X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotree.h;h=e0002209e4d83aaaf9468573173858d9b0602b61;hp=a961721a77dad0f32624aa1ff7941651007fc757;hb=615301e57c25e241356a9c2380648d117709458d;hpb=62568a297aaf939ab753334f17abde82ec8e8531

diff --git a/phylotree.h b/phylotree.h
index a961721..e000220 100644
--- a/phylotree.h
+++ b/phylotree.h
@@ -44,15 +44,17 @@ 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
-	int getMaxLevel()				{	return maxLevel;						}
-	int getNumSeqs()  {  return numSeqs;  }
+	
+	int getMaxLevel()		{	return maxLevel;	}
+	int getNumSeqs()		{	return numSeqs;		}
+	int getNumNodes()		{	return tree.size();	}
+	
 	bool ErrorCheck(vector<string>);
 	
 private:
-	string getNextTaxon(string&);
+	string getNextTaxon(string&, string);
 	void print(ofstream&, vector<TaxNode>&); //used to create static reference taxonomy file
 	void fillOutTree(int, vector<TaxNode>&); //used to create static reference taxonomy file
 	void binUnclassified(string);
@@ -61,7 +63,8 @@ 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;