X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=7ffd1e7003154d672d544aa8a993f371a7f9a28a;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=fc9c3690fef8900ad3484147ae3fa0487a514b73;hpb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63;p=mothur.git

diff --git a/treemap.h b/treemap.h
index fc9c369..7ffd1e7 100644
--- 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.