X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;h=ee76f05697cfce07213857432c9d786b150fc033;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=95276921149b5237a923928bc9f23a5e8e7aed1b;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 9527692..ee76f05 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"
 
@@ -33,11 +33,11 @@ class PhyloDiversityCommand : public Command {
 		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);