void addSeqToTree(string, string);
void assignHeirarchyIDs(int);
void print(ofstream&);
- vector<int> getGenusNodes();
- TaxNode get(int i) { return tree[i]; }
+ vector<int> getGenusNodes();
+ void binUnclassified();
+
+ TaxNode get(int i) { return tree[i]; }
TaxNode get(string seqName) { return tree[name2Taxonomy[seqName]]; }
- int getIndex(string seqName) { return name2Taxonomy[seqName]; }
- string getName(int i) { return tree[i].name; }
+ int getIndex(string seqName) { return name2Taxonomy[seqName]; }
+ string getName(int i) { return tree[i].name; }
+ string getFullTaxonomy(string); //pass a sequence name return taxonomy
+ int getMaxLevel() { return maxLevel; }
+
private:
string getNextTaxon(string&);
vector<TaxNode> tree;
void print(int, ofstream&);
int numNodes;
int numSeqs;
+ int maxLevel;
};
/**************************************************************************************************/