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; }
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);
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;