moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
deleted file mode 100644 (file)
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
-