working on adding count file to mgcluster

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 7ed8d04f0886367f5a17a5baeec4848e75687358..57822e02d4b8c3a57f7d0ddf26947c470bf9400b 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -10,7 +10,6 @@
  */
 
 #include "mothur.h"
-#include "groupmap.h"
 #include "listvector.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
@@ -20,15 +19,14 @@ struct GroupIndex {
        int             vectorIndex;
 };
 
-class GroupMap;
-class ListVector;
-
 class TreeMap {
 public:
        TreeMap() { m = MothurOut::getInstance(); }
        TreeMap(string);
        ~TreeMap();
+    
        int readMap();
+    int readMap(string);
        int getNumGroups();
        int getNumSeqs();
        void setIndex(string, int);  //sequencename, index
@@ -42,13 +40,19 @@ public:
                sort(namesOfGroups.begin(), namesOfGroups.end());
                return namesOfGroups;
        }
-       vector<string> namesOfSeqs;
-    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 print(ostream&);
        void makeSim(vector<string>);  //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.   
-       
+    vector<string> getNamesSeqs();
+       vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
+    int getCopy(TreeMap&);
+    
+    vector<string> namesOfSeqs;
+    map<string,int> seqsPerGroup;      //groupname, number of seqs in that group.
+       map<string, GroupIndex> treemap; //sequence name and <groupname, vector index>
+
+    
 private:
        vector<string> namesOfGroups;
        ifstream fileHandle;