From 89e28cbf46242a64dfa7e75c9ed1632a899a7667 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 15 Jan 2019 15:04:14 +0100
Subject: [PATCH] separate fasta file output in worker thread with dedicated
output object
---
src/CMakeLists.txt | 1 +
src/gui/mainwindow.cpp | 41 +++----------------
src/gui/mainwindow.h | 3 ++
src/gui/workerthread.cpp | 34 ++++++++++++++++
src/gui/workerthread.h | 3 ++
src/main.cpp | 1 +
src/output/exportfastafile.cpp | 74 ++++++++++++++++++++++++++++++++++
src/output/exportfastafile.h | 43 ++++++++++++++++++++
src/utils/types.h | 12 ++++++
9 files changed, 177 insertions(+), 35 deletions(-)
create mode 100644 src/output/exportfastafile.cpp
create mode 100644 src/output/exportfastafile.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 798433f06..65b17ed76 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -146,6 +146,7 @@ SET(CPP_FILES
output/ods/samplesheet.cpp
output/ods/simplesheet.cpp
output/ods/spectrasheet.cpp
+ output/exportfastafile.cpp
output/masschroqml.cpp
output/masschroqprm.cpp
output/mcqrspectralcount.cpp
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 938cfcd81..492888c67 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -32,7 +32,6 @@
#include "ui_main.h"
#include <pappsomspp/pappsoexception.h>
-#include <pappsomspp/fasta/fastaoutputstream.h>
#include "../utils/utils.h"
#include "workerthread.h"
#include "output/xpip.h"
@@ -503,6 +502,9 @@ MainWindow::doActionFasta()
{
try
{
+ // export all grouped proteins
+ // or only one protein by sub grouped
+ // or only one protein by group
QSettings settings;
QString default_location =
@@ -521,41 +523,10 @@ MainWindow::doActionFasta()
settings.setValue("path/fastafile", QFileInfo(filename).absolutePath());
+ showWaitingMessage(
+ tr("Writing %1 FASTA file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingFastaFile(filename, _project_sp, ExportFastaType::all);
- QFile outFile;
- outFile.setFileName(filename);
- outFile.open(QIODevice::WriteOnly);
- QTextStream *p_outputStream = new QTextStream(&outFile);
-
-
- pappso::FastaOutputStream fasta_output(*p_outputStream);
-
- for(IdentificationGroup *identification :
- _project_sp.get()->getIdentificationGroupList())
- {
- for(ProteinMatch *protein_match :
- identification->getProteinMatchList())
- {
- if(protein_match->getValidationState() >=
- ValidationState::grouped)
- {
- pappso::Protein protein(
- QString("%1 %2")
- .arg(
- protein_match->getProteinXtpSp().get()->getAccession())
- .arg(protein_match->getProteinXtpSp()
- .get()
- ->getDescription()),
- protein_match->getProteinXtpSp().get()->getSequence());
- fasta_output.writeProtein(protein);
- }
- }
- }
-
- p_outputStream->flush();
- delete p_outputStream;
- outFile.close();
- // emit operateXpipFile(filename);
}
catch(pappso::PappsoException &error)
{
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 21762189b..4acaa6c1c 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -109,6 +109,9 @@ class MainWindow : public QMainWindow
void operateWritingProticFile(QString filename, ProjectSp project_sp);
void operateWritingMcqrSpectralCountFile(QString filename,
ProjectSp project_sp);
+ void operateWritingFastaFile(QString filename,
+ ProjectSp project_sp,
+ ExportFastaType type);
void operateGrouping(ProjectSp project_sp);
void operateRunningXtandem(TandemRunBatch tandem_run_batch);
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 5c0d3dd46..add639e0d 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -34,6 +34,7 @@
#include <odsstream/odsexception.h>
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
+#include "../output/exportfastafile.h"
#include "../output/masschroqml.h"
#include "../output/masschroqprm.h"
#include "../output/proticdbml.h"
@@ -153,6 +154,11 @@ WorkerThread::WorkerThread(MainWindow *p_main_window)
&WorkerThread::operationFinished,
p_main_window,
&MainWindow::doOperationFinished);
+ // FASTA file write
+ connect(p_main_window,
+ &MainWindow::operateWritingFastaFile,
+ this,
+ &WorkerThread::doWritingFastaFile);
#else
// Qt4 code
@@ -730,3 +736,31 @@ WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
+
+
+void
+WorkerThread::doWritingFastaFile(QString filename,
+ ProjectSp project_sp,
+ ExportFastaType type)
+{
+
+ try
+ {
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ emit loadingMessage(tr("writing FASTA file, please wait"));
+
+
+ ExportFastaFile output(filename, type);
+ output.write(project_sp);
+ output.close();
+
+ // emit operateXpipFile(filename);
+ emit operationFinished();
+ }
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing FASTA file :\n%1").arg(error.qwhat()));
+ }
+}
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 309a35dc0..6bb87eaec 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -64,6 +64,9 @@ class WorkerThread : public QObject
void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void doWritingProticFile(QString filename, ProjectSp project_sp);
void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
+ void doWritingFastaFile(QString filename,
+ ProjectSp project_sp,
+ ExportFastaType type);
void doGrouping(ProjectSp project_sp);
void doGroupingOnIdentification(IdentificationGroup *p_identification_group,
GroupingType grouping_type);
diff --git a/src/main.cpp b/src/main.cpp
index c42ce2257..8cf6312fc 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -48,6 +48,7 @@ main(int argc, char *argv[])
qRegisterMetaType<MsRunSp>("MsRunSp");
qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
"std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
+ qRegisterMetaType<ExportFastaType>("ExportFastaType");
try
{
diff --git a/src/output/exportfastafile.cpp b/src/output/exportfastafile.cpp
new file mode 100644
index 000000000..c8cbf49e1
--- /dev/null
+++ b/src/output/exportfastafile.cpp
@@ -0,0 +1,74 @@
+/**
+ * \file output/exportfastafile.cpp
+ * \date 15/01/2019
+ * \author Olivier Langella
+ * \brief FASTA file writer
+ */
+
+/*******************************************************************************
+ * 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/>.
+ *
+ ******************************************************************************/
+
+#include "exportfastafile.h"
+#include <pappsomspp/fasta/fastaoutputstream.h>
+
+ExportFastaFile::ExportFastaFile(QString filename, ExportFastaType type)
+{
+ p_outputFastaFile = new QFile(filename);
+}
+
+void
+ExportFastaFile::write(ProjectSp project_sp)
+{
+
+ p_outputFastaFile->open(QIODevice::WriteOnly);
+ QTextStream *p_outputStream = new QTextStream(p_outputFastaFile);
+
+
+ pappso::FastaOutputStream fasta_output(*p_outputStream);
+
+ for(IdentificationGroup *identification :
+ project_sp.get()->getIdentificationGroupList())
+ {
+ for(ProteinMatch *protein_match : identification->getProteinMatchList())
+ {
+ if(protein_match->getValidationState() >= ValidationState::grouped)
+ {
+ pappso::Protein protein(
+ QString("%1 %2")
+ .arg(protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(
+ protein_match->getProteinXtpSp().get()->getDescription()),
+ protein_match->getProteinXtpSp().get()->getSequence());
+ fasta_output.writeProtein(protein);
+ }
+ }
+ }
+
+ p_outputStream->flush();
+ delete p_outputStream;
+ p_outputFastaFile->close();
+}
+
+void
+ExportFastaFile::close()
+{
+ delete p_outputFastaFile;
+ p_outputFastaFile = nullptr;
+}
diff --git a/src/output/exportfastafile.h b/src/output/exportfastafile.h
new file mode 100644
index 000000000..c681f63d0
--- /dev/null
+++ b/src/output/exportfastafile.h
@@ -0,0 +1,43 @@
+/**
+ * \file output/exportfastafile.h
+ * \date 15/01/2019
+ * \author Olivier Langella
+ * \brief FASTA file writer
+ */
+
+/*******************************************************************************
+ * 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/>.
+ *
+ ******************************************************************************/
+
+#pragma once
+
+#include <QString>
+#include "../utils/types.h"
+#include "../core/project.h"
+
+class ExportFastaFile
+{
+ private:
+ QFile *p_outputFastaFile = nullptr;
+
+ public:
+ ExportFastaFile(QString filename, ExportFastaType type);
+ void write(ProjectSp project_sp);
+ void close();
+};
diff --git a/src/utils/types.h b/src/utils/types.h
index 91f06ca30..03d3cb6d6 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -168,4 +168,16 @@ enum class ValidationState : std::int8_t
};
+/** \def export fasta files
+ *
+ */
+
+enum class ExportFastaType : std::int8_t
+{
+ all = 0, ///< all grouped proteins
+ oneBySubgroup = 1, ///< export only one by subgroup
+ oneByGroup = 2, ///< export only one by group
+};
+
+
#endif /* _TYPES_H_ */
--
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