X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=7ed8d04f0886367f5a17a5baeec4848e75687358;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=d4b506e6fb1d26675937f89f2cc1591e21a98c07;hpb=e03de8796670a0c747aed63483daa09c8b86aea0;p=mothur.git

diff --git a/treemap.h b/treemap.h
index d4b506e..7ed8d04 100644
--- 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;