sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / hclustercommand.h

diff --git a/hclustercommand.h b/hclustercommand.h
index 8bbc655fd7c30a9708b8292a81de0bb6a7b6c478..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"
@@ -32,13 +31,24 @@
 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;
@@ -46,7 +56,7 @@ private:
        ListVector oldList;
        ReadCluster* read;
        
-       bool abort, sorted, print_start;
+       bool abort, sorted, print_start, hard;
        string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
        double cutoff;
        int precision, length;