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.