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Bio::Graphics::FeatureUser Contributed Perl DocumentaBio::Graphics::Feature(3)

NAME
       Bio::Graphics::Feature - A simple feature object for use with
       Bio::Graphics::Panel

SYNOPSIS
	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');

DESCRIPTION
       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:

	 -seq_id      the reference sequence
	 -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())
	 -primary_tag the same as -type
	 -source      the source tag
	 -score	      the feature score (for GFF compatibility)
	 -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)
	 -phase	      the phase of the feature (0..2)
	 -id	      an alias for -name
	 -seqname     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?)
	 -primary_id  unique database ID
	 -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:

       attributes()
	   An alternative interface to get_tag_values. Pass the name of an
	   attribute to get the value(s) of that attribute:

	      $expression_level = $gene->attributes('expression');

	   Call attributes() without any arguments to get a hash of all
	   attributes:

	     %attributes = $gene->attributes;

       url()
	   Get/set the URL that the graphical rendering of this feature will
	   link to.

       add_segment(@segments)
	   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.

       my @features = get_SeqFeatures('type1','type2','type3'...)
	   Get the subfeatures of this feature. If an optional list of types
	   is provided, then only returns subfeatures with the indicated
	   primary_tag. (This is an extension of the Bio::SeqFeatureI
	   interface).

       $feature->add_hit($hit)
	   For nucleotide alignments, add a feature that is a "hit" on the
	   feature.

       $hit = $feature->hit
	   Return the hit.

       segments()
	   An alias for get_SeqFeatures().

       get_all_SeqFeatures()
	   Alias for get_SeqFeatures()

       merged_segments()
	   Another alias for sub_SeqFeature().

       stop()
	   An alias for end().

       name()
	   An alias for seqname().

       exons()
	   An alias for sub_SeqFeature() (you don't want to know why!)

       configurator()
	   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

   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.

   configurator
	Title	: configurator
	Usage	: my $configurator = $seqfeature->configurator([$new_configurator])
	Function: Get/set an object that provides configuration information for this feature
	Returns : configurator object
	Args	: new configurator object (optional)

       A configurator object provides hints to the Bio::Graphics::Feature as
       to how to display itself on a canvas. Currently this stores the
       Bio::Graphics::FeatureFile and descendents.

   url
	Title	: url
	Usage	: my $url = $seqfeature->url([$new_url])
	Function: Get/set the URL associated with this feature
	Returns : a URL string
	Args	: new URL (optional)

       Features link to URLs when displayed as a clickable image map. This
       field holds that information.

   make_link
	Title	: make_link
	Usage	: my $url = $seqfeature->make_link()
	Function: Create a URL for the feature
	Returns : a URL string
	Args	: none

       This method will invoke the configurator in order to turn the feature
       into a link. Used by Bio::Graphics::Panel to create imagemaps.

SEE ALSO
       Bio::Graphics::Panel,Bio::Graphics::Glyph, Bio::Graphics::FeatureBase
       GD

AUTHOR
       Lincoln Stein <lstein@cshl.edu>.

       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.

perl v5.14.1			  2011-07-22	     Bio::Graphics::Feature(3)
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