added get.repseqs command, started matrix output command

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 60fb924278c8df36a405ca363c2584d5ae2fa42a..73d02fcc4b0c58f29de00c130e3fa8a197dd3d53 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -9,11 +9,8 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "groupmap.h"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -22,7 +19,7 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-
+class GroupMap;
 
 class TreeMap {
 public:
@@ -41,6 +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.shared command.
+       
        
 private:
        ifstream fileHandle;
@@ -50,6 +49,7 @@ private:
        map<string, int>::iterator it2;
        void setNamesOfGroups(string); 
        
+       
 };
 
 #endif