added subsample and consensus parameters to unifrac.weighted command

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index b1db317de0add4b28352315e20dc282110fad789..e1ebd16c6151e373eb86971f53295d2036b4e4c2 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -51,21 +51,18 @@ class UnifracWeightedCommand : public Command {
                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...
                TreeMap* tmap;
-               Weighted* weighted;
                string sumFile, outputDir;
                int iters, numGroups, numComp, counter;
-               EstOutput userData;                     //weighted score info for user tree
-               EstOutput randomData;           //weighted score info for random trees
                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;
+               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, numUniquesInName;
+               int processors, numUniquesInName, subsampleSize, subsampleIters;
                ofstream outSum;
                map<string, string> nameMap;
                
@@ -78,6 +75,11 @@ class UnifracWeightedCommand : public Command {
                int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
                int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
                int readNamesFile();
+        int runRandomCalcs(Tree*, vector<double>);
+        int readTrees();
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap*);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
                
 };