added count.groups command and paralellized align.seqs for windows

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index d4b506e6fb1d26675937f89f2cc1591e21a98c07..244348ef1f52d3768a585e1960fd0d1b20424d49 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -28,7 +28,7 @@ public:
        TreeMap() { m = MothurOut::getInstance(); }
        TreeMap(string);
        ~TreeMap();
-       void readMap();
+       int readMap();
        int getNumGroups();
        int getNumSeqs();
        void setIndex(string, int);  //sequencename, index
@@ -42,7 +42,7 @@ 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.
+       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: