Reference

Bio::DB::GFF::Typename(3pm)

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 <[email protected]>.

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.

History