From f0100c37a2579dd1e0812ed4ec757f6f0c0b2b51 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 20 Apr 2017 13:46:42 +0200
Subject: [PATCH] check psimod compliance
---
src/core/project.cpp | 4 +++-
src/core/project.h | 4 ++++
src/gui/mainwindow.cpp | 20 +++++++++++---------
src/utils/peptidestore.cpp | 14 +++++++++++++-
src/utils/peptidestore.h | 4 ++++
5 files changed, 35 insertions(+), 11 deletions(-)
diff --git a/src/core/project.cpp b/src/core/project.cpp
index ad3de8ff1..e21a90c2c 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -39,7 +39,9 @@ Project::~Project()
}
}
-
+bool Project::checkPsimodCompliance() const {
+ return _peptide_store.checkPsimodCompliance();
+}
void Project::readResultFile(QString filename) {
IdentificationDataSourceSp ident_source = _identification_data_source_store.getInstance(filename);
diff --git a/src/core/project.h b/src/core/project.h
index ead40c37e..544de7dc9 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -65,6 +65,10 @@ public:
void setCombineMode(bool is_combine_mode);
bool isCombineMode() const;
void readResultFile(QString filename);
+
+ /** @brief check that modifications are coded with PSI MOD accessions
+ */
+ bool checkPsimodCompliance() const;
private :
bool _is_combine_mode =true;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 43a3fab5c..1068cfe0a 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -179,11 +179,11 @@ void MainWindow::doAcceptedExportSpreadsheetDialog() {
}
settings.setValue("path/export_ods", QFileInfo(filename).absolutePath());
-
+
OdsDocWriter writer(filename);
OdsExport export_ods(_project_sp.get());
export_ods.write(&writer);
-
+
writer.close();
//emit operateXpipFile(filename);
}
@@ -222,7 +222,7 @@ void MainWindow::doProjectReady(ProjectSp project_sp) {
viewError(tr("Error while grouping :\n%1").arg(error.qwhat()));
}
_project_window->setProjectSp(project_sp);
-ui->menu_export_files->setDisabled(false);
+ ui->menu_export_files->setDisabled(false);
qDebug() << "MainWindow::doProjectReady end";
}
@@ -259,22 +259,24 @@ void MainWindow::selectXpipFile() {
}
- void MainWindow::doActionSpreadsheet() {
+void MainWindow::doActionSpreadsheet() {
qDebug() << "MainWindow::doActionSpreadsheet begin";
try {
-
- _p_export_spreadsheet_dialog->show();
- _p_export_spreadsheet_dialog->raise();
- _p_export_spreadsheet_dialog->activateWindow();
+
+ _p_export_spreadsheet_dialog->show();
+ _p_export_spreadsheet_dialog->raise();
+ _p_export_spreadsheet_dialog->activateWindow();
}
catch (pappso::PappsoException & error) {
viewError(tr("Error doActionSpreadsheet :\n%1").arg(error.qwhat()));
}
qDebug() << "MainWindow::doActionSpreadsheet end";
- }
+}
void MainWindow::doActionMassChroQ() {
qDebug() << "MainWindow::doActionMassChroQ begin";
try {
+ _project_sp.get()->checkPsimodCompliance();
+
QSettings settings;
QString default_location = settings.value("path/mcqfile", "").toString();
diff --git a/src/utils/peptidestore.cpp b/src/utils/peptidestore.cpp
index 1fe1dcf1a..f1bd04adb 100644
--- a/src/utils/peptidestore.cpp
+++ b/src/utils/peptidestore.cpp
@@ -29,6 +29,7 @@
#include "peptidestore.h"
#include <pappsomspp/amino_acid/Aa.h>
+#include <pappsomspp/pappsoexception.h>
PeptideStore::PeptideStore()
{
@@ -52,9 +53,20 @@ PeptideXtpSp & PeptideStore::getInstance(PeptideXtpSp & peptide_in) {
for (auto && aa : *(ret.first->second.get())) {
std::list<pappso::AaModificationP> mod_list = aa.getModificationList();
- _modification_collection.insert(mod_list.begin(), mod_list.end());
+ _modification_collection.insert(mod_list.begin(), mod_list.end());
}
}
return ret.first->second;
}
+
+bool PeptideStore::checkPsimodCompliance() const {
+ for (pappso::AaModificationP modification :_modification_collection) {
+ if (modification->getAccession().startsWith("MOD:")) {
+ }
+ else {
+ throw pappso::PappsoException(QObject::tr("Modification %1 is not a PSIMOD accession").arg(modification->getAccession()));
+ }
+ }
+ return true;
+}
diff --git a/src/utils/peptidestore.h b/src/utils/peptidestore.h
index 1d5d9de2e..5221b31a4 100644
--- a/src/utils/peptidestore.h
+++ b/src/utils/peptidestore.h
@@ -41,6 +41,10 @@ public:
~PeptideStore();
PeptideXtpSp & getInstance(PeptideXtpSp & peptide_in);
+
+ /** @brief check that modifications are coded with PSI MOD accessions
+ */
+ bool checkPsimodCompliance() const;
private :
--
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