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Commit fd70b054 authored by Langella Olivier's avatar Langella Olivier
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error if fasta file is not found

parent 0d70f987
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src/core/proteinmatch.cpp
+ 3
− 3
View file @ fd70b054
......@@ -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 {
......
src/files/fastafile.cpp
+ 5
− 0
View file @ fd70b054
......@@ -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()));
}
}
src/gui/project_view/projectwindow.cpp
+ 65
− 39
View file @ fd70b054
......@@ -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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