added subsample and consensus parameters to unifrac.weighted command

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index 244348ef1f52d3768a585e1960fd0d1b20424d49..fc9c3690fef8900ad3484147ae3fa0487a514b73 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -37,15 +37,26 @@ public:
        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 addGroup(string s) { setNamesOfGroups(s); }
+       vector<string> getNamesOfGroups() {
+               sort(namesOfGroups.begin(), namesOfGroups.end());
+               return namesOfGroups;
+       }
+    
+    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;
        string groupFileName;
        int numGroups;