#
# BioPerl module for Bio::SeqFeature::FeaturePair
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
=head1 SYNOPSIS
my $feat = Bio::SeqFeature::FeaturePair->new(
-feature1 => $f1,
-feature2 => $f2,
);
# Bio::SeqFeatureI methods can be used
my $start = $feat->start;
my $end = $feat->end;
# Bio::FeaturePair methods can be used
my $hstart = $feat->hstart;
my $hend = $feat->hend;
my $feature1 = $feat->feature1; # returns feature1 object
=head1 DESCRIPTION
A sequence feature object where the feature is itself a feature on
another sequence - e.g. a blast hit where residues 1-40 of a protein
sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence
HS120G22. The genomic sequence coordinates are used to create one
sequence feature $f1 and the protein coordinates are used to create
feature $f2. A FeaturePair object can then be made
my $fp = Bio::SeqFeature::FeaturePair->new(
-feature1 => $f1, # genomic
-feature2 => $f2, # protein
);
This object can be used as a standard Bio::SeqFeatureI in which case
my $gstart = $fp->start # returns start coord on feature1 - genomic seq.
my $gend = $fp->end # returns end coord on feature1.
In general standard Bio::SeqFeatureI method calls return information
in feature1.
Data in the feature 2 object are generally obtained using the standard
methods prefixed by h (for hit!)
my $pstart = $fp->hstart # returns start coord on feature2 = protein seq.
my $pend = $fp->hend # returns end coord on feature2.
If you wish to swap feature1 and feature2 around :
$feat->invert
so...
$feat->start # etc. returns data in $feature2 object
No sub_SeqFeatures or tags can be stored in this object directly. Any
features or tags are expected to be stored in the contained objects
feature1, and feature2.
=head1 CONTACT
Ewan Birney E<lt>birney@sanger.ac.ukE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqFeature::FeaturePair;
use vars qw($AUTOLOAD);
use strict;
use Bio::SeqFeatureI;
use Bio::Factory::ObjectFactory;
use base qw(Bio::SeqFeature::Generic);
=head2 new
Title : new
Usage :
Function: Constructor for this module. Accepts the following parameters:
-feature1 Bio::SeqFeatureI-compliant object
-feature2 Bio::SeqFeatureI-compliant object
-feature_factory Bio::Factory::ObjectFactoryI compliant
object to be used when feature1 and/or feature2
are accessed without explicitly set before. This
is mostly useful for derived classes who want to
set their preferred class for feature objects.
Example :
Returns :
Args : see above
=cut
sub new {
my ($class, @args) = @_;
#
# We've got a certain problem here that somewhat relates to chicken and
# eggs. The problem is, we override a lot of SeqFeatureI methods here
# to delegate them to either feature1 or feature2. If we pass along
# those attributes right away, we need feature1 or feature2 or the feature
# factory in place, or there is no way around the dreaded default, which
# is ugly too (as it necessitates subsequent copying if you wanted a
# different feature object class).
#
# So I decided to go with the lesser of two evils here: we need to assume
# here that we can set all attributes through set_attributes(), which we
# assume is no different from setting them through the constructor. This
# gives us a window to set the feature objects and the factory, such that
# any derived class doesn't have to worry about this any more.
#
# I'm happy to hear a better solution, but I think this one isn't so bad.
#
my $self = $class->SUPER::new();
my ($feature1,$feature2,$featfact) =
$self->_rearrange([qw( FEATURE1
FEATURE2
FEATURE_FACTORY )],@args);
$self->_register_for_cleanup(\&cleanup_fp);
# initialize the feature object factory if not provided
if(! $featfact) {
$featfact = Bio::Factory::ObjectFactory->new(
-type => "Bio::SeqFeature::Generic",
-interface => "Bio::SeqFeatureI"
);
}
$self->feature_factory($featfact);
# Store the features in the object
$feature1 && $self->feature1($feature1);
$feature2 && $self->feature2($feature2);
# OK. Now we're setup to store all the attributes, and they'll go right
# away into the right objects.
$self->set_attributes(@args);
# done - we hope
return $self;
}
=head2 feature1
Title : feature1
Usage : $f = $featpair->feature1
$featpair->feature1($feature)
Function: Get/set for the query feature
Returns : Bio::SeqFeatureI
Args : Bio::SeqFeatureI
=cut
sub feature1 {
my ($self,$arg) = @_;
if ( defined($arg) || !defined $self->{'feature1'} ) {
$self->throw("internal error: feature factory not set!")
unless $self->feature_factory;
$arg = $self->feature_factory->create_object() unless( defined $arg);
$self->throw("Argument [$arg] must be a Bio::SeqFeatureI")
unless (ref($arg) && $arg->isa("Bio::SeqFeatureI"));
$self->{'feature1'} = $arg;
}
return $self->{'feature1'};
}
=head2 feature2
Title : feature2
Usage : $f = $featpair->feature2
$featpair->feature2($feature)
Function: Get/set for the hit feature
Returns : Bio::SeqFeatureI
Args : Bio::SeqFeatureI
=cut
sub feature2 {
my ($self,$arg) = @_;
if ( defined($arg) || ! defined $self->{'feature2'}) {
$self->throw("internal error: feature factory not set!")
unless $self->feature_factory;
$arg = $self->feature_factory->create_object() unless( defined $arg);
$self->throw("Argument [$arg] must be a Bio::SeqFeatureI")
unless (ref($arg) && $arg->isa("Bio::SeqFeatureI"));
$self->{'feature2'} = $arg;
}
return $self->{'feature2'};
}
=head2 start
Title : start
Usage : $start = $featpair->start
$featpair->start(20)
Function: Get/set on the start coordinate of feature1
Returns : integer
Args : [optional] beginning of feature
=cut
sub start {
return shift->feature1->start(@_);
}
=head2 end
Title : end
Usage : $end = $featpair->end
$featpair->end($end)
Function: get/set on the end coordinate of feature1
Returns : integer
Args : [optional] ending point of feature
=cut
sub end {
return shift->feature1->end(@_);
}
=head2 strand
Title : strand
Usage : $strand = $feat->strand()
$feat->strand($strand)
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : [optional] strand information to set
=cut
sub strand {
return shift->feature1->strand(@_);
}
=head2 location
Title : location
Usage : $location = $featpair->location
$featpair->location($location)
Function: Get/set location object (using feature1)
Returns : Bio::LocationI object
Args : [optional] LocationI to store
=cut
sub location {
return shift->feature1->location(@_);
}
=head2 score
Title : score
Usage : $score = $feat->score()
$feat->score($score)
Function: get/set on score information
Returns : float
Args : none if get, the new value if set
=cut
sub score {
return shift->feature1->score(@_);
}
=head2 frame
Title : frame
Usage : $frame = $feat->frame()
$feat->frame($frame)
Function: get/set on frame information
Returns : 0,1,2
Args : none if get, the new value if set
=cut
sub frame {
return shift->feature1->frame(@_);
}
=head2 primary_tag
Title : primary_tag
Usage : $ptag = $featpair->primary_tag
Function: get/set on the primary_tag of feature1
Returns : 0,1,2
Args : none if get, the new value if set
=cut
sub primary_tag {
return shift->feature1->primary_tag(@_);
}
=head2 source_tag
Title : source_tag
Usage : $tag = $feat->source_tag()
$feat->source_tag('genscan');
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
=cut
sub source_tag {
return shift->feature1->source_tag(@_);
}
=head2 seqname
Title : seqname
Usage : $obj->seq_id($newval)
Function: There are many cases when you make a feature that you
do know the sequence name, but do not know its actual
sequence. This is an attribute such that you can store
the seqname.
This attribute should *not* be used in GFF dumping, as
that should come from the collection in which the seq
feature was found.
Returns : value of seqname
Args : newvalue (optional)
=cut
sub seq_id {
return shift->feature1->seq_id(@_);
}
=head2 hseqname
Title : hseqname
Usage : $featpair->hseqname($newval)
Function: Get/set method for the name of
feature2.
Returns : value of $feature2->seq_id
Args : newvalue (optional)
=cut
sub hseq_id {
return shift->feature2->seq_id(@_);
}
=head2 hstart
Title : hstart
Usage : $start = $featpair->hstart
$featpair->hstart(20)
Function: Get/set on the start coordinate of feature2
Returns : integer
Args : none
=cut
sub hstart {
return shift->feature2->start(@_);
}
=head2 hend
Title : hend
Usage : $end = $featpair->hend
$featpair->hend($end)
Function: get/set on the end coordinate of feature2
Returns : integer
Args : none
=cut
sub hend {
return shift->feature2->end(@_);
}
=head2 hstrand
Title : hstrand
Usage : $strand = $feat->strand()
$feat->strand($strand)
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : none
=cut
sub hstrand {
return shift->feature2->strand(@_);
}
=head2 hscore
Title : hscore
Usage : $score = $feat->score()
$feat->score($score)
Function: get/set on score information
Returns : float
Args : none if get, the new value if set
=cut
sub hscore {
return shift->feature2->score(@_);
}
=head2 hframe
Title : hframe
Usage : $frame = $feat->frame()
$feat->frame($frame)
Function: get/set on frame information
Returns : 0,1,2
Args : none if get, the new value if set
=cut
sub hframe {
return shift->feature2->frame(@_);
}
=head2 hprimary_tag
Title : hprimary_tag
Usage : $ptag = $featpair->hprimary_tag
Function: Get/set on the primary_tag of feature2
Returns : 0,1,2
Args : none if get, the new value if set
=cut
sub hprimary_tag {
return shift->feature2->primary_tag(@_);
}
=head2 hsource_tag
Title : hsource_tag
Usage : $tag = $feat->hsource_tag()
$feat->source_tag('genscan');
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
=cut
sub hsource_tag {
return shift->feature2->source_tag(@_);
}
=head2 invert
Title : invert
Usage : $tag = $feat->invert
Function: Swaps feature1 and feature2 around
Returns : Nothing
Args : none
=cut
sub invert {
my ($self) = @_;
my $tmp = $self->feature1;
$self->feature1($self->feature2);
$self->feature2($tmp);
return 1;
}
=head2 feature_factory
Title : feature_factory
Usage : $obj->feature_factory($newval)
Function: Get/set the feature object factory for this feature pair.
The feature object factory will be used to create a feature
object if feature1() or feature2() is called in get mode
without having been set before.
The default is an instance of Bio::Factory::ObjectFactory
and hence allows the type to be changed dynamically at any
time.
Example :
Returns : The feature object factory in use (a
Bio::Factory::ObjectFactoryI compliant object)
Args : on set, a Bio::Factory::ObjectFactoryI compliant object
=cut
sub feature_factory {
my $self = shift;
return $self->{'feature_factory'} = shift if @_;
return $self->{'feature_factory'};
}
#################################################################
# aliases for backwards compatibility #
#################################################################
# seqname() is already aliased in Generic.pm, and we overwrite seq_id
sub hseqname {
my $self = shift;
$self->warn("SeqFeatureI::seqname() is deprecated. Please use seq_id() instead.");
return $self->hseq_id(@_);
}
sub cleanup_fp {
my $self = shift;
$self->{'feature1'} = $self->{'feature2'} = undef;
}
1;