X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=treegroupscommand.h;h=10a2e31c88ea6a177b55a6a2e8f19f99d07e520d;hp=3c40eff6ab95c0dcb12e931e5f785f30654243db;hb=b22853b5cfbf5c47949ad2a084f2fad88b2e4be4;hpb=bdb56fb93c1f0acfb8fa6542ebc444a0701c1f5a

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3c40eff..10a2e31 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -11,15 +11,12 @@
  */
  
 #include "command.hpp"
-#include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
-#include "sharedutilities.h"
 
 
 /* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups. 
@@ -37,10 +34,9 @@ public:
 	
 private:
 	void createTree();
-	void printSims();
+	void printSims(ostream&);
 	
 	GlobalData* globaldata;
-	SharedUtil* util;
 	ReadOTUFile* read;
 	TreeMap* tmap;
 	Tree* t;
@@ -49,11 +45,10 @@ private:
 	map<int, int> index;  //maps row in simMatrix to vector index in the tree	
 	InputData* input;
 	ValidCalculators* validCalculator;
-	SharedListVector* SharedList;
-	SharedOrderVector* order;
 	vector<SharedRAbundVector*> lookup;
 	string format, outputFile, groupNames;
 	int numGroups;
+	ofstream out;
 
 };