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

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 93e8c776918ec9fa2d6f661d7c178380a4f47d66..20b11a85ac05e57b453906475d73ab4fd2ecb2e0 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -18,7 +18,12 @@
 class TrimSeqsCommand : public Command {
 public:
        TrimSeqsCommand(string);
+       TrimSeqsCommand();
        ~TrimSeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -39,6 +44,7 @@ private:
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
        int countDiffs(string, string);
+       map<string, vector<string> > outputTypes;
 
        bool abort;
        string fastaFile, oligoFile, qFileName, outputDir;