X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=unifracunweightedcommand.h;h=3961e53cb68c96e70dd5bcd55449ed5d72346cd9;hp=fd39ae43852bee7ad970d77035fa839c50f62422;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=b3296231bac975d0c655bd62075909786a23e270

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index fd39ae4..3961e53 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -12,7 +12,7 @@
 
 #include "command.hpp"
 #include "unweighted.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "sharedutilities.h"
 #include "fileoutput.h"
 #include "readtree.h"
@@ -27,7 +27,9 @@ class UnifracUnweightedCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "unifrac.unweighted";		}
 		string getCommandCategory()		{ return "Hypothesis Testing";		}
-		string getHelpString();	
+		
+	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"; }
 
@@ -38,7 +40,7 @@ class UnifracUnweightedCommand : public Command {
 	private:
 		FileOutput* output;
 		vector<Tree*> T;	   //user trees
-		TreeMap* tmap;
+		CountTable* ct;
 		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
 		int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
@@ -49,7 +51,7 @@ class UnifracUnweightedCommand : public Command {
 		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, consensus, subsample;
-		string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile;
+		string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
 		vector<string> Groups, outputNames; //holds groups to be used
 
 		ofstream outSum, out;
@@ -59,7 +61,7 @@ class UnifracUnweightedCommand : public Command {
 		void printUWSummaryFile(int);
 		void printUnweightedFile();
 		void createPhylipFile(int);
-        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);