read contaminant and decoy XML tag

src/input/xtpxpipsaxhandler.cpp

@@ -123,6 +123,10 @@ bool XtpXpipSaxHandler::startElement(const QString & namespaceURI, const QString
             is_ok = startElement_description(attributes);
         } else if (qName == "fasta_file") {
             is_ok = startElement_fasta_file(attributes);
+        } else if (qName == "contaminants") {
+            is_ok = startElement_contaminants(attributes);
+        } else if (qName == "decoys") {
+            is_ok = startElement_decoys(attributes);
         }
 
         _current_text.clear();
@@ -193,6 +197,41 @@ bool XtpXpipSaxHandler::endElement(const QString & namespaceURI, const QString &
     return is_ok;
 }
 
+bool XtpXpipSaxHandler::startElement_contaminants(QXmlAttributes attributes) {
+//    <contaminants regexp="^contatruc\|" fasta_id=""/>
+
+    qDebug() << "startElement_contaminants ";
+    QString regexp(attributes.value("regexp"));
+    QString fasta_id_list(attributes.value("fasta_id"));
+    if (!regexp.isEmpty()) {
+        _p_project->getProteinStore().setRegexpContaminantPattern(regexp);
+    }
+    if (!fasta_id_list.isEmpty()) {
+        for (QString fasta_id:fasta_id_list.split(" ")) {
+            _p_project->getProteinStore().addContaminantFastaFile(_map_fasta_files.at(fasta_id).get());
+        }
+    }
+    qDebug() << "startElement_contaminants end" ;
+    return true;
+}
+
+bool XtpXpipSaxHandler::startElement_decoys(QXmlAttributes attributes) {
+//    <decoys regexp=".*reversedi" fasta_id=""/>
+    qDebug() << "startElement_decoys ";
+    QString regexp(attributes.value("regexp"));
+    QString fasta_id_list(attributes.value("fasta_id"));
+    if (!regexp.isEmpty()) {
+        _p_project->getProteinStore().setRegexpDecoyPattern(regexp);
+    }
+    if (!fasta_id_list.isEmpty()) {
+        for (QString fasta_id:fasta_id_list.split(" ")) {
+            _p_project->getProteinStore().addDecoyFastaFile(_map_fasta_files.at(fasta_id).get());
+        }
+    }
+    qDebug() << "startElement_decoys end" ;
+    return true;
+}
+
 bool XtpXpipSaxHandler::startElement_label_method(QXmlAttributes attributes) {
 //    <label_method id="dimethyl">
     qDebug() << "startElement_label_method ";

src/input/xtpxpipsaxhandler.h

@@ -85,6 +85,8 @@ private:
     bool startElement_stat(QXmlAttributes attributes);
     bool startElement_counts(QXmlAttributes attributes);
     bool startElement_label_method(QXmlAttributes attributes);
+    bool startElement_contaminants(QXmlAttributes attributes);
+    bool startElement_decoys(QXmlAttributes attributes);
     
     //bool endElement_identification();
     bool endElement_sequence();