fixed unifrac.weighted

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 9aa86d4441e5c5f1202a6d552fef31162337c00d..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();
        
@@ -36,20 +41,21 @@ private:
        HCluster* hcluster;
        ListVector* list;
        ListVector oldList;
-       vector<DistNode> overlapMatrix;
-       DistNode next;
-
+       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, exitedBreak, merge;
+       bool abort, minWanted, hclusterWanted, merge, hard;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
-       vector<DistNode> getSeqs(ifstream&);
+       vector<seqDist> getSeqs(ifstream&);
 
 };