X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=8f744c80a3e92873699aca320032cedeea59a007;hb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;hp=60f75b388571aff503ac95b96df5946e6fcfa89f;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/treemap.h b/treemap.h
index 60f75b3..8f744c8 100644
--- a/treemap.h
+++ b/treemap.h
@@ -9,11 +9,9 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#include "mothur.h"
+#include "groupmap.h"
+#include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
 
@@ -22,7 +20,8 @@ struct GroupIndex {
 	int		vectorIndex;
 };
 
-
+class GroupMap;
+class ListVector;
 
 class TreeMap {
 public:
@@ -34,12 +33,15 @@ public:
 	int getNumSeqs();
 	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
 	string getGroup(string);
 	vector<string> namesOfGroups;
 	vector<string> namesOfSeqs;
     map<string,int> seqsPerGroup;	//groupname, number of seqs in that group.
-	map<string, GroupIndex> treemap; //sequence name and groupname
+	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;
@@ -49,6 +51,7 @@ private:
 	map<string, int>::iterator it2;
 	void setNamesOfGroups(string); 
 	
+	
 };
 
 #endif