X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;h=ec372ba20acac93709ca4fff0b58c8a42dadf048;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=95276921149b5237a923928bc9f23a5e8e7aed1b;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 9527692..ec372ba 100644
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -11,7 +11,7 @@
  */
 
 #include "command.hpp"
-#include "treemap.h"
+#include "counttable.h"
 #include "sharedutilities.h"
 #include "tree.h"
 
@@ -25,19 +25,20 @@ class PhyloDiversityCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "phylo.diversity";			}
 		string getCommandCategory()		{ return "Hypothesis Testing";		}
-		string getOutputFileNameTag(string, string);
+		
 	string getHelpString();	
+    string getOutputPattern(string);	
 		string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
 		string getDescription()		{ return "phylo.diversity"; }
 
 		int execute();
 		void help() { m->mothurOut(getHelpString()); }
 private:
-		TreeMap* tmap;
+		CountTable* ct;
 		float freq;
 		int iters, processors, numUniquesInName;  
 		bool abort, rarefy, summary, collect, scale;
-		string groups, outputDir, treefile, groupfile, namefile;
+		string groups, outputDir, treefile, groupfile, namefile, countfile;
 		vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
 		
         map<string, int> getRootForGroups(Tree* t);