Provided by: libbio-perl-perl_1.7.2-3_all bug

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 implementation, 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.