changing command name classify.shared to classifyrf.shared

[mothur.git] / phylotree.h

diff --git a/phylotree.h b/phylotree.h
index 50bbb1dd86f3148e10110e3f10407ce754a30766..e0002209e4d83aaaf9468573173858d9b0602b61 100644 (file)
--- a/phylotree.h
+++ b/phylotree.h
@@ -44,7 +44,7 @@ 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;        }
@@ -54,7 +54,7 @@ public:
        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);
@@ -63,7 +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;