FDR and contaminant selection now works selecting fasta files

src/files/fastafile.cpp

@@ -32,9 +32,10 @@ public:
     };
 
     void setSequence(const QString& description, const QString& sequence) override {
-        qDebug() << "PeptideReader::setSequence " << description << " " <<sequence;
+        //qDebug() << "PeptideReader::setSequence " << description << " " <<sequence;
         QStringList descr_split = description.simplified().split(" ");
         QString accession = descr_split.at(0);
+        //qDebug() << "PeptideReader::setSequence " << accession << " " <<accession;
         _protein_store.setContaminantAccession(accession);
     };
 private:

src/gui/project_view/projectwindow.cpp

@@ -54,6 +54,7 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
     ui->contaminant_database_listview->setModel(_p_fasta_str_li);
     QItemSelectionModel * selection_model = ui->contaminant_database_listview->selectionModel();
     ui->contaminant_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
+    ui->decoy_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
 
     _p_automatic_filter_widget = new AutomaticFilterWidget(this);
     ui->filter_parameter_layout->addWidget(_p_automatic_filter_widget);
@@ -259,7 +260,22 @@ void ProjectWindow::doFdrChanged() {
     qDebug() << "ProjectWindow::doFdrChanged begin ";
     showWaitingMessage(tr("FDR modifications"));
     doDisplayLoadingMessage(tr("tagging decoy proteins"));
-    _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
+    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 *>()"));
+            }
+        }
+    }
+    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());
 

src/utils/proteinstore.cpp

@@ -34,12 +34,12 @@
 
 ProteinStore::ProteinStore()
 {
-      QSettings settings;
+    QSettings settings;
 
     _regexp_contaminant.setPattern(settings.value("automatic_filter/contaminant_regexp","^conta\\|").toString());
     _regexp_decoy.setPattern(settings.value("automatic_filter/decoy_regexp",".*\\|reversed$").toString());
-    
-    
+
+
 }
 
 ProteinStore::~ProteinStore()
@@ -51,7 +51,7 @@ QRegExp ProteinStore::getRegexpContaminant() const {
 }
 void ProteinStore::setRegexpContaminantPattern(const QString & pattern) {
     _regexp_contaminant.setPattern(pattern);
-    
+
     for  (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
         setProteinInformations(acc_protein.second);
     }
@@ -63,11 +63,11 @@ QRegExp ProteinStore::getRegexpDecoy() const {
 }
 void ProteinStore::setRegexpDecoyPattern(const QString & pattern) {
     _regexp_decoy.setPattern(pattern);
-    
+
     for  (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
         setProteinInformations(acc_protein.second);
     }
-        QSettings settings;
+    QSettings settings;
     settings.setValue("automatic_filter/decoy_regexp", pattern);
 
 }
@@ -84,10 +84,16 @@ void ProteinStore::clearContaminants() {
 }
 
 void ProteinStore::setDecoyAccession(QString accession) {
-    _map_accession_protein_list.at(accession).get()->setIsDecoy(true);
+    std::map<QString, ProteinXtpSp>::iterator it =  _map_accession_protein_list.find(accession);
+    if (it != _map_accession_protein_list.end()) {
+        it->second.get()->setIsDecoy(true);
+    }
 }
 void ProteinStore::setContaminantAccession(QString accession) {
-    _map_accession_protein_list.at(accession).get()->setIsContaminant(true);
+    std::map<QString, ProteinXtpSp>::iterator it =  _map_accession_protein_list.find(accession);
+    if (it != _map_accession_protein_list.end()) {
+        it->second.get()->setIsContaminant(true);
+    }
 }
 ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
 
@@ -106,7 +112,7 @@ void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
     peptide_in.get()->setIsDecoy(false);
     QString accession = peptide_in.get()->getAccession();
     peptide_in.get()->parseAccession2dbxref();
-    
+
     if ((!_regexp_contaminant.isEmpty()) && (_regexp_contaminant.indexIn(accession, 0)>-1)) {
         //qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
         peptide_in.get()->setIsContaminant(true);