- void print(ofstream&);
- vector<int> getGenusNodes();
- 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; }
+ void printTreeNodes(string); //used by bayesian to save time
+ vector<int> getGenusNodes();
+ vector<int> getGenusTotals();
+ void setUp(string); //used to create file needed for summary file if you use () constructor and add seqs manually instead of passing taxonomyfile
+
+ TaxNode get(int i);
+ TaxNode get(string seqName);
+ string getName(int i);
+ int getIndex(string seqName);
+
+ string getFullTaxonomy(string); //pass a sequence name return taxonomy
+ int getMaxLevel() { return maxLevel; }
+ int getNumSeqs() { return numSeqs; }
+ bool ErrorCheck(vector<string>);
+