Bio::DB::GFF::TypenameUser Contributed Perl DocumentaBio::DB::GFF::Typename(3)NAMEBio::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);
DESCRIPTIONBio::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.
perl v5.14.1 2011-07-22 Bio::DB::GFF::Typename(3)