added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
index d4b506e6fb1d26675937f89f2cc1591e21a98c07..7ed8d04f0886367f5a17a5baeec4848e75687358 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
@@ -37,15 +37,20 @@ 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;
+       void addGroup(string s) { setNamesOfGroups(s); }
+       vector<string> getNamesOfGroups() {
+               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 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:
+       vector<string> namesOfGroups;
        ifstream fileHandle;
        string groupFileName;
        int numGroups;