Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => 'transcript', -name => 'alpha-1 antitrypsin', -desc => 'an enzyme inhibitor', ); # create a feature composed of multiple segments, all of type "similarity" $f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]], -name => 'ABC-3', -type => 'gapped_alignment', -subtype => 'similarity'); # build up a gene exon by exon $e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>'exon'); $e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>'exon'); $e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>'exon'); $f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>'gene'); This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing. All methods are as described in Bio::SeqFeatureI with the following additions:

The new() Constructor
$feature = Bio::Graphics::Feature->new(@args); This method creates a new feature object. You can create a simple feature that contains no subfeatures, or a hierarchically nested object. Arguments are as follows: -start the start position of the feature -end the stop position of the feature -stop an alias for end -name the feature name (returned by seqname()) -type the feature type (returned by primary_tag()) -source the source tag -desc a description of the feature -segments a list of subfeatures (see below) -subtype the type to use when creating subfeatures -strand the strand of the feature (one of -1, 0 or +1) -id an alias for -name -seqname an alias for -name -primary_id an alias for -name -display_id an alias for -name -display_name an alias for -name (do you get the idea the API has changed?) -url a URL to link to when rendered with Bio::Graphics -configurator an object (like a Bio::Graphics::FeatureFile) that knows how to configure the graphical representation of the object based on its type. -attributes a hashref of tag value attributes, in which the key is the tag and the value is an array reference of values -factory a reference to a feature factory, used for compatibility with more obscure parts of Bio::DB::GFF The subfeatures passed in -segments may be an array of Bio::Graphics::Feature objects, or an array of [$start,$stop] pairs. Each pair should be a two-element array reference. In the latter case, the feature type passed in -subtype will be used when creating the subfeatures. If no feature type is passed, then it defaults to "feature".

Non-SeqFeatureI methods
A number of new methods are provided for compatibility with Ace::Sequence, which has a slightly different API from SeqFeatureI: Get/set the URL that the graphical rendering of this feature will link to. Add one or more segments (a subfeature). Segments can either be Feature objects, or [start,stop] arrays, as in the -segments argument to new(). The feature endpoints are automatically adjusted. An alias for sub_SeqFeature(). Alias for sub_SeqFeature() Alias for sub_SeqFeature() Another alias for sub_SeqFeature(). An alias for end(). An alias for seqname(). An alias for sub_SeqFeature() (you don't want to know why!) Get/set the configurator that knows how to adjust the graphical representation of this feature based on its type. Currently the only configurator that will work is Bio::Graphics::FeatureFile.

factory
Title : factory Usage : $factory = $obj->factory([$new_factory]) Function: Returns the feature factory from which this feature was generated. Mostly for compatibility with weird dependencies in gbrowse. Returns : A feature factory Args : None

display_name
Title : display_name Usage : $id = $obj->display_name or $obj->display_name($newid); Function: Gets or sets the display id, also known as the common name of the Seq object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the LOCUS field of the GenBank/EMBL databanks and the ID field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience issues. Returns : A string Args : None or a new id

accession_number
Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implemetation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None

alphabet
Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called <type> because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none Status : Virtual

desc
Title : desc Usage : $seqobj->desc($string) or $seqobj->desc() Function: Sets or gets the description of the sequence Example : Returns : The description Args : The description or none

location
Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none Bio::Graphics::Panel,Bio::Graphics::Glyph, GD 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. See DISCLAIMER.txt for disclaimers of warranty.