added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index b44e6caed27037ddb177acdd1416df40550dee5c..5d0cccf249099ac51d86b58e41e5098793ef3f3c 100644 (file)
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -12,9 +12,8 @@
 
 #include "command.hpp"
 #include "treemap.h"
-#include "readtree.h"
 #include "sharedutilities.h"
-
+#include "tree.h"
 
 class PhyloDiversityCommand : public Command {
        
@@ -33,14 +32,12 @@ class PhyloDiversityCommand : public Command {
                int execute();
                void help() { m->mothurOut(getHelpString()); }
 private:
-               ReadTree* read;
                TreeMap* tmap;
                float freq;
                int iters, processors, numUniquesInName;  
                bool abort, rarefy, summary, collect, scale;
                string groups, outputDir, treefile, groupfile, namefile;
                vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
-               map<string, string> nameMap;
                
                int readNamesFile();
                void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);