X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;fp=unifracunweightedcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=fd39ae43852bee7ad970d77035fa839c50f62422;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
deleted file mode 100644
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--- a/unifracunweightedcommand.h
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-#ifndef UNIFRACUNWEIGHTEDCOMMAND_H
-#define UNIFRACUNWEIGHTEDCOMMAND_H
-
-/*
- *  unifracunweightedcommand.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 2/9/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "unweighted.h"
-#include "treemap.h"
-#include "sharedutilities.h"
-#include "fileoutput.h"
-#include "readtree.h"
-
-class UnifracUnweightedCommand : public Command {
-	
-	public:
-		UnifracUnweightedCommand(string);	
-		UnifracUnweightedCommand();
-		~UnifracUnweightedCommand() {}
-	
-		vector<string> setParameters();
-		string getCommandName()			{ return "unifrac.unweighted";		}
-		string getCommandCategory()		{ return "Hypothesis Testing";		}
-		string getHelpString();	
-		string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
-		string getDescription()		{ return "generic tests that describes whether two or more communities have the same structure"; }
-
-		int execute();
-		void help() { m->mothurOut(getHelpString()); }
-	
-	
-	private:
-		FileOutput* output;
-		vector<Tree*> T;	   //user trees
-		TreeMap* tmap;
-		string sumFile, allGroups;
-		vector<string> groupComb; // AB. AC, BC...
-		int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
-		vector< vector<float> > utreeScores; //scores for users trees for each comb.
-		vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
-		map<float, float>  validScores;  //map contains scores from random
-		vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
-		vector< map<float, float> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
-		
-		bool abort, phylip, random, includeRoot, consensus, subsample;
-		string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
-		vector<string> Groups, outputNames; //holds groups to be used
-
-		ofstream outSum, out;
-		ifstream inFile;
-		
-        int runRandomCalcs(Tree*, vector<double>);
-		void printUWSummaryFile(int);
-		void printUnweightedFile();
-		void createPhylipFile(int);
-        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
-        int getConsensusTrees(vector< vector<double> >&, int);
-        int getAverageSTDMatrices(vector< vector<double> >&, int);
-		
-};
-
-#endif