added pipeline commands which involved change to command factory and command class...

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 1eb2576d2b6867f132be866b4b3e96b1cc7a1c44..983383bdc3b6842db303685e2dd96f421e30d614 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -41,7 +41,12 @@ struct Compare {
 class SeqErrorCommand : public Command {
 public:
        SeqErrorCommand(string);
+       SeqErrorCommand();
        ~SeqErrorCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -58,6 +63,8 @@ private:
        double threshold;
        int numRefs;
        ofstream errorFile;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        vector<Sequence> referenceSeqs;
 };