Erick Antezana > ONTO-PERL > OBO::XO::OBO_ID_Term_Map

Download:
ONTO-PERL/ONTO-PERL-1.44.tar.gz

Dependencies

Annotate this POD

CPAN RT

Open  0
View/Report Bugs
Source  

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), seed_id (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

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', 'cel cycle');

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) 2006-2014 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.

syntax highlighting: