started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 0dc74eec2fad5ebc157b4fd12e63a7b8b37c967a..12299731f89e10741926cd797fad2a02ed267c2d 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,7 @@
  */
 
 #include "mothur.h"
-#include "utilities.hpp"
+#include "groupmap.h"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -19,7 +19,7 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-
+class GroupMap;
 
 class TreeMap {
 public:
@@ -38,6 +38,8 @@ 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.groups command.
+       
        
 private:
        ifstream fileHandle;
@@ -47,6 +49,7 @@ private:
        map<string, int>::iterator it2;
        void setNamesOfGroups(string); 
        
+       
 };
 
 #endif