Raw content of Bio::EnsEMBL::ProteinFeature
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::ProteinFeature
=head1 SYNOPSIS
my $feature = Bio::EnsEMBL::ProteinFeature->new(
-start => $start,
-end => $end,
-hstart => $hit_start,
-hend => $hit_end,
-hname => $hit_name
);
=head1 DESCRIPTION
ProteinFeature objects represent domains or other features of interest
on a peptide sequence.
=head1 METHODS
=cut
package Bio::EnsEMBL::ProteinFeature;
use strict;
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::FeaturePair);
=head2 new
Arg [IDESC] : (optional) string An interpro description
Arg [INTERPRO_AC] : (optional) string An interpro accession
Arg [...] : named arguments to FeaturePair superclass
Example : $pf = Bio::EnsEMBL::ProteinFeature->new(-IDESC => $idesc,
-INTERPRO_AC => $iac,
@fp_args);
Description: Instantiates a Bio::EnsEMBL::ProteinFeature
Returntype : Bio::EnsEMBL::FeaturePair
Exceptions : none
Caller : general
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ($idesc, $interpro_ac, $translation_id) = rearrange(['IDESC', 'INTERPRO_AC', 'TRANSLATION_ID'], @_);
my $self = $class->SUPER::new(@_);
#the strand of protein features is always 0
$self->{'strand'} = 0;
$self->{'idesc'} = $idesc || '';
$self->{'interpro_ac'} = $interpro_ac || '';
$self->{'translation_id'} = $translation_id || '';
return $self;
}
=head2 strand
Arg [1] : Ignored
Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
: the strand to be set.
Returntype : int
Status : Stable
=cut
#do not allow the strand to be set
sub strand {
my $self = shift;
return $self->{'strand'};
}
=head2 idesc
Arg [1] : (optional) string The interpro description
Example : print $protein_feature->idesc();
Description: Getter/Setter for the interpro description of this protein
feature.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub idesc{
my $self = shift;
$self->{'idesc'} = shift if(@_);
return $self->{'idesc'};
}
=head2 interpro_ac
Arg [1] : (optional) string The interpro accession
Example : print $protein_feature->interpro_ac();
Description: Getter/Setter for the interpro accession of this protein
feature.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub interpro_ac{
my $self = shift;
$self->{'interpro_ac'} = shift if(@_);
return $self->{'interpro_ac'};
}
=head2 idesc
Arg [1] : (optional) string The interpro description
Example : print $protein_feature->idesc();
Description: Getter/Setter for the interpro description of this protein
feature.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub translation_id{
my $self = shift;
$self->{'translation_id'} = shift if(@_);
return $self->{'translation_id'};
}
1;
]]>