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08 Jan 2020 20:41:58 UTC
- Distribution: Bio-DB-GFF
- Module version: 1.7.4
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Bus factor: 2- License: perl_5
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- Dependencies
- Apache::DBI
- Bio::Annotation::Collection
- Bio::DB::BioFetch
- Bio::DB::Fasta
- Bio::DB::GFF::Util::Binning
- Bio::DB::GFF::Util::Rearrange
- Bio::Das::FeatureTypeI
- Bio::Das::SegmentI
- Bio::DasI
- Bio::Location::Simple
- Bio::Location::Split
- Bio::LocationI
- Bio::PrimarySeq
- Bio::RangeI
- Bio::Root::Root
- Bio::Root::RootI
- Bio::Root::Version
- Bio::SeqFeatureI
- Bio::SeqI
- Bio::SeqIO
- CGI
- Carp
- DBI
- DB_File
- Data::Dumper
- Digest::MD5
- Exporter
- Fcntl
- File::Basename
- File::Glob
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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.
Module Install Instructions
To install Bio::DB::GFF, copy and paste the appropriate command in to your terminal.
cpanm Bio::DB::GFF
perl -MCPAN -e shell install Bio::DB::GFF
For more information on module installation, please visit the detailed CPAN module installation guide.