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

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
deleted file mode 100644 (file)
index fd39ae4..0000000
--- a/unifracunweightedcommand.h
+++ /dev/null
@@ -1,68 +0,0 @@
-#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