added mothur.h and fixed includes in many files

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 60f75b388571aff503ac95b96df5946e6fcfa89f..0dc74eec2fad5ebc157b4fd12e63a7b8b37c967a 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -9,10 +9,7 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
+#include "mothur.h"
 #include "utilities.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
@@ -34,11 +31,12 @@ 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&);
        
 private: