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

[mothur.git] / degapseqscommand.h

diff --git a/degapseqscommand.h b/degapseqscommand.h
index 192d6eb7397e143e5ff91389ca37a5be98857a6e..5501d49b6affcdfe7e24fb8b444f837800d08ff5 100644 (file)
--- a/degapseqscommand.h
+++ b/degapseqscommand.h
@@ -16,7 +16,12 @@
 class DegapSeqsCommand : public Command {
 public:
        DegapSeqsCommand(string);
+       DegapSeqsCommand();
        ~DegapSeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -26,7 +31,7 @@ private:
        string fastafile, outputDir;
        vector<string> outputNames;
        vector<string> fastaFileNames;
-       
+       map<string, vector<string> > outputTypes;
 };
 
 #endif