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[mothur.git] / 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