NAME
Bio::Graphics::FeatureBase - Base class for Bio::Graphics::Feature
SYNOPSIS
See Bio::Graphics::Feature for full synopsis.
DESCRIPTION
This is the base class for Bio::Graphics::Feature. It has all the methods of Bio::Graphics::Feature except for those that are required to interface with Bio::Graphics::FeatureFile, namely factory(), configurator(), url(), and make_link(). Please see Bio::Graphics::Feature for full documentation.
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
location_string
Title : location_string
Usage : my $string = $seqfeature->location_string()
Function: Returns a location string in a format recognized by gbrowse
Returns : a string
Args : none
This is a convenience function used by the generic genome browser. It returns the location of the feature and its subfeatures in the compact form "start1..end1,start2..end2,...". Use $seqfeature->location()->toFTString() to obtain a standard GenBank/EMBL location representation.
clone
Title : clone
Usage : my $feature = $seqfeature->clone
Function: Create a deep copy of the feature
Returns : A copy of the feature
Args : none
SEE ALSO
Bio::Graphics::Feature, Bio::Graphics::FeatureFile, Bio::Graphics::Panel,Bio::Graphics::Glyph, GD
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2006 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.