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

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 9082204bf80af5ccb83cba072078ef8b276f6e3a..d2b2e03a3196d61cf7036ff879f1a18bec741ae6 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -22,7 +22,12 @@ class ChimeraPintailCommand : public Command {
 public:
 
        ChimeraPintailCommand(string);
+       ChimeraPintailCommand();
        ~ChimeraPintailCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -49,6 +54,7 @@ private:
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;