vector<string> setParameters();
string getCommandName() { return "classify.tree"; }
string getCommandCategory() { return "Phylotype Analysis"; }
vector<string> setParameters();
string getCommandName() { return "classify.tree"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- ReadTree* read;
- TreeMap* tmap;
- string treefile, taxonomyfile, groupfile, namefile, outputDir;
+ string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
string getTaxonomy(set<string>, int&);
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
string getTaxonomy(set<string>, int&);