#include <RaaSpeciesTree.h>
Public Member Functions | |
int | findNode (const std::string &taxon, bool allowsynonym=false) |
Returns the database rank of a taxon identified by its name. | |
int | findNode (int tid) |
Returns the database rank of a taxon identified by a TID. | |
std::string | getName (int rank) |
Returns the name of a taxon identified by its database rank. | |
int | parent (int rank) |
Returns the database rank of the parent of a taxon in the tree. | |
int | getTid (int rank) |
Returns the TID of a taxon. | |
int | count (int rank) |
Returns the number of sequences attached to a taxon or to taxa below it in the species tree. | |
std::string | label (int rank) |
Returns the label of a taxon of given rank. | |
int | firstChild (int rank) |
Returns the rank of the first child taxon of a given taxon. | |
int | nextChild (int parent, int child) |
Allows to loop around all child taxa of a given taxon. | |
bool | isChild (int parent, int child) |
Tells whether there is a downward path from taxon parent to taxon child in the species tree. | |
int | nextSynonym (int rank) |
Allows to loop around all synonymous taxa of a given taxon. | |
int | getMajor (int rank) |
Gives the major taxon among all synonyms of a given taxon. | |
Friends | |
class | RAA |
The tree can be walked up or down starting from a string, a database species rank, or an NCBI taxonID (TID) value. The species tree also contains synonymous names. The root of the tree is named "ROOT" and has database rank 2.
int RaaSpeciesTree::count | ( | int | rank | ) |
Returns the number of sequences attached to a taxon or to taxa below it in the species tree.
rank | The database rank of a taxon. |
int RaaSpeciesTree::findNode | ( | int | tid | ) |
Returns the database rank of a taxon identified by a TID.
tid | A TID value. |
int bpp::RaaSpeciesTree::findNode | ( | const std::string & | taxon, | |
bool | allowsynonym = false | |||
) |
Returns the database rank of a taxon identified by its name.
taxon | A taxon name. Case is not significant. | |
allowsynonym | If true, the return value will give the synonym's rank rather than the rank of its major taxon. |
int RaaSpeciesTree::firstChild | ( | int | rank | ) |
Returns the rank of the first child taxon of a given taxon.
rank | The database rank of a taxon. |
int RaaSpeciesTree::getMajor | ( | int | rank | ) |
Gives the major taxon among all synonyms of a given taxon.
rank | The database rank of a taxon. |
string RaaSpeciesTree::getName | ( | int | rank | ) |
Returns the name of a taxon identified by its database rank.
rank | The database rank of a taxon. |
int RaaSpeciesTree::getTid | ( | int | rank | ) |
Returns the TID of a taxon.
rank | The database rank of a taxon. |
bool RaaSpeciesTree::isChild | ( | int | parent, | |
int | child | |||
) |
Tells whether there is a downward path from taxon parent to taxon child in the species tree.
parent | The database rank of a taxon. | |
child | The database rank of another taxon. |
string RaaSpeciesTree::label | ( | int | rank | ) |
Returns the label of a taxon of given rank.
Labels may contain taxon common names, genetic code information, TID values, and taxonomic level information (e.g., genus, order).
rank | The database rank of a taxon. |
int RaaSpeciesTree::nextChild | ( | int | parent, | |
int | child | |||
) |
Allows to loop around all child taxa of a given taxon.
parent | The database rank of a taxon. | |
child | The database rank of a child of taxon of rank parent. |
int RaaSpeciesTree::nextSynonym | ( | int | rank | ) |
Allows to loop around all synonymous taxa of a given taxon.
Synonymous taxa of a taxon are chained in a closed loop, among which only one, the major taxon, has a parent taxon.
rank | The database rank of a taxon. |
int RaaSpeciesTree::parent | ( | int | rank | ) |
Returns the database rank of the parent of a taxon in the tree.
rank | The database rank of a taxon. |