Bio::SeqFeature::Lite(3pm)				User Contributed Perl Documentation				Bio::SeqFeature::Lite(3pm)

NAME

       Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class

SYNOPSIS

	# create a simple feature with no internal structure
	$f = Bio::SeqFeature::Lite->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::SeqFeature::Lite->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::SeqFeature::Lite->new(-start=>1,-stop=>100,-type=>'exon');
	$e2 = Bio::SeqFeature::Lite->new(-start=>150,-stop=>200,-type=>'exon');
	$e3 = Bio::SeqFeature::Lite->new(-start=>300,-stop=>500,-type=>'exon');
	$f  = Bio::SeqFeature::Lite->new(-segments=>[$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::SeqFeature::Lite->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)
	 -seq	      a dna or protein sequence string to attach to feature
	 -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
	 -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::SeqFeature::Lite 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:

       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.

       segments()
	   An alias for sub_SeqFeature().

       get_SeqFeatures()
	   Alias for sub_SeqFeature()

       get_all_SeqFeatures()
	   Alias for sub_SeqFeature()

       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!)

   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

   refseq
	Title	: refseq
	Usage	: $ref = $s->refseq([$newseq] [,$newseqclass])
	Function: get/set reference sequence
	Returns : current reference sequence
	Args	: new reference sequence and class (optional)
	Status	: Public

       This method will get or set the reference sequence.  Called with no arguments, it returns the current reference sequence.  Called with any
       Bio::SeqFeatureI object that provides the seq_id(), start(), end() and strand() methods.

       The method will generate an exception if you attempt to set the reference sequence to a sequence that has a different seq_id from the
       current feature.

SEE ALSO

       Bio::Graphics::Feature

AUTHOR

       Lincoln Stein <lstein@cshl.edu>.

       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.

perl v5.14.2							    2012-03-02						Bio::SeqFeature::Lite(3pm)