Raw content of Bio::SeqFeature::PositionProxy
<![CDATA[# $Id: PositionProxy.pm,v 1.4 2002/10/22 07:38:41 lapp Exp $
#
# BioPerl module for Bio::SeqFeature::PositionProxy
#
# Cared for by Ewan Birney <birney@ebi.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::PositionProxy - handle features when truncation/revcom sequences span a feature
=head1 SYNOPSIS
$proxy = new Bio::SeqFeature::PositionProxy ( -loc => $loc,
-parent => $basefeature);
$seq->add_SeqFeature($feat);
=head1 DESCRIPTION
PositionProxy is a Proxy Sequence Feature to handle truncation
and revcomp without duplicating all the data within the sequence features.
It holds a new location for a sequence feature and the original feature
it came from to provide the additional annotation information.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Ewan Birney E<lt>birney@sanger.ac.ukE<gt>
=head1 DEVELOPERS
This class has been written with an eye out of inheritence. The fields
the actual object hash are:
_gsf_tag_hash = reference to a hash for the tags
_gsf_sub_array = reference to an array for sub arrays
_gsf_start = scalar of the start point
_gsf_end = scalar of the end point
_gsf_strand = scalar of the strand
=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::PositionProxy;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::SeqFeatureI;
use Bio::Tools::GFF;
@ISA = qw(Bio::Root::Root Bio::SeqFeatureI);
sub new {
my ($caller, @args) = @_;
my $self = $caller->SUPER::new(@args);
my ($feature,$location) = $self->_rearrange([qw(PARENT LOC)],@args);
if( !defined $feature || !ref $feature || !$feature->isa('Bio::SeqFeatureI') ) {
$self->throw("Must have a parent feature, not a [$feature]");
}
if( $feature->isa("Bio::SeqFeature::PositionProxy") ) {
$feature = $feature->parent();
}
if( !defined $location || !ref $location || !$location->isa('Bio::LocationI') ) {
$self->throw("Must have a location, not a [$location]");
}
return $self;
}
=head2 location
Title : location
Usage : my $location = $seqfeature->location()
Function: returns a location object suitable for identifying location
of feature on sequence or parent feature
Returns : Bio::LocationI object
Args : none
=cut
sub location {
my($self, $value ) = @_;
if (defined($value)) {
unless (ref($value) and $value->isa('Bio::LocationI')) {
$self->throw("object $value pretends to be a location but ".
"does not implement Bio::LocationI");
}
$self->{'_location'} = $value;
}
elsif (! $self->{'_location'}) {
# guarantees a real location object is returned every time
$self->{'_location'} = Bio::Location::Simple->new();
}
return $self->{'_location'};
}
=head2 parent
Title : parent
Usage : my $sf = $proxy->parent()
Function: returns the seqfeature parent of this proxy
Returns : Bio::SeqFeatureI object
Args : none
=cut
sub parent {
my($self, $value ) = @_;
if (defined($value)) {
unless (ref($value) and $value->isa('Bio::SeqFeatureI')) {
$self->throw("object $value pretends to be a location but ".
"does not implement Bio::SeqFeatureI");
}
$self->{'_parent'} = $value;
}
return $self->{'_parent'};
}
=head2 start
Title : start
Usage : $start = $feat->start
$feat->start(20)
Function: Get
Returns : integer
Args : none
=cut
sub start {
my ($self,$value) = @_;
return $self->location->start($value);
}
=head2 end
Title : end
Usage : $end = $feat->end
$feat->end($end)
Function: get
Returns : integer
Args : none
=cut
sub end {
my ($self,$value) = @_;
return $self->location->end($value);
}
=head2 length
Title : length
Usage :
Function:
Example :
Returns :
Args :
=cut
sub length {
my ($self) = @_;
return $self->end - $self->start() + 1;
}
=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 : none
=cut
sub strand {
my ($self,$value) = @_;
return $self->location->strand($value);
}
=head2 attach_seq
Title : attach_seq
Usage : $sf->attach_seq($seq)
Function: Attaches a Bio::Seq object to this feature. This
Bio::Seq object is for the *entire* sequence: ie
from 1 to 10000
Example :
Returns : TRUE on success
Args :
=cut
sub attach_seq {
my ($self, $seq) = @_;
if ( !defined $seq || !ref $seq || ! $seq->isa("Bio::PrimarySeqI") ) {
$self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures");
}
$self->{'_gsf_seq'} = $seq;
# attach to sub features if they want it
foreach my $sf ( $self->sub_SeqFeature() ) {
if ( $sf->can("attach_seq") ) {
$sf->attach_seq($seq);
}
}
return 1;
}
=head2 seq
Title : seq
Usage : $tseq = $sf->seq()
Function: returns the truncated sequence (if there) for this
Example :
Returns : sub seq on attached sequence bounded by start & end
Args : none
=cut
sub seq {
my ($self, $arg) = @_;
if ( defined $arg ) {
$self->throw("Calling SeqFeature::PositionProxy->seq with an argument. You probably want attach_seq");
}
if ( ! exists $self->{'_gsf_seq'} ) {
return undef;
}
# assumming our seq object is sensible, it should not have to yank
# the entire sequence out here.
my $seq = $self->{'_gsf_seq'}->trunc($self->start(), $self->end());
if ( $self->strand == -1 ) {
$seq = $seq->revcom;
}
return $seq;
}
=head2 entire_seq
Title : entire_seq
Usage : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns :
Args :
=cut
sub entire_seq {
my ($self) = @_;
return undef unless exists($self->{'_gsf_seq'});
return $self->{'_gsf_seq'};
}
=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 seqname {
my ($obj,$value) = @_;
if ( defined $value ) {
$obj->{'_gsf_seqname'} = $value;
}
return $obj->{'_gsf_seqname'};
}
=head2 Proxies
These functions chain back to the parent for all non sequence related stuff.
=cut
=head2 primary_tag
Title : primary_tag
Usage : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
eg 'exon'
Returns : a string
Args : none
=cut
sub primary_tag{
my ($self,@args) = @_;
return $self->parent->primary_tag();
}
=head2 source_tag
Title : source_tag
Usage : $tag = $feat->source_tag()
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
=cut
sub source_tag{
my ($self) = @_;
return $self->parent->source_tag();
}
=head2 has_tag
Title : has_tag
Usage : $tag_exists = $self->has_tag('some_tag')
Function:
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args :
=cut
sub has_tag{
my ($self,$tag) = @_;
return $self->parent->has_tag($tag);
}
=head2 each_tag_value
Title : each_tag_value
Usage : @values = $self->each_tag_value('some_tag')
Function:
Returns : An array comprising the values of the specified tag.
Args :
=cut
sub each_tag_value {
my ($self,$tag) = @_;
return $self->parent->each_tag_value($tag);
}
=head2 all_tags
Title : all_tags
Usage : @tags = $feat->all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args : none
=cut
sub all_tags{
my ($self) = @_;
return $self->parent->all_tags();
}
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