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

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
deleted file mode 100644 (file)
index 9deb065..0000000
--- a/unifracweightedcommand.h
+++ /dev/null
@@ -1,83 +0,0 @@
-#ifndef UNIFRACWEIGHTEDCOMMAND_H
-#define UNIFRACWEIGHTEDCOMMAND_H
-
-/*
- *  unifracweightedcommand.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 2/9/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "weighted.h"
-#include "treemap.h"
-#include "progress.hpp"
-#include "sharedutilities.h"
-#include "fileoutput.h"
-#include "readtree.h"
-
-class UnifracWeightedCommand : public Command {
-       
-       public:
-               UnifracWeightedCommand(string);
-               UnifracWeightedCommand();
-               ~UnifracWeightedCommand() {}
-       
-               vector<string> setParameters();
-               string getCommandName()                 { return "unifrac.weighted";            }
-               string getCommandCategory()             { return "Hypothesis Testing";          }
-               string getHelpString(); 
-               string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
-               string getDescription()         { return "generic tests that describes whether two or more communities have the same structure"; }
-
-               int execute();
-               void help() { m->mothurOut(getHelpString()); }
-       
-       private:
-               struct linePair {
-                       int start;
-                       int num;
-                       linePair(int i, int j) : start(i), num(j) {}
-               };
-               vector<linePair> lines;
-        TreeMap* tmap;
-               FileOutput* output;
-               vector<Tree*> T;           //user trees
-               vector<double> utreeScores;  //user tree unweighted scores
-               vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
-               vector<string> groupComb; // AB. AC, BC...
-               string sumFile, outputDir;
-               int iters, numGroups, numComp, counter;
-               vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
-               vector< vector<double> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
-               vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
-               vector< map<float, float> > rCumul;  //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c                                                                
-               map<float, float>  validScores;  //map contains scores from random
-               
-               bool abort, phylip, random, includeRoot, subsample, consensus;
-               string groups, itersString, outputForm, treefile, groupfile, namefile;
-               vector<string> Groups, outputNames; //holds groups to be used
-               int processors, subsampleSize, subsampleIters;
-               ofstream outSum;
-               map<string, string> nameMap;
-               
-               void printWSummaryFile();
-               void printWeightedFile();  
-               void createPhylipFile();
-               //void removeValidScoresDuplicates();
-               int findIndex(float, int);
-               void calculateFreqsCumuls();
-               int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
-               int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
-        int runRandomCalcs(Tree*, vector<double>);
-        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
-        int getConsensusTrees(vector< vector<double> >&, int);
-        int getAverageSTDMatrices(vector< vector<double> >&, int);
-               
-};
-
-
-
-#endif