From 608dea92f0a71b4283a9302ddd3447b15c4dc4ad Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 21 Dec 2017 10:03:07 +0100
Subject: [PATCH] export MassChroqPRM files
---
src/CMakeLists.txt | 1 +
src/gui/main.ui | 25 +++++++++++++-
src/gui/mainwindow.cpp | 28 ++++++++++++++++
src/gui/mainwindow.h | 2 ++
src/gui/workerthread.cpp | 16 +++++++++
src/gui/workerthread.h | 1 +
src/output/masschroqprm.cpp | 65 ++++++++++++++++++++-----------------
src/output/masschroqprm.h | 11 +------
8 files changed, 109 insertions(+), 40 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index d576d6d8c..78e9cbc05 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -101,6 +101,7 @@ SET(CPP_FILES
output/ods/simplesheet.cpp
output/ods/spectrasheet.cpp
output/masschroqml.cpp
+ output/masschroqprm.cpp
output/proticdbml.cpp
output/xpip.cpp
utils/fastafilestore.cpp
diff --git a/src/gui/main.ui b/src/gui/main.ui
index b7bcf9354..f3387e1bd 100644
--- a/src/gui/main.ui
+++ b/src/gui/main.ui
@@ -67,6 +67,7 @@
</property>
<addaction name="actionFasta"/>
<addaction name="actionMassChroQ"/>
+ <addaction name="actionMassChroqPRM"/>
<addaction name="actionSpreadsheet"/>
<addaction name="actionProticDb"/>
<addaction name="action_spectral_counting_mcq"/>
@@ -163,7 +164,12 @@
</action>
<action name="action_save_project">
<property name="text">
- <string>Save project</string>
+ <string>&Save project</string>
+ </property>
+ </action>
+ <action name="actionMassChroqPRM">
+ <property name="text">
+ <string>MassChroqPRM</string>
</property>
</action>
</widget>
@@ -427,6 +433,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>actionMassChroqPRM</sender>
+ <signal>triggered()</signal>
+ <receiver>Main</receiver>
+ <slot>doActionMassChroqPRM()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>-1</x>
+ <y>-1</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>231</x>
+ <y>191</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>selectXpipFile()</slot>
@@ -442,5 +464,6 @@
<slot>doActionAbout()</slot>
<slot>doActionTandemRun()</slot>
<slot>doActionSaveProject()</slot>
+ <slot>doActionMassChroqPRM()</slot>
</slots>
</ui>
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 5b22c3743..2c511d6ef 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -464,6 +464,34 @@ void MainWindow::doActionMassChroQ() {
qDebug() << "MainWindow::doActionMassChroQ end";
}
+void MainWindow::doActionMassChroqPRM() {
+ qDebug() << "MainWindow::doActionMassChroqPRM begin";
+ try {
+ _project_sp.get()->checkPsimodCompliance();
+
+ QSettings settings;
+ QString default_location = settings.value("path/mcqprmfile", "").toString();
+
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save MassChroqPRM file"),
+ QString("%1/untitled.masschroqprm").arg(default_location),
+ tr("MassChroqPRM (*.masschroqprm)"));
+
+ if (filename.isEmpty()) {
+ return;
+ }
+
+ settings.setValue("path/mcqprmfile", QFileInfo(filename).absolutePath());
+
+ showWaitingMessage(tr("Writing %1 MassChroqPRM file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingMassChroqPrmFile(filename, _project_sp);
+ //emit operateXpipFile(filename);
+ }
+ catch (pappso::PappsoException & error) {
+ viewError(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+ }
+ qDebug() << "MainWindow::doActionMassChroqPRM end";
+}
+
void MainWindow::doActionProticDb() {
qDebug() << "MainWindow::doActionProticDb begin";
try {
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 2ee0090c1..629751d03 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -69,6 +69,7 @@ public slots:
void doActionQuit();
void doActionFasta();
void doActionMassChroQ();
+ void doActionMassChroqPRM();
void doActionProticDb();
void doActionLabelingMethods();
void doActionTandemRun();
@@ -99,6 +100,7 @@ signals:
void operateWritingXpipFile(QString filename, ProjectSp project_sp);
void operateWritingOdsFile(QString filename, ProjectSp project_sp);
void operateWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void operateWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void operateWritingProticFile(QString filename, ProjectSp project_sp);
void operateGrouping(ProjectSp project_sp);
void operateRunningXtandem(TandemRunBatch tandem_run_batch);
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 47ea9ae0d..55561bb88 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -32,6 +32,7 @@
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
#include "../output/masschroqml.h"
+#include "../output/masschroqprm.h"
#include "../output/proticdbml.h"
#include "../output/ods/odsexport.h"
#include "../output/xpip.h"
@@ -73,6 +74,7 @@ WorkerThread::WorkerThread(MainWindow * p_main_window)
connect(this, &WorkerThread::groupingFinished, p_main_window,&MainWindow::doGroupingFinished);
//masschroq write
connect(p_main_window, &MainWindow::operateWritingMassChroqFile, this,&WorkerThread::doWritingMassChroqFile);
+ connect(p_main_window, &MainWindow::operateWritingMassChroqPrmFile, this,&WorkerThread::doWritingMassChroqPrmFile);
//protic write
connect(p_main_window, &MainWindow::operateWritingProticFile, this,&WorkerThread::doWritingProticFile);
//writing ODS file :
@@ -306,6 +308,20 @@ void WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp
}
}
+void WorkerThread::doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp) {
+
+ try {
+ emit loadingMessage(tr("writing MassChroqPRM file, please wait"));
+ MassChroqPrm output(filename);
+ output.write(project_sp);
+ output.close();
+ emit operationFinished();
+ }
+ catch (pappso::PappsoException & error) {
+ emit operationFailed(tr("Error while writing MassChroqPRM file :\n%1").arg(error.qwhat()));
+ }
+}
+
void WorkerThread::doWritingProticFile(QString filename, ProjectSp project_sp) {
try {
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index dd120d7a1..35ccd0e1d 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -61,6 +61,7 @@ public slots:
void doWritingXpipFile(QString filename, ProjectSp project_sp);
void doWritingOdsFile(QString filename, ProjectSp project_sp);
void doWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void doWritingProticFile(QString filename, ProjectSp project_sp);
void doGrouping(ProjectSp project_sp);
void doGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
diff --git a/src/output/masschroqprm.cpp b/src/output/masschroqprm.cpp
index 1bde93c9c..8f5c272c9 100644
--- a/src/output/masschroqprm.cpp
+++ b/src/output/masschroqprm.cpp
@@ -29,6 +29,7 @@
#include "masschroqprm.h"
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/utils.h>
MassChroqPrm::MassChroqPrm(const QString & out_filename) {
//_p_digestion_pipeline = p_digestion_pipeline;
@@ -73,7 +74,7 @@ void MassChroqPrm::write(ProjectSp sp_project) {
//<masschroq>
_output_stream->writeStartElement("masschroqprm");
/*
- *
+ *
<parameters>
<parentIonMassTolerance>
<daltonPrecision value="1.5"/>
@@ -102,6 +103,7 @@ void MassChroqPrm::write(ProjectSp sp_project) {
}
void MassChroqPrm::writePeptides() {
+
/*
*
*
@@ -112,36 +114,42 @@ void MassChroqPrm::writePeptides() {
_output_stream->writeStartElement("peptideList");
- for (IdentificationGroup * p_ident_group : _sp_project.get()->getIdentificationGroupList()) {
- for () {
- PeptideMassSet pepMassSet = new PeptideMassSet();
-
- logger.debug("pepMassSet size : " + pepMassSet.size());
-
- logger.debug("pepMassSet numbering");
- pepMassSet.numberingGetPepMass2PeptideList(group);
-
- // iterated current pepid to write buffer peptide element
- for (PeptideMass pepMass : pepMassSet) {
- _output_stream->writeStartElement("peptide");
- _output_stream->writeAttribute("id",
- Utils.getPappsoPeptideMassId(group, pepMass));
- Peptide bestPeptide = pepMass.getBestEvaluePeptide();
- _output_stream->writeAttribute("seq", bestPeptide.getSequence());
-
- ArrayList<Modifs> arrModif = bestPeptide.get_Modifs();
- for (Modifs modif : arrModif) {
- _output_stream->writeStartElement("psimod");
- _output_stream->writeAttribute("at", "" + modif.get_posi());
-
- _output_stream->writeAttribute("acc", ""
- + modif.getPsiMod().getAccession());
- _output_stream->writeEndElement();
+ for (IdentificationDataSourceSp identification_data_source_sp :_sp_project.get()->getIdentificationDataSourceStore().getIdentificationDataSourceList()) {
+ for (const PeptideEvidenceSp & peptide_evidence_sp: identification_data_source_sp.get()->getPeptideEvidenceStore().getPeptideEvidenceList()) {
+ const pappso::GrpPeptide * p_grp_peptide =peptide_evidence_sp.get()->getGrpPeptideSp().get();
+
+ if (p_grp_peptide != nullptr) {
+ std::set<const pappso::GrpPeptide *> _already_writed;
+ if (_already_writed.find(p_grp_peptide) == _already_writed.end()) {
+ _already_writed.insert(p_grp_peptide);
+ PeptideXtp * p_peptide = peptide_evidence_sp.get()->getPeptideXtpSp().get();
+ _output_stream->writeStartElement("peptide");
+ _output_stream->writeAttribute("id",p_grp_peptide->getGroupingId());
+ _output_stream->writeAttribute("seq", p_peptide->getSequence());
+
+
+ unsigned int i=0;
+ for (const pappso::Aa & amino_acid: *p_peptide) {
+
+ std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
+
+
+ for (auto && aa_modif : aa_modif_list) {
+ if (!aa_modif->isInternal()) {
+ _output_stream->writeStartElement("psimod");
+ _output_stream->writeAttribute("acc", aa_modif->getAccession());
+ _output_stream->writeAttribute("at", QString ("%1").arg(i));
+ _output_stream->writeEndElement();// mod
+ }
+ }
+ i++;
+ }
+ _output_stream->writeEndElement();
+ }
}
- _output_stream->writeEndElement();
}
-
}
+ //peptideList
_output_stream->writeEndElement();
}
catch (pappso::PappsoException &error)
@@ -152,6 +160,5 @@ void MassChroqPrm::writePeptides() {
{
throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides stdex :\n%1").arg(error.what()));
}
-}
}
diff --git a/src/output/masschroqprm.h b/src/output/masschroqprm.h
index 31aca8f40..bc2e8e04c 100644
--- a/src/output/masschroqprm.h
+++ b/src/output/masschroqprm.h
@@ -45,16 +45,7 @@ class MassChroqPrm
void write(ProjectSp sp_project);
void close();
private:
- void writeGroups();
- void writeProteinList();
- void writePeptideList();
- void writePeptideListInGroup(const GroupingGroup * p_group);
- void writeIsotopeLabelList();
- void writeAlignments();
- void writeQuantificationMethods();
- void writeQuantificationResults();
- void writeQuantificationTraces();
- void writeQuantify();
+ void writePeptides();
private :
QFile * _output_file;
--
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