X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.h;h=d4b506e6fb1d26675937f89f2cc1591e21a98c07;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=8f744c80a3e92873699aca320032cedeea59a007;hpb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;p=mothur.git

diff --git a/treemap.h b/treemap.h
index 8f744c8..d4b506e 100644
--- 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();
@@ -34,7 +34,9 @@ public:
 	void setIndex(string, int);  //sequencename, index
 	int getIndex(string);		//returns vector index of sequence
 	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.
@@ -50,6 +52,7 @@ private:
 	map<string, GroupIndex>::iterator it;
 	map<string, int>::iterator it2;
 	void setNamesOfGroups(string); 
+	MothurOut* m;
 	
 	
 };