changes while testing

[mothur.git] / otuhierarchycommand.h

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index dd5f3a7adc759733bf3972392485c79b94669977..cd106ece49d90dcfe28a0d272b672919281a912b 100644 (file)
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -19,20 +19,27 @@ class OtuHierarchyCommand : public Command {
 public:
        OtuHierarchyCommand(string);
        OtuHierarchyCommand();
-       ~OtuHierarchyCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~OtuHierarchyCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "otu.hierarchy";                       }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
+       string getDescription()         { return "relates OTUs at different distances"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        bool abort;
        set<string> labels; //holds labels to be used
        string label, listFile, outputDir, output;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        vector<ListVector> getListVectors();