X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=1c67c32f81afb2535943934ab82d66629bbc05b2;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=e1ebd16c6151e373eb86971f53295d2036b4e4c2;hpb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index e1ebd16..1c67c32 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -12,7 +12,7 @@
 
 #include "command.hpp"
 #include "weighted.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
@@ -28,7 +28,9 @@ class UnifracWeightedCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "unifrac.weighted";		}
 		string getCommandCategory()		{ return "Hypothesis Testing";		}
-		string getHelpString();	
+		
+	string getHelpString();	
+    string getOutputPattern(string);	
 		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"; }
 
@@ -42,15 +44,12 @@ class UnifracWeightedCommand : public Command {
 			linePair(int i, int j) : start(i), num(j) {}
 		};
 		vector<linePair> lines;
-		
-		ReadTree* read;
-		SharedUtil* util;
+        CountTable* ct;
 		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;
 		string sumFile, outputDir;
 		int iters, numGroups, numComp, counter;
 		vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
@@ -60,9 +59,9 @@ class UnifracWeightedCommand : public Command {
 		map<float, float>  validScores;  //map contains scores from random
 		
 		bool abort, phylip, random, includeRoot, subsample, consensus;
-		string groups, itersString, outputForm, treefile, groupfile, namefile;
+		string groups, itersString, outputForm, treefile, groupfile, namefile, countfile;
 		vector<string> Groups, outputNames; //holds groups to be used
-		int processors, numUniquesInName, subsampleSize, subsampleIters;
+		int processors, subsampleSize, subsampleIters;
 		ofstream outSum;
 		map<string, string> nameMap;
 		
@@ -74,10 +73,8 @@ 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>);
-        int readTrees();
-        vector<Tree*> buildTrees(vector< vector<double> >&, int, TreeMap*);
+        vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
         int getConsensusTrees(vector< vector<double> >&, int);
         int getAverageSTDMatrices(vector< vector<double> >&, int);