forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index cd8d51dcad76a44dbc0ca064bd79a5ef3e0fbe80..fd39ae43852bee7ad970d77035fa839c50f62422 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -36,36 +36,32 @@ class UnifracUnweightedCommand : public Command {
        
        
        private:
-               ReadTree* read;
-               SharedUtil* util;
                FileOutput* output;
                vector<Tree*> T;           //user trees
                TreeMap* tmap;
-               Unweighted* unweighted;
                string sumFile, allGroups;
                vector<string> groupComb; // AB. AC, BC...
-               int iters, numGroups, numComp, counter, processors, numUniquesInName;
-               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, includeRoot;
+               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;
-               map<string, string> nameMap;
                
+        int runRandomCalcs(Tree*, vector<double>);
                void printUWSummaryFile(int);
                void printUnweightedFile();
                void createPhylipFile(int);
-               int readNamesFile();
-                
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
                
 };