Bio::Graphics Feature
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel
Package variables
No package variables defined.
Inherit
Bio::Graphics::FeatureBase
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:
 $feature = Bio::Graphics::Feature->new(@args);
This method creates a new feature object. You can create a simple
feature that contains no subfeatures, or a hierarchically nested object.
Arguments are as follows:
  -seq_id      the reference sequence
-start the start position of the feature
-end the stop position of the feature
-stop an alias for end
-name the feature name (returned by seqname())
-type the feature type (returned by primary_tag())
-primary_tag the same as -type
-source the source tag
-score the feature score (for GFF compatibility)
-desc a description of the feature
-segments a list of subfeatures (see below)
-subtype the type to use when creating subfeatures
-strand the strand of the feature (one of -1, 0 or +1)
-phase the phase of the feature (0..2)
-id an alias for -name
-seqname an alias for -name
-display_id an alias for -name
-display_name an alias for -name (do you get the idea the API has changed?)
-primary_id unique database ID
-url a URL to link to when rendered with Bio::Graphics
-configurator an object (like a Bio::Graphics::FeatureFile) that knows how
to configure the graphical representation of the object based
on its type.
-attributes a hashref of tag value attributes, in which the key is the tag
and the value is an array reference of values
-factory a reference to a feature factory, used for compatibility with
more obscure parts of Bio::DB::GFF
The subfeatures passed in -segments may be an array of
Bio::Graphics::Feature objects, or an array of [$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". 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!)
    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.
Methods
new
No description
Code
factoryDescriptionCode
configuratorDescriptionCode
urlDescriptionCode
make_linkDescriptionCode
Methods description
factorycode    nextTop
 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
configuratorcodeprevnextTop
 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.
urlcodeprevnextTop
 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_linkcodeprevnextTop
 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.
Methods code
newdescriptionprevnextTop
sub new {
  my $self = shift->SUPER::new(@_);

  my %arg = @_;
  for my $option (qw(factory configurator)) {
    $self->{$option} = $arg{"-$option"} if exists $arg{"-$option"};
  }
  $self;
}
factorydescriptionprevnextTop
sub factory {
  my $self = shift;
  my $d = $self->{factory};
  $self->{factory} = shift if @_;
  $d;
}
configuratordescriptionprevnextTop
sub configurator {
  my $self = shift;
  my $d = $self->{configurator};
  $self->{configurator} = shift if @_;
  $d;
}
urldescriptionprevnextTop
sub url {
  my $self = shift;
  my $d = $self->{url};
  $self->{url} = shift if @_;
  $d;
}
make_linkdescriptionprevnextTop
sub make_link {
  my $self = shift;

  if (my $url = $self->url) {
    return $url;
  }

  elsif (my $configurator = $self->configurator) {
    return $configurator->make_link($self) if $configurator->can('make_link');
  }

  else {
    return;
  }
}
General documentation
display_nameTop
 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_numberTop
 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
alphabetTop
 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 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
descTop
 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
locationTop
 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_stringTop
 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.
SEE ALSOTop
Bio::Graphics::Panel,Bio::Graphics::Glyph, Bio::Graphics::FeatureBase
GD
AUTHORTop
Lincoln Stein <lstein@cshl.org>.
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.