X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=979612f4aea3aa41187ea520483afadfa05b1782;hb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;hp=d3c1b3e47615fb6d3b342c8d41758aa7b9d9178a;hpb=bb8d942036365d2a66330944269f17841ed2388a;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index d3c1b3e..979612f 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -15,11 +15,10 @@
 #include "groupmap.h"
 #include "validcalculator.h"
 #include "tree.h"
-#include "treemap.h"
+#include "counttable.h"
 #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:
@@ -81,7 +78,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "tree.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
 	string getDescription()		{ return "generate a tree file that describes the dissimilarity among groups"; }
 
@@ -100,21 +99,19 @@ 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;
+	CountTable* ct;
 	Tree* t;
     InputData* input;
 	vector<Calculator*> treeCalculators;
 	vector<SharedRAbundVector*> lookup;
 	string lastLabel;
-	string format, groupNames, filename, sharedfile, inputfile;
+	string format, groupNames, filename, sharedfile, countfile, inputfile;
 	int numGroups, subsampleSize, iters, processors;
 	ofstream out;
 	float precision, cutoff;