1.18.1

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 0824ebf7f7e6cd109db4d3adb344c46d09738b21..9f10f375660be529a2b2b53e6a87745d426bba19 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -25,7 +25,7 @@ class ListVector;
 
 class TreeMap {
 public:
-       TreeMap() {};
+       TreeMap() { m = MothurOut::getInstance(); }
        TreeMap(string);
        ~TreeMap();
        void readMap();
@@ -36,12 +36,13 @@ public:
        bool isValidGroup(string);  //return true if string is a valid group
        void removeSeq(string);  //removes a sequence, this is to accomadate trees that do not contain all the seqs in your groupfile
        string getGroup(string);
+       void addSeq(string, 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, vector index>
        void print(ostream&);
-       void makeSim(GroupMap*);  //takes groupmap info and fills treemap for use by tree.shared command.
+       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.   
        
 private:
@@ -51,6 +52,7 @@ private:
        map<string, GroupIndex>::iterator it;
        map<string, int>::iterator it2;
        void setNamesOfGroups(string); 
+       MothurOut* m;
        
        
 };