fixes while building

[mothur.git] / otuhierarchycommand.h

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index 1cd427f1a7af8442d4747e65662bbf431ccdcbbd..2b9e8e7f042e5f63a8805a427a8c3f8693f6cad9 100644 (file)
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -18,16 +18,31 @@ class OtuHierarchyCommand : public Command {
 
 public:
        OtuHierarchyCommand(string);
-       ~OtuHierarchyCommand();
-       int execute();
-       void help();
+       OtuHierarchyCommand();
+       ~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;
+       set<string> mylabels; //holds labels to be used
+       string label, listFile, outputDir, output, list1Label, list2Label;
+       vector<string> outputNames;
        
-       vector<ListVector> getListVectors();
+       vector< vector<string> > getListVectors();
+    vector< vector<string> > getListVector(string, string&);
                
 };