added modify names parameter to set.dir

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 3e6d8354af5eda2c21f85c632a09b886962afb37..3961e53cb68c96e70dd5bcd55449ed5d72346cd9 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -12,50 +12,58 @@
 
 #include "command.hpp"
 #include "unweighted.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "sharedutilities.h"
 #include "fileoutput.h"
-
-
-class GlobalData;
+#include "readtree.h"
 
 class UnifracUnweightedCommand : public Command {
        
        public:
                UnifracUnweightedCommand(string);       
-               ~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
+               UnifracUnweightedCommand();
+               ~UnifracUnweightedCommand() {}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "unifrac.unweighted";          }
+               string getCommandCategory()             { return "Hypothesis Testing";          }
+               
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               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();    
+               void help() { m->mothurOut(getHelpString()); }
+       
        
        private:
-               GlobalData* globaldata;
-               SharedUtil* util;
                FileOutput* output;
                vector<Tree*> T;           //user trees
-               TreeMap* tmap;
-               Unweighted* unweighted;
+               CountTable* ct;
                string sumFile, allGroups;
                vector<string> groupComb; // AB. AC, BC...
-               int iters, numGroups, numComp, counter, processors;
-               EstOutput userData;                     //unweighted score info for user tree
-               EstOutput randomData;           //unweighted score info for random trees
+               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;
-               string groups, itersString, outputDir;
+               bool abort, phylip, random, includeRoot, consensus, subsample;
+               string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
                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, CountTable&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
                
 };