sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / hclustercommand.h

diff --git a/hclustercommand.h b/hclustercommand.h
index fc0333174a87b111a0cda756dc24ff4669202cc9..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"
@@ -34,16 +33,22 @@ class HClusterCommand : public Command {
 public:
        HClusterCommand(string);
        HClusterCommand();      
-       ~HClusterCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~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;
@@ -59,7 +64,6 @@ private:
        time_t start;
        unsigned long loops;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        void printData(string label);
 };