From adc54b07132090bb9eacc3af968dcb884d732ea0 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 7 Mar 2018 22:08:53 +0100
Subject: [PATCH] economic accession parsing
---
src/gui/project_view/projectwindow.cpp | 1 +
.../contaminant_widget/contaminantwidget.cpp | 1 +
src/utils/proteinstore.cpp | 17 ++++++++++-------
3 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 2a2fc3123..f52b45355 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -568,6 +568,7 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
_project_sp = project_sp;
ui->decoy_regexp_radiobutton->setChecked(true);
+ ui->decoy_regexp_groupbox->setVisible(true);
ui->decoy_database_groupbox->setVisible(false);
if (_project_sp.get()->getProteinStore().getDecoyFastaFileList().size() > 0) {
ui->decoy_database_files_radiobutton->setChecked(true);
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
index e316b142b..7c4f95820 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
@@ -83,6 +83,7 @@ void ContaminantWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_lis
void ContaminantWidget::getProjectContaminants(const Project * p_project) {
ui->contaminant_regexp_radiobutton->setChecked(true);
+ ui->contaminant_protein_regexp_line_edit->setVisible(true);
ui->contaminant_database_listview->setVisible(false);
if (p_project->getProteinStore().getContaminantFastaFileList().size() > 0) {
ui->contaminant_file_radiobutton->setChecked(true);
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index a08f89ed4..e7312b0b6 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -128,24 +128,27 @@ ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
if (ret.second) {
//the protein is new in the store, update content
setProteinInformations(ret.first->second);
+
+ if (ret.first->second.get()->getDbxrefList().size() == 0) {
+ ret.first->second.get()->parseAccession2dbxref();
+ }
}
return (ret.first->second);
}
-void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
+void ProteinStore::setProteinInformations(ProteinXtpSp & protein_in) {
//qDebug() << "ProteinStore::setProteinInformations begin" << peptide_in.get()->getSequence();
- peptide_in.get()->setIsContaminant(false);
- peptide_in.get()->setIsDecoy(false);
- QString accession = peptide_in.get()->getAccession();
- peptide_in.get()->parseAccession2dbxref();
+ protein_in.get()->setIsContaminant(false);
+ protein_in.get()->setIsDecoy(false);
+ QString accession = protein_in.get()->getAccession();
if ((!_regexp_contaminant.isEmpty()) && (_regexp_contaminant.indexIn(accession, 0)>-1)) {
//qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
- peptide_in.get()->setIsContaminant(true);
+ protein_in.get()->setIsContaminant(true);
}
if ((!_regexp_decoy.isEmpty()) && (_regexp_decoy.indexIn(accession, 0)>-1) ) {
- peptide_in.get()->setIsDecoy(true);
+ protein_in.get()->setIsDecoy(true);
}
//qDebug() << "ProteinStore::setProteinInformations end";
}
--
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