params(params)
{
//_p_digestion_pipeline = p_digestion_pipeline;
@@ -186,8 +188,15 @@ MassChroQml::writeQuantificationResults()
//<quantification_result output_file="result1"
// format="tsv" />
_output_stream->writeStartElement("quantification_result");
- _output_stream->writeAttribute("output_file", "result1");
- _output_stream->writeAttribute("format", "tsv");
+ _output_stream->writeAttribute("output_file", m_params.result_file_name);
+ if(m_params.result_file_format == TableFileFormat::ods)
+ {
+ _output_stream->writeAttribute("format", "ods");
+ }
+ else
+ {
+ _output_stream->writeAttribute("format", "tsv");
+ }
_output_stream->writeEndElement();
//<quantification_result output_file="result2"
// format="ods" />
@@ -196,10 +205,20 @@ MassChroQml::writeQuantificationResults()
//<compar_result output_file="compar"
// format="ods" />
- _output_stream->writeStartElement("compar_result");
- _output_stream->writeAttribute("output_file", "result1");
- _output_stream->writeAttribute("format", "ods");
- _output_stream->writeEndElement();
+ if(m_params.export_compar_file)
+ {
+ _output_stream->writeStartElement("compar_result");
+ _output_stream->writeAttribute("output_file", m_params.compar_file_name);
+ if(m_params.compar_file_format == TableFileFormat::ods)
+ {
+ _output_stream->writeAttribute("format", "ods");
+ }
+ else
+ {
+ _output_stream->writeAttribute("format", "tsv");
+ }
+ _output_stream->writeEndElement();
+ }
//</quantification_results>
_output_stream->writeEndElement();
}
@@ -212,8 +231,9 @@ MassChroQml::writeQuantificationTraces()
_output_stream->writeStartElement("quantification_traces");
//<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces"
// format="tsv" />
- _output_stream->writeComment("<peptide_traces peptide_ids=\"pep0 pep1\" "
- "output_dir=\"pep_traces\" format=\"tsv\" />");
+ _output_stream->writeComment(
+ "<peptide_traces peptide_ids=\"pep0 pep1\" "
+ "output_dir=\"pep_traces\" format=\"tsv\" />");
/*
<all_xics_traces output_dir="all_xics_traces" format="tsv" />
<mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces"
@@ -258,8 +278,9 @@ MassChroQml::writeQuantify()
}
_output_stream->writeEndElement();
- _output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 "
- "381.577 569.771 575.256</mz_list>");
+ _output_stream->writeComment(
+ "<mz_list>732.317 449.754 552.234 464.251 "
+ "381.577 569.771 575.256</mz_list>");
_output_stream->writeComment(
"<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt "
"mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
@@ -356,8 +377,9 @@ MassChroQml::writeAlignments()
// corrections -->
_output_stream->writeStartElement("ms2");
- _output_stream->writeComment("write_time_values_output_dir=\"directory\" to "
- "write retention time corrections");
+ _output_stream->writeComment(
+ "write_time_values_output_dir=\"directory\" to "
+ "write retention time corrections");
//<ms2_tendency_halfwindow>10</ms2_tendency_halfwindow>
_output_stream->writeStartElement("ms2_tendency_halfwindow");
_output_stream->writeCharacters("10");
@@ -455,7 +477,8 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
}
// sort list
- std::sort(mcq_peptide_list.begin(), mcq_peptide_list.end(),
+ std::sort(mcq_peptide_list.begin(),
+ mcq_peptide_list.end(),
[](const McqPeptide &first, const McqPeptide &second) {
return (first.id < second.id);
});
@@ -541,7 +564,8 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
}
//<observed_in data="samp0" scan="655" z="2" />
- std::sort(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end(),
+ std::sort(mcq_peptide.observed_in.begin(),
+ mcq_peptide.observed_in.end(),
[](const McqObserved &first, const McqObserved &second) {
return std::tie(first.charge, first.scan, first.msrun) <
std::tie(second.charge, second.scan, second.msrun);
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index bfe322690..1dffd898d 100644
--- a/src/output/masschroqml.h
+++ b/src/output/masschroqml.h
@@ -38,11 +38,13 @@
#include "../core/project.h"
#include "../grouping/groupinggroup.h"
#include "../gui/xic_view/xic_widgets/zivywidget.h"
+#include "../gui/export/export_masschroq_dialog/masschroqfileparameters.h"
class MassChroQml
{
public:
- MassChroQml(const QString &out_filename);
+ MassChroQml(const QString &out_filename,
+ const MasschroqFileParameters ¶ms);
~MassChroQml();
void write(ProjectSp sp_project);
@@ -61,6 +63,7 @@ class MassChroQml
void writeQuantify();
private:
+ const MasschroqFileParameters &m_params;
QFile *_output_file;
QXmlStreamWriter *_output_stream;
ProjectSp _sp_project;
diff --git a/src/utils/types.h b/src/utils/types.h
index 03d3cb6d6..6615853b2 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -180,4 +180,14 @@ enum class ExportFastaType : std::int8_t
};
+/** \def TableFileFormat file format of tables
+ *
+ */
+enum class TableFileFormat : std::int8_t
+{
+ ods = 1, ///< Open Document Spreadsheet
+ tsv = 2, ///< tabulated separated values
+};
+
+
#endif /* _TYPES_H_ */
--
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