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.

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq