/ 
ONTO-PERL-1.25
River stage zero No dependents
/ OBO::XO::OBO_ID_Term_Map

NAME

OBO::XO::OBO_ID_Term_Map - A map between OBO IDs and term names.

SYNOPSIS

use OBO::XO::OBO_ID_Term_Map;

$obo_id_set = OBO_ID_Term_Map->new();

$obo_id_set->file("gene_ontology.ids");

$file = $obo_id_set->file();

$size = $obo_id_set->size();

$obo_id_set->file("OBO");

if ($obo_id_set->add("OBO:0007049")) { ... }

$new_id = $obo_id_set->get_new_id("GO");

DESCRIPTION

The OBO::XO::OBO_ID_Term_Map class implements a map for storing OBO IDs and their corresponding names.

AUTHOR

Erick Antezana, <erick.antezana -@- gmail.com>

COPYRIGHT AND LICENSE

Copyright (C) 2006, 2007, 2008, 2009, 2010 by Erick Antezana

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.

put

Usage    - $map->put("GO:0007049", "cell cycle")
Returns  - the size of map
Args     - OBO id (string), term name (string)
Function - either puts a new entry in the map or modifies an existing entry by changing the term name
Remark   - prior to adding new entries to the map, use method get_new_id()

get_new_id

Usage    - $map->get_new_id("GO", "cell cycle")
Returns  - a new OBO ID (string)
Args     - idspace (string), term (string)
Function - get a new OBO ID and insert it (put) into this map

get_term_by_id

Usage    - $map->get_term_by_id($obo_id)
Returns  - the term name (string) associated to the given OBO id
Args     - an OBO id (string)
Function - the term name associated to the given OBO id

get_id_by_term

Usage    - $map->get_id_by_term($term_name)
Returns  - the OBO id associated to the given term name
Args     - a term name (string)
Function - the term associated to the given term

keys_set

Usage    - $map->keys_set()
Returns  - the keys (or OBO ids)
Args     - none
Function - the keys (or OBO ids)

values_set

Usage    - $map->values_set()
Returns  - the values (or terms names)
Args     - none
Function - the keys (or terms names)

contains_key

Usage    - $map->contains_key($k)
Returns  - 1 (true) or 0 (false)
Args     - a key or OBO id
Function - 1 (true) or 0 (false)

contains_value

Usage    - $map->contains_value($v)
Returns  - 1 (true) or 0 (false)
Args     - a value or term
Function - 1 (true) or 0 (false)

equals

Usage    - $map->equals($other_map)
Returns  - 1 (true) or 0 (false)
Args     - another map
Function - compares two maps and tells whether they are identical or not

size

Usage    - $map->size()
Returns  - the size of this map
Args     - none
Function - the size of this map

file

Usage    - $map->file()
Returns  - the file of this map
Args     - none
Function - the file of this map

clear

Usage    - $map->clear()
Returns  - clears this map
Args     - none
Function - clears this map

is_empty

Usage    - $map->is_empty()
Returns  - 1 (true) or 0 (false)
Args     - none
Function - tells if this map is empty

write_map

Usage    - $map->write_map()
Returns  - none
Args     - none
Function - prints the contents of the map to the file associated to this object

remove_by_key

Usage    - $map->remove_by_key('OBO:B0000001')
Returns  - the value corresponding to the given key that will be eventually removed
Args     - the key (OBO ID as string) of the entry to be removed (string)
Function - removes one entry  from the map