changes while testing

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index fc9c3690fef8900ad3484147ae3fa0487a514b73..7ffd1e7003154d672d544aa8a993f371a7f9a28a 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,6 @@
  */
 
 #include "mothur.h"
-#include "groupmap.h"
 #include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
@@ -20,19 +19,18 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-class GroupMap;
-class ListVector;
-
 class TreeMap {
 public:
        TreeMap() { m = MothurOut::getInstance(); }
        TreeMap(string);
        ~TreeMap();
+    
        int readMap();
+    int readMap(string);
        int getNumGroups();
        int getNumSeqs();
-       void setIndex(string, int);  //sequencename, index
-       int getIndex(string);           //returns vector index of sequence
+       //void setIndex(string, int);  //sequencename, index
+       //int getIndex(string);         //returns vector index of sequence
        bool isValidGroup(string);  //return true if string is a valid group
        void removeSeq(string);  //removes a sequence, this is to accomadate trees that do not contain all the seqs in your groupfile
        string getGroup(string);
@@ -48,7 +46,7 @@ public:
        void makeSim(ListVector*);  //takes listvector info and fills treemap for use by tree.shared command.   
     vector<string> getNamesSeqs();
        vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
-    int getCopy(TreeMap*);
+    int getCopy(TreeMap&);
     
     vector<string> namesOfSeqs;
     map<string,int> seqsPerGroup;      //groupname, number of seqs in that group.