From fd70b054cca8189f469223d8fbd13bb041375435 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 29 Sep 2017 21:43:14 +0200
Subject: [PATCH] error if fasta file is not found
---
src/core/proteinmatch.cpp | 6 +-
src/files/fastafile.cpp | 5 ++
src/gui/project_view/projectwindow.cpp | 104 +++++++++++++++----------
3 files changed, 73 insertions(+), 42 deletions(-)
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 6866522fe..4400d062c 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -64,7 +64,7 @@ bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
}
void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
+ //qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
_proxy_valid = false;
unsigned int number_of_valid_peptides =0;
bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
@@ -91,7 +91,7 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
}
}
- qDebug() <<"ProteinMatch::updateAutomaticFilters begin 2" ;
+ // qDebug() <<"ProteinMatch::updateAutomaticFilters begin 2" ;
if (number_of_valid_peptides == 0) {
_proxy_valid = false;
@@ -105,7 +105,7 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
}
}
}
- qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
+ // qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
}
const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index cc1bf229e..f4eb6876d 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -25,6 +25,7 @@
#include <pappsomspp/fasta/fastareader.h>
#include <QStringList>
#include <QDebug>
+#include <pappsomspp/exception/exceptionnotfound.h>
class AccessionContaminantReader: public pappso::FastaHandlerInterface {
public:
@@ -94,10 +95,12 @@ void FastaFile::setContaminants(ProteinStore & protein_store) const {
}
else {
qDebug() << "FastaFile::setContaminants "<< _fasta_source.absoluteFilePath() << " not open";
+ throw pappso::ExceptionNotFound(QObject::tr("unable to open contaminant fasta file \"%1\"").arg(_fasta_source.absoluteFilePath()));
}
}
else {
qDebug() << "FastaFile::setContaminants "<< _fasta_source.absoluteFilePath() << " does not exists";
+ throw pappso::ExceptionNotFound(QObject::tr("contaminant fasta file \"%1\" not found").arg(_fasta_source.absoluteFilePath()));
}
}
@@ -113,9 +116,11 @@ void FastaFile::setDecoys(ProteinStore & protein_store) const {
}
else {
qDebug() << "FastaFile::setDecoys "<< _fasta_source.absoluteFilePath() << " not open";
+ throw pappso::ExceptionNotFound(QObject::tr("unable to open decoy fasta file \"%1\"").arg(_fasta_source.absoluteFilePath()));
}
}
else {
qDebug() << "FastaFile::setDecoys "<< _fasta_source.absoluteFilePath() << " does not exists";
+ throw pappso::ExceptionNotFound(QObject::tr("decoy fasta file \"%1\" not found").arg(_fasta_source.absoluteFilePath()));
}
}
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 10723c89f..75f0e264c 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -282,29 +282,42 @@ void ProjectWindow::computeMassPrecision() {
void ProjectWindow::doFdrChanged() {
qDebug() << "ProjectWindow::doFdrChanged begin ";
- showWaitingMessage(tr("FDR modifications"));
- doDisplayLoadingMessage(tr("tagging decoy proteins"));
- QModelIndexList index_list = ui->decoy_database_listview->selectionModel()->selectedIndexes();
- if (index_list.size() > 0) {
- _project_sp.get()->getProteinStore().clearDecoys();
- for (QModelIndex index :index_list) {
- if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
- FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
- p_fasta_file->setDecoys(_project_sp.get()->getProteinStore());
- }
- else {
- throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ try {
+ showWaitingMessage(tr("FDR modifications"));
+ doDisplayLoadingMessage(tr("tagging decoy proteins"));
+ QModelIndexList index_list = ui->decoy_database_listview->selectionModel()->selectedIndexes();
+ if (index_list.size() > 0) {
+ qDebug() << "ProjectWindow::doFdrChanged index_list.size()=" << index_list.size();
+ _project_sp.get()->getProteinStore().clearDecoys();
+ for (QModelIndex index :index_list) {
+ if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
+ FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
+ p_fasta_file->setDecoys(_project_sp.get()->getProteinStore());
+ }
+ else {
+ throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ }
}
}
+ else {
+ _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
+ }
+ doDisplayLoadingMessage(tr("updating filters"));
+ _project_sp.get()->updateAutomaticFilters(_project_sp.get()->getAutomaticFilterParameters());
+
+ //re group
+ emit operateGrouping(_project_sp);
}
- else {
- _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
+ catch (pappso::PappsoException exception_pappso) {
+ hideWaitingMessage();
+ QMessageBox::warning(this,
+ tr("Unable to compute FDR :"), exception_pappso.qwhat());
+ }
+ catch (std::exception exception_std) {
+ hideWaitingMessage();
+ QMessageBox::warning(this,
+ tr("Unable to compute FDR :"), exception_std.what());
}
- doDisplayLoadingMessage(tr("updating filters"));
- _project_sp.get()->updateAutomaticFilters(_project_sp.get()->getAutomaticFilterParameters());
-
- //re group
- emit operateGrouping(_project_sp);
qDebug() << "ProjectWindow::doFdrChanged end ";
}
@@ -317,30 +330,42 @@ void ProjectWindow::refresh() {
}
void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters) {
qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged begin ";
- showWaitingMessage(tr("Updating filters"));
-
- doDisplayLoadingMessage(tr("tagging contaminant proteins"));
- QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
- if (index_list.size() > 0) {
- _project_sp.get()->getProteinStore().clearContaminants();
- for (QModelIndex index :index_list) {
- if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
- FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
- p_fasta_file->setContaminants(_project_sp.get()->getProteinStore());
- }
- else {
- throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ try {
+ showWaitingMessage(tr("Updating filters"));
+
+ doDisplayLoadingMessage(tr("tagging contaminant proteins"));
+ QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
+ if (index_list.size() > 0) {
+ _project_sp.get()->getProteinStore().clearContaminants();
+ for (QModelIndex index :index_list) {
+ if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
+ FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
+ p_fasta_file->setContaminants(_project_sp.get()->getProteinStore());
+ }
+ else {
+ throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ }
}
}
+ else {
+ _project_sp.get()->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
+ }
+ doDisplayLoadingMessage(tr("updating filters"));
+ _project_sp.get()->updateAutomaticFilters(parameters);
+
+ qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged emit operateGrouping(_project_sp) ";
+ emit operateGrouping(_project_sp);
}
- else {
- _project_sp.get()->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
+ catch (pappso::PappsoException exception_pappso) {
+ hideWaitingMessage();
+ QMessageBox::warning(this,
+ tr("Error filtering results :"), exception_pappso.qwhat());
+ }
+ catch (std::exception exception_std) {
+ hideWaitingMessage();
+ QMessageBox::warning(this,
+ tr("Error filtering results :"), exception_std.what());
}
- doDisplayLoadingMessage(tr("updating filters"));
- _project_sp.get()->updateAutomaticFilters(parameters);
-
- qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged emit operateGrouping(_project_sp) ";
- emit operateGrouping(_project_sp);
qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged end ";
}
@@ -653,3 +678,4 @@ void ProjectWindow::doAcceptedLabelingMethod() {
emit operateGrouping(_project_sp);
}
+
--
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