sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / hclustercommand.h

diff --git a/hclustercommand.h b/hclustercommand.h
index 7351cef71a6edad1a3b1484cbe437d9dd6899e39..d1074070420fc89347a65b8fa8c0448c953c8881 100644 (file)
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -11,7 +11,6 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
@@ -28,27 +27,28 @@
 //University of Florida, Gainesville, FL 32610-3622 and 3Materials Technology Directorate, Air Force Technical 
 //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();
-       int execute();  
-       void help();
+       HClusterCommand(string);
+       HClusterCommand();      
+       ~HClusterCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "hcluster";    }
+       string getCommandCategory()             { return "Clustering";  }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
+       string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        HCluster* cluster;
        ListVector* list;
        RAbundVector* rabund;
@@ -56,23 +56,16 @@ 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;
        
        void printData(string label);
-       vector<seqDist> getSeqs(ifstream&);
 };
 
 /************************************************************/