Bio::Graphics::FeatureBase(3)

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.