major change to the tree class to use the count table class instead of tree map....

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 95276921149b5237a923928bc9f23a5e8e7aed1b..ee76f05697cfce07213857432c9d786b150fc033 100644 (file)
--- 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);