X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotree.h;h=4b7a35a24547b155c857f140496b6cc03654c66d;hp=7aae8f1adedcf5f1db6b94d1bbe76a968a8e3100;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/phylotree.h b/phylotree.h
index 7aae8f1..4b7a35a 100644
--- a/phylotree.h
+++ b/phylotree.h
@@ -44,8 +44,9 @@ public:
 	TaxNode get(int i);				
 	TaxNode get(string seqName);
 	string getName(int i);			
-	int getIndex(string seqName);	
+	int getGenusIndex(string seqName);	
 	string getFullTaxonomy(string);	 //pass a sequence name return taxonomy
+    vector<string> getSeqs(string);	 //returns names of sequences in given taxonomy
 	
 	int getMaxLevel()		{	return maxLevel;	}
 	int getNumSeqs()		{	return numSeqs;		}
@@ -63,7 +64,8 @@ private:
 	vector<int> genusIndex; //holds the indexes in tree where the genus level taxonomies are stored
 	vector<int> totals; //holds the numSeqs at each genus level taxonomy
 	map<string, int> name2Taxonomy;  //maps name to index in tree
-	map<int, int> uniqueTaxonomies;  //map of unique taxonomies
+    map<string, int> name2GenusNodeIndex;
+	set<int> uniqueTaxonomies;  //map of unique taxonomies
 	map<int, int> leafNodes; //used to create static reference taxonomy file
 	//void print(int, ofstream&);
 	int numNodes;