From af6d966bf18c0555786b5242d01b872923db2155 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 15 May 2018 22:03:01 +0200
Subject: [PATCH] back to spectral count in one single file
---
src/gui/mainwindow.cpp | 6 +-
src/gui/workerthread.cpp | 26 ++++++---
src/output/mcqrspectralcount.cpp | 99 ++++++++++++++++++++++++++++----
src/output/mcqrspectralcount.h | 10 +++-
4 files changed, 117 insertions(+), 24 deletions(-)
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index da0dca12f..232e0049d 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -357,9 +357,9 @@ void MainWindow::doActionSpectralCountingMcq()
QSettings settings;
QString default_location = settings.value("path/scmcqfile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save spectral count TSV files in a directory"),
- QString("%1/untitled.d").arg(default_location),
- tr("TSV (*.d)"));
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save spectral count TSV file"),
+ QString("%1/untitled.tsv").arg(default_location),
+ tr("TSV (*.tsv)"));
if (filename.isEmpty()) {
return;
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 19833b647..c09396e11 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -29,7 +29,8 @@
#include "workerthread.h"
#include <odsstream/odsdocwriter.h>
-#include <odsstream/tsvdirectorywriter.h>
+#include <odsstream/tsvoutputstream.h>
+#include <odsstream/odsexception.h>
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
#include "../output/masschroqml.h"
@@ -347,21 +348,30 @@ void WorkerThread::doWritingProticFile(QString filename, ProjectSp project_sp) {
}
-void WorkerThread::doWritingMcqrSpectralCountFile(QString directory_name, ProjectSp project_sp) {
-
+void WorkerThread::doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp) {
try {
- emit loadingMessage(tr("Writing spectral count files for MassChroqR in directory %1").arg(directory_name));
- TsvDirectoryWriter * p_writer = new TsvDirectoryWriter(directory_name);
- McqrSpectralCount spectra_sheet(project_sp.get());
- spectra_sheet.write(p_writer, _p_work_monitor);
+ emit loadingMessage(tr("Writing %1 spectral count file for MassChroqR").arg(filename));
+ QFile outFile;
+ outFile.setFileName(filename);
+ outFile.open(QIODevice::WriteOnly);
+ QTextStream * p_outputStream = new QTextStream(&outFile);
+ TsvOutputStream * p_writer = new TsvOutputStream(*p_outputStream);
+ p_writer->setNoSheetName(true);
+ McqrSpectralCount spectra_sheet(p_writer, project_sp.get());
+ spectra_sheet.writeSheet();
p_writer->close();
delete p_writer;
+ delete p_outputStream;
+ outFile.close();
emit operationFinished();
}
- catch (pappso::PappsoException & error) {
+ catch (OdsException & error) {
emit operationFailed(tr("Error while writing spectral count file for MassChroqR :\n%1").arg(error.qwhat()));
}
+ catch (pappso::PappsoException & errorb) {
+ emit operationFailed(tr("Error while writing spectral count file for MassChroqR :\n%1").arg(errorb.qwhat()));
+ }
}
diff --git a/src/output/mcqrspectralcount.cpp b/src/output/mcqrspectralcount.cpp
index da69431bd..3e5b13774 100644
--- a/src/output/mcqrspectralcount.cpp
+++ b/src/output/mcqrspectralcount.cpp
@@ -1,5 +1,5 @@
/**
- * \file /output/mcqrspectralcount.cpp
+ * \file /output/mcqrspectralcount.h
* \date 23/3/2018
* \author Olivier Langella
* \brief write simple TSV file for MassChroqR spectral count studies
@@ -29,21 +29,98 @@
#include "mcqrspectralcount.h"
#include <pappsomspp/pappsoexception.h>
-#include <QSettings>
-#include "mcqr/mcqrscpeptide.h"
-#include "mcqr/mcqrscprotein.h"
-McqrSpectralCount::McqrSpectralCount (const Project * p_project): _p_project(p_project) {
+
+McqrSpectralCount::McqrSpectralCount (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+ _p_writer = p_writer;
}
+void McqrSpectralCount::writeSheet () {
+ _p_writer->writeSheet("MassChroqR spectral counting");
+
+ std::vector<IdentificationGroup *> identification_list = _p_project->getIdentificationGroupList();
+ if (identification_list.size() > 1) {
+ throw pappso::PappsoException(QObject::tr("error : cannot write MassChroqR spectral count file in individual mode"));
+ }
+
+ for (IdentificationGroup * p_ident:identification_list) {
+ //writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
+ }
+}
+
+
+void McqrSpectralCount::writeHeaders(IdentificationGroup * p_ident) {
+
+//ProteinID, msrun, msrunfile, accession, description, q
+ _p_writer->writeCell("protein");
+ _p_writer->writeCell("msrun");
+ _p_writer->writeCell("msrunfile");
+ _p_writer->writeCell("accession");
+ _p_writer->writeCell("description");
+ _p_writer->writeCell("sc");
+ //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
+
+}
+
+
+
+void McqrSpectralCount::writeIdentificationGroup(IdentificationGroup * p_ident) {
+
+ _ms_run_sp_list = p_ident->getMsRunSpList();
+ writeHeaders(p_ident);
+ for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+
+ std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
+
+ std::sort(protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch * a, const ProteinMatch * b)
+ {
+ return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
+ });
+
+ for (auto & protein_match:protein_match_list) {
+ writeOneProtein(group_pair.second.get(), protein_match);
+ }
+
+ }
+ _p_writer->writeLine();
+}
+
+
+void McqrSpectralCount::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
+ try {
+
+ qDebug() << "McqrSpectralCount::writeOneProtein begin" ;
+ ValidationState validation_state = ValidationState::validAndChecked;
+
+ pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
+
+ ProteinXtp * p_protein = p_protein_match->getProteinXtpSp().get();
+
+ for (MsRunSp & msrun_sp : _ms_run_sp_list) {
+ _p_writer->writeLine();
+
+ _p_writer->writeCell(p_grp_protein->getGroupingId());
-void McqrSpectralCount::write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_monitor) {
- QSettings settings;
+ _p_writer->writeCell(msrun_sp.get()->getXmlId());
+ _p_writer->writeCell(msrun_sp.get()->getFilename());
- p_monitor->message(QObject::tr("writing MassChroqR protein file"));
- McqRscProtein( p_writer, _p_project).writeSheet();
- p_monitor->message(QObject::tr("writing MassChroqR peptide file"));
- McqRscPeptide( p_writer, _p_project).writeSheet();
+ //const std::list<DbXref> & dbxref_list = p_protein->getDbxrefList();
+ //if (dbxref_list.size() == 0) {
+ _p_writer->writeCell(p_protein->getAccession());
+ //}
+ //else {
+ // _p_writer->writeCell(dbxref_list.front().getUrl(), p_protein->getAccession());
+ //}
+ _p_writer->writeCell(p_protein->getDescription());
+ _p_writer->writeCell(p_protein_match->countSampleScan(validation_state, msrun_sp.get()));
+ }
+ qDebug() << "McqrSpectralCount::writeOneProtein end" ;
+ }
+ catch (pappso::PappsoException error) {
+ throw pappso::PappsoException(QObject::tr("Error writing protein %1 :\n%2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ }
}
diff --git a/src/output/mcqrspectralcount.h b/src/output/mcqrspectralcount.h
index ef1c882f1..1a3d6c3ed 100644
--- a/src/output/mcqrspectralcount.h
+++ b/src/output/mcqrspectralcount.h
@@ -36,12 +36,18 @@
class McqrSpectralCount
{
public :
- McqrSpectralCount (const Project * project);
+ McqrSpectralCount (CalcWriterInterface * p_writer, const Project * p_project);
- void write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_monitor);
+ void writeSheet();
+private :
+ void writeIdentificationGroup(IdentificationGroup * p_ident);
+ void writeHeaders(IdentificationGroup * p_ident);
+ void writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match);
private :
const Project * _p_project;
+ CalcWriterInterface * _p_writer;
+ std::vector<MsRunSp> _ms_run_sp_list;
};
#endif // MCQRSPECTRALCOUNT_H
--
GitLab