Bio::Graphics::FeatureBase.3pm

Langue: en

Version: 2008-06-24 (ubuntu - 08/07/09)

Section: 3 (Bibliothèques de fonctions)

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.