/usr/include/Bpp/Raa/RaaSpeciesTree.h is in libbpp-raa-dev 2.2.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 | #ifndef _RAASPECIESTREE_H_
#define _RAASPECIESTREE_H_
extern "C" {
#include "RAA_acnuc.h"
}
#include <string>
namespace bpp {
/**
* @brief To work with the species tree classification of the database.
*
* 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.
*/
class RaaSpeciesTree {
friend class RAA;
public:
/**
* @brief Returns the database rank of a taxon identified by its name.
*
* @param taxon A taxon name. Case is not significant.
* @param allowsynonym If true, the return value will give the synonym's rank rather than the rank of its
* major taxon.
* @return The database rank of this taxon, or 0 if no such taxon exists in tree.
*/
int findNode(const std::string &taxon, bool allowsynonym = false);
/**
* @brief Returns the database rank of a taxon identified by a TID.
*
* @param tid A TID value.
* @return The database rank of this taxon, or 0 if no such taxon exists in tree.
*/
int findNode(int tid);
/**
* @brief Returns the name of a taxon identified by its database rank.
*
* @param rank The database rank of a taxon.
* @return The name of this taxon.
*/
std::string getName(int rank);
/**
* @brief Returns the database rank of the parent of a taxon in the tree.
*
* @param rank The database rank of a taxon.
* @return The database rank of the parent of this taxon in the tree, or 0 if no such taxon exists in tree.
*/
int parent(int rank);
/**
* @brief Returns the TID of a taxon.
*
* @param rank The database rank of a taxon.
* @return The TID of this taxon, or 0 if no such taxon exists in tree.
*/
int getTid(int rank);
/**
* @brief Returns the number of sequences attached to a taxon or to taxa below it in the species tree.
*
* @param rank The database rank of a taxon.
* @return The number of sequences attached to this taxon or to taxa below it, or 0 if no such taxon exists in tree.
*/
int count(int rank);
/**
* @brief 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).
* @param rank The database rank of a taxon.
* @return The label of this taxon, or "" if no such taxon or label exists in tree.
*/
std::string label(int rank);
/**
* @brief Returns the rank of the first child taxon of a given taxon.
*
* @param rank The database rank of a taxon.
* @return The rank of its first child taxon, or 0 if no child taxon exists in tree.
*/
int firstChild(int rank);
/**
* @brief Allows to loop around all child taxa of a given taxon.
*
* @param parent The database rank of a taxon.
* @param child The database rank of a child of taxon of rank parent.
* @return The rank of the next child taxon of parent after taxon child, or 0 if no more child taxon exists in tree.
*/
int nextChild(int parent, int child);
/**
* @brief Tells whether there is a downward path from taxon parent to taxon child in the species tree.
*
* @param parent The database rank of a taxon.
* @param child The database rank of another taxon.
* @return true iff child is below parent (possibly with intermediate nodes) in the species tree.
*/
bool isChild(int parent, int child);
/**
* @brief 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.
*
* @param rank The database rank of a taxon.
* @return The rank of the next synonymous taxon, or 0 if taxon rank has no synonymous taxon.
*/
int nextSynonym(int rank);
/**
* @brief Gives the major taxon among all synonyms of a given taxon.
*
* @param rank The database rank of a taxon.
* @return The rank of the major taxon of taxon rank (can be itself).
*/
int getMajor(int rank);
private:
raa_db_access *raa_data;
raa_node **sp_tree;
int *tid_to_rank;
int max_tid;
int max_sp;
};
} //namespace bpp.
#endif // _RAASPECIESTREE_H_
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