check psimod compliance

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);
     

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;

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();
 

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;
+}

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 :