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[mothur.git] / otuhierarchycommand.h

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
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+#ifndef OTUHIERARCHYCOMMAND_H
+#define OTUHIERARCHYCOMMAND_H
+/*
+ *  otuhierarchycommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 1/19/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "listvector.hpp"
+
+//**********************************************************************************************************************
+
+class OtuHierarchyCommand : public Command {
+
+public:
+       OtuHierarchyCommand(string);
+       OtuHierarchyCommand();
+       ~OtuHierarchyCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "otu.hierarchy";                       }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       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;
+       
+       vector<ListVector> getListVectors();
+               
+};
+
+//**********************************************************************************************************************
+
+#endif
+
+