default use of regexp to remove reversed proteins

src/cpp/libgroupingprotein/gp_params.cpp

@@ -24,7 +24,7 @@ GpParams::GpParams(QCoreApplication *p_app) :
     _p_in = new QTextStream(stdin, QIODevice::ReadOnly);
     _pepByProt = 2;
     _pepRepro = 1;
-    //_decoy_regexp.setPattern(".*\\|reversed$");
+    _decoy_regexp.setPattern(".*\\|reversed$");
 
     QCommandLineParser parser;
     //const QStringList args = parser.positionalArguments();
@@ -57,10 +57,10 @@ GpParams::GpParams(QCoreApplication *p_app) :
                                     QString(), QString());
 
     QCommandLineOption fastaOption(QStringList() << "fasta",
-                                   QCoreApplication::translate("main", "Remove proteins from this fasta file default:no"),
+                                   QCoreApplication::translate("main", "Remove contaminant proteins from this fasta file default:no"),
                                    QCoreApplication::translate("main", "FILE"), QString());
     QCommandLineOption decoyOption(QStringList() << "decoy-regexp",
-                                   QCoreApplication::translate("main", "regular expression to select decoy protein accessions and remove them before grouping. default is empty : decoy sequences are NOT removed"),
+                                   QCoreApplication::translate("main", "regular expression to select decoy protein accessions and remove them before grouping. default : .*\\|reversed$"),
                                    QCoreApplication::translate("main", "string"), QString());
 
     parser.addOption(inputOption);
@@ -92,7 +92,7 @@ GpParams::GpParams(QCoreApplication *p_app) :
 
     _only_peptide_sequence = parser.isSet(nomassOption);
     _only_count = parser.isSet(countOption);
-    
+
 
     value = parser.value(decoyOption);
     if (value.isEmpty()) {