fixed cluster.classic and added weighted method to hcluster

[mothur.git] / hclustercommand.h

diff --git a/hclustercommand.h b/hclustercommand.h
index 1dd46b9ad96890c5576e18ae500cff6359270795..fc0333174a87b111a0cda756dc24ff4669202cc9 100644 (file)
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -29,17 +29,16 @@
 //Applications Center, 1030 S. Highway A1A, Patrick AFB, FL 32925-3002, USA 
 //Received January 28, 2009; Revised April 14, 2009; Accepted April 15, 2009 
 /************************************************************/
-struct seqDist {
-       int seq1;
-       int seq2;
-       float dist;
-};
-/************************************************************/
 class HClusterCommand : public Command {
        
 public:
-       HClusterCommand(string);        
+       HClusterCommand(string);
+       HClusterCommand();      
        ~HClusterCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -52,23 +51,17 @@ private:
        ListVector oldList;
        ReadCluster* read;
        
-       bool abort;
-
-       string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort;
+       bool abort, sorted, print_start, hard;
+       string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
        double cutoff;
-       string showabund, timing;
        int precision, length;
        ofstream sabundFile, rabundFile, listFile;
-       //ifstream in;
-       seqDist next;
-       bool exitedBreak, sorted;
-
-       bool print_start;
        time_t start;
        unsigned long loops;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        void printData(string label);
-       vector<seqDist> getSeqs(ifstream&);
 };
 
 /************************************************************/