X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;fp=phylodiversitycommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=5d0cccf249099ac51d86b58e41e5098793ef3f3c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
deleted file mode 100644
index 5d0cccf..0000000
--- a/phylodiversitycommand.h
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef PHYLODIVERSITYCOMMAND_H
-#define PHYLODIVERSITYCOMMAND_H
-
-/*
- *  phylodiversitycommand.h
- *  Mothur
- *
- *  Created by westcott on 4/30/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "treemap.h"
-#include "sharedutilities.h"
-#include "tree.h"
-
-class PhyloDiversityCommand : public Command {
-	
-	public:
-		PhyloDiversityCommand(string);
-		PhyloDiversityCommand();
-		~PhyloDiversityCommand(){}
-	
-		vector<string> setParameters();
-		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:
-		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
-		
-		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, 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
-