X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;h=5d0cccf249099ac51d86b58e41e5098793ef3f3c;hb=f67ace597e7147f3ca35201e3623abe6440a9d24;hp=df04b35d66f1c0dc36893074f6c840711395c49b;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index df04b35..5d0cccf 100644
--- 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 {
 	
@@ -27,18 +26,18 @@ class PhyloDiversityCommand : public Command {
 		string getCommandName()			{ return "phylo.diversity";			}
 		string getCommandCategory()		{ return "Hypothesis Testing";		}
 		string getHelpString();	
-	
+		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:
-		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);