added count file to chimera.uchime. found issue with uchime program that indicated...

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index d3c1b3e47615fb6d3b342c8d41758aa7b9d9178a..6790afb73984377c1aba8f6488a3cf1c2e544280 100644 (file)
--- 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;