Bio::DB::GFF::Typename.3pm

Langue: en

Autres versions - même langue

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::DB::GFF::Typename -- The name of a feature type

SYNOPSIS

   use Bio::DB::GFF;
 
   my $type = Bio::DB::GFF::Typename->new(similarity => 'BLAT_EST_GENOME');
   my $segment = $segment->features($type);

DESCRIPTION

Bio::DB::GFF::Typename objects encapsulate the combination of feature method and source used by the GFF flat file format. They can be used in the Bio::DB::GFF modules wherever a feature type is called for.

Since there are relatively few types and many features, this module maintains a memory cache of unique types so that two features of the same type will share the same Bio::DB::GFF::Typename object.

METHODS

new

  Title   : new
  Usage   : $type = Bio::DB::GFF::Typename->new($method,$source)
  Function: create a new Bio::DB::GFF::Typename object
  Returns : a new Bio::DB::GFF::Typename object
  Args    : method and source
  Status  : Public

method

  Title   : method
  Usage   : $method = $type->method([$newmethod])
  Function: get or set the method
  Returns : a method name
  Args    : new method name (optional)
  Status  : Public

source

  Title   : source
  Usage   : $source = $type->source([$newsource])
  Function: get or set the source
  Returns : a source name
  Args    : new source name (optional)
  Status  : Public

asString

  Title   : asString
  Usage   : $string = $type->asString
  Function: get the method and source as a string
  Returns : a string in "method:source" format
  Args    : none
  Status  : Public

This method is used by operator overloading to overload the '""' operator.

clone

  Title   : clone
  Usage   : $new_clone = $type->clone;
  Function: clone this object
  Returns : a new Bio::DB::GFF::Typename object
  Args    : none
  Status  : Public

This method creates an exact copy of the object.

match

  Title   : match
  Usage   : $boolean = $type->match($type_or_string)
  Function: fuzzy match on types
  Returns : a flag indicating that the argument matches the object
  Args    : a Bio::DB::GFF::typename object, or a string in method:source format
  Status  : Public

This match allows Sequence:Link and Sequence: to match, but not Sequence:Link and Sequence:Genomic_canonical.

BUGS

This module is still under development.

SEE ALSO

bioperl, Bio::DB::GFF, Bio::DB::RelSegment

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.