added get.repseqs command, started matrix output command

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3c40eff6ab95c0dcb12e931e5f785f30654243db..10a2e31c88ea6a177b55a6a2e8f19f99d07e520d 100644 (file)
--- 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;
 
 };