broke up globaldata and moved error checking and help into commands

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 941ca9a8f79e4de463f99719d6ffd37fe7733961..8f744c80a3e92873699aca320032cedeea59a007 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,8 @@
  */
 
 #include "mothur.h"
-#include "utilities.hpp"
+#include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -19,7 +20,8 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-
+class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
@@ -38,7 +40,8 @@ public:
     map<string,int> seqsPerGroup;      //groupname, number of seqs in that group.
        map<string, GroupIndex> treemap; //sequence name and <groupname, vector index>
        void print(ostream&);
-       
+       void makeSim(GroupMap*);  //takes groupmap info and fills treemap for use by tree.shared command.
+       void makeSim(ListVector*);  //takes listvector info and fills treemap for use by tree.shared command.   
        
 private:
        ifstream fileHandle;