From 83e75fdc835bbabc32e468170a60130abd5000e2 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 10 Jun 2019 07:49:43 +0200
Subject: [PATCH] WIP: finding best msrun for alignment reference
---
src/core/project.cpp | 78 +++++++++++++++----
src/core/project.h | 6 +-
.../exportmasschroqdialog.cpp | 39 +++-------
3 files changed, 80 insertions(+), 43 deletions(-)
diff --git a/src/core/project.cpp b/src/core/project.cpp
index effd7a3af..534f40989 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -27,6 +27,7 @@
#include "peptidematch.h"
#include "proteinmatch.h"
#include <QDebug>
+#include <pappsomspp/exception/exceptionnotfound.h>
Project::Project()
{
@@ -54,7 +55,7 @@ Project::readResultFile(QString filename)
_identification_data_source_store.getInstance(filename);
ident_source.get()->parseTo(this);
- qDebug() << "Project::readResultFile end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
const ProjectMode
@@ -143,14 +144,13 @@ Project::updateAutomaticFilters(
const AutomaticFilterParameters &automatic_filter_parameters)
{
- qDebug() << "Project::updateAutomaticFilters begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_automatic_filter_parameters = automatic_filter_parameters;
for(auto &p_id_group : _identification_goup_list)
{
p_id_group->updateAutomaticFilters(_automatic_filter_parameters);
}
-
- qDebug() << "Project::updateAutomaticFilters end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
ProjectSp
Project::makeProjectSp() const
@@ -168,16 +168,16 @@ Project::newIdentificationGroup()
void
Project::readXpipFile(WorkMonitorInterface *p_monitor, QFileInfo xpip_fileinfo)
{
- qDebug() << "Project::readXpipFile begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
XpipSaxHandler *parser_java_xpip = new XpipSaxHandler(p_monitor, this);
QXmlSimpleReader simplereader;
simplereader.setContentHandler(parser_java_xpip);
simplereader.setErrorHandler(parser_java_xpip);
-
- qDebug() << "Project::readXpipFile Read XPIP XML result file '"
- << xpip_fileinfo.absoluteFilePath() << "'";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << " Read XPIP XML result file '" << xpip_fileinfo.absoluteFilePath()
+ << "'";
QFile qfile(xpip_fileinfo.absoluteFilePath());
QXmlInputSource xmlInputSource(&qfile);
@@ -189,7 +189,8 @@ Project::readXpipFile(WorkMonitorInterface *p_monitor, QFileInfo xpip_fileinfo)
}
else
{
- qDebug() << parser_java_xpip->errorString();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << parser_java_xpip->errorString();
// throw PappsoException(
// QObject::tr("error reading tandem XML result file :\n").append(
// parser->errorString()));
@@ -213,7 +214,8 @@ Project::readXpipFile(WorkMonitorInterface *p_monitor, QFileInfo xpip_fileinfo)
simplereaderb.setContentHandler(parser_xtp_xpip);
simplereaderb.setErrorHandler(parser_xtp_xpip);
- qDebug() << "Project::readXpipFile Read XPIP XML result file '"
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << " Read XPIP XML result file '"
<< xpip_fileinfo.absoluteFilePath() << "'";
QFile qfileb(xpip_fileinfo.absoluteFilePath());
@@ -235,7 +237,8 @@ Project::readXpipFile(WorkMonitorInterface *p_monitor, QFileInfo xpip_fileinfo)
}
else
{
- qDebug() << parser_xtp_xpip->errorString();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+ << __LINE__;
throw pappso::PappsoException(
QObject::tr(
"Error reading %1 XPIP file :\n it is not an XPIP file")
@@ -281,11 +284,58 @@ Project::hasPtmExperiment() const
void
Project::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
{
for(const IdentificationGroup *p_ident_group : _identification_goup_list)
{
- p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list,
- p_msrun, p_peptide, charge);
+ p_ident_group->getSameXicPeptideEvidenceList(
+ peptide_evidence_list, p_msrun, p_peptide, charge);
+ }
+}
+
+void
+Project::prepareMsrunRetentionTimesForAlignment() const
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ bool is_ok = true;
+ for(IdentificationDataSourceSp p_ident_data_source :
+ this->getIdentificationDataSourceStore()
+ .getIdentificationDataSourceList())
+ {
+ MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
+
+ if(msrun_sp->findMsRunFile())
+ {
+ // msrun_sp->checkMsRunStatistics();
+ msrun_sp->buildMsRunRetentionTime(
+ p_ident_data_source->getPeptideEvidenceStore());
+ }
+ else
+ {
+ is_ok = false;
+
+ throw pappso::ExceptionNotFound(
+ QObject::tr("MS run file %1 not found.")
+ .arg(msrun_sp.get()->getFileName()));
+ break;
+ }
+ }
+ if(is_ok)
+ {
+ for(auto &msrun_sp : this->getMsRunStore().getMsRunList())
+ {
+ msrun_sp->computeMsRunRetentionTime();
+ }
+ // find the best reference
+ }
+ else
+ {
+ for(auto &msrun_sp : this->getMsRunStore().getMsRunList())
+ {
+ msrun_sp->clearMsRunRetentionTime();
+ }
}
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
diff --git a/src/core/project.h b/src/core/project.h
index e79d02b91..5f0120f21 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -97,9 +97,13 @@ class Project
*/
void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
unsigned int charge) const;
+
+ void prepareMsrunRetentionTimesForAlignment() const;
+
private:
LabelingMethodSp _labeling_method_sp;
ProjectMode _project_mode = ProjectMode::combined;
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index 6d615df0b..dd20c7972 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -38,6 +38,7 @@
#include <QFileDialog>
#include <pappsomspp/msrun/alignment/msrunretentiontime.h>
#include <pappsomspp/msfile/msfileaccessor.h>
+#include <pappsomspp/pappsoexception.h>
ExportMasschroqDialog::ExportMasschroqDialog(QWidget *parent)
: QDialog(parent), ui(new Ui::ExportMasschroqDialog)
@@ -268,27 +269,11 @@ ExportMasschroqDialog::doBrowseMsrunDirectory()
void
ExportMasschroqDialog::doFindBestMsrunForAlignment()
{
- IdentificationGroup *p_identification_group = nullptr;
- if(mp_project->getIdentificationGroupList().size() != 1)
- {
- }
- else
- {
- // p_identification_group =
- // mp_project->getIdentificationGroupList()[0]->get
- }
bool is_ok = true;
- for(IdentificationDataSourceSp p_ident_data_source :
- mp_project->getIdentificationDataSourceStore()
- .getIdentificationDataSourceList())
+ for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
{
- MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
-
if(msrun_sp->findMsRunFile())
{
- // msrun_sp->checkMsRunStatistics();
- msrun_sp->buildMsRunRetentionTime(
- p_ident_data_source->getPeptideEvidenceStore());
}
else
{
@@ -301,19 +286,17 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
break;
}
}
- if(is_ok)
+ try
{
- for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
- {
- msrun_sp->computeMsRunRetentionTime();
- }
- //find the best reference
+ mp_project->prepareMsrunRetentionTimesForAlignment();
}
- else
+ catch(pappso::PappsoException &error)
{
- for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
- {
- msrun_sp->clearMsRunRetentionTime();
- }
+ QMessageBox msgBox;
+ msgBox.setWindowTitle("Error");
+ msgBox.setText(
+ tr("Error preparing MS run retention times: %1").arg(error.qwhat()));
+ msgBox.setIcon(QMessageBox::Critical);
+ msgBox.exec();
}
}
--
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