X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;h=95276921149b5237a923928bc9f23a5e8e7aed1b;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=0aafb8dbc53305a327f7a2b825a2b9c74df8bdb9;hpb=515c3398ea27e2105f616fc5662b2a7ceb486aa0;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 0aafb8d..9527692 100644
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -12,27 +12,42 @@
 
 #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;  
-		bool abort, rarefy;
-		string groups, outputDir;
+		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
 		
-		void printData(set<int>&, map< string, vector<float> >&, string);
-		float calcBranchLength(Tree*, int);
+        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);
+        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&);
+
 };
 
 #endif