X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=9deb065b21da66b0bd83ef50d6d7d457e750025a;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=b1db317de0add4b28352315e20dc282110fad789;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index b1db317..9deb065 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -42,30 +42,24 @@ class UnifracWeightedCommand : public Command {
 			linePair(int i, int j) : start(i), num(j) {}
 		};
 		vector<linePair> lines;
-		
-		ReadTree* read;
-		SharedUtil* util;
+        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...
-		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, subsampleSize, subsampleIters;
 		ofstream outSum;
 		map<string, string> nameMap;
 		
@@ -77,7 +71,10 @@ class UnifracWeightedCommand : public Command {
 		void calculateFreqsCumuls();
 		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>);
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap&);
+        int getConsensusTrees(vector< vector<double> >&, int);
+        int getAverageSTDMatrices(vector< vector<double> >&, int);
 		
 };