X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;h=f5e205c4e40ce010239c0cc8beba6798e1a17aa4;hb=af27acb766f6947c45e1eb65438d878c7ea48ef3;hp=8dd569bbcf567d1990465a2c17bf62ed4ad55831;hpb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 8dd569b..f5e205c 100644
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -18,7 +18,12 @@ class PhyloDiversityCommand : public Command {
 	
 	public:
 		PhyloDiversityCommand(string);
+		PhyloDiversityCommand();
 		~PhyloDiversityCommand();
+		vector<string> getRequiredParameters();
+		vector<string> getValidParameters();
+		vector<string> getRequiredFiles();
+		map<string, vector<string> > getOutputFiles() { return outputTypes; }
 		int execute();	
 		void help();
 	
@@ -26,12 +31,18 @@ class PhyloDiversityCommand : public Command {
 		GlobalData* globaldata;
 		
 		float freq;
-		int iters;  
-		bool abort, rarefy;
+		int iters, processors;  
+		bool abort, rarefy, summary, collect, scale;
 		string groups, outputDir;
 		vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
+		map<string, vector<string> > outputTypes;
 		
-		void printData(vector<int>&, vector< vector<float> >&, string);
+		void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
+		void printSumData(map< string, vector<float> >&, ofstream&, int);
+		vector<float> calcBranchLength(Tree*, int, map< string, set<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