X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=6790afb73984377c1aba8f6488a3cf1c2e544280;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=d3c1b3e47615fb6d3b342c8d41758aa7b9d9178a;hpb=82723a54e6109e2d46d84c10e87727cebd5a18ea;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index d3c1b3e..6790afb 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -19,7 +19,6 @@
 #include "readmatrix.hpp"
 #include "readcolumn.h"
 #include "readphylip.h"
-#include "sparsematrix.hpp"
 #include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
@@ -69,8 +68,6 @@
 	They can also use as many or as few calculators as they wish. */
 	
 
-typedef list<PCell>::iterator MatData;
-
 class TreeGroupCommand : public Command {
 	
 public:
@@ -81,6 +78,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "tree.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
 	string getDescription()		{ return "generate a tree file that describes the dissimilarity among groups"; }
@@ -100,12 +98,10 @@ private:
 	Tree* createTree(vector< vector<double> >&);
 	void printSims(ostream&, vector< vector<double> >&);
 	int makeSimsShared();
-	vector< vector<double> > makeSimsDist();
+	vector< vector<double> > makeSimsDist(SparseDistanceMatrix*);
     int writeTree(string, Tree*);
     int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
 	
-	ReadMatrix* readMatrix;
-	SparseMatrix* matrix;
 	NameAssignment* nameMap;
 	ListVector* list;
 	TreeMap* tmap;