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

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 2ac80c91dd65fa7cf56f71331e4c4486c68c8b87..f16a8f0c5ebc75bf07039a54d910d266e418b94e 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -24,7 +24,12 @@ class MGClusterCommand : public Command {
 
 public:
        MGClusterCommand(string);
+       MGClusterCommand();
        ~MGClusterCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -37,12 +42,15 @@ private:
        ListVector* list;
        ListVector oldList;
        vector<seqDist> overlapMatrix;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
-       string blastfile, method, namefile, overlapFile, distFile;
+       string blastfile, method, namefile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
-       float cutoff, penalty;
+       double cutoff;
+       float penalty;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge;
+       bool abort, minWanted, hclusterWanted, merge, hard;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);