X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;h=95276921149b5237a923928bc9f23a5e8e7aed1b;hb=44f3a3c81a34fdee62550d98838a4b421e8df08e;hp=7d4b2d89484a88e4bc5016f19e2e24c89ab07a4e;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 7d4b2d8..9527692 100644
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -12,28 +12,39 @@
 
 #include "command.hpp"
 #include "treemap.h"
-#include "globaldata.hpp"
+#include "sharedutilities.h"
+#include "tree.h"
 
 class PhyloDiversityCommand : public Command {
 	
 	public:
 		PhyloDiversityCommand(string);
-		~PhyloDiversityCommand();
-		int execute();	
-		void help();
+		PhyloDiversityCommand();
+		~PhyloDiversityCommand(){}
 	
-	private:
-		GlobalData* globaldata;
-		
+		vector<string> setParameters();
+		string getCommandName()			{ return "phylo.diversity";			}
+		string getCommandCategory()		{ return "Hypothesis Testing";		}
+		string getOutputFileNameTag(string, string);
+	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:
+		TreeMap* tmap;
 		float freq;
-		int iters, processors;  
+		int iters, processors, numUniquesInName;  
 		bool abort, rarefy, summary, collect, scale;
-		string groups, outputDir;
+		string groups, outputDir, treefile, groupfile, namefile;
 		vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
 		
+        map<string, int> getRootForGroups(Tree* t);
+		int readNamesFile();
 		void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
 		void printSumData(map< string, vector<float> >&, ofstream&, int);
-		float calcBranchLength(Tree*, int, map< string, set<int> >&);
+        vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, int>);
 		int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
 		int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);