Raw content of Bio::Tools::HMMER::Domain
<![CDATA[# $Id: Domain.pm,v 1.11 2002/10/08 08:38:34 lapp Exp $
#
# BioPerl module for Bio::Tools::HMMER::Domain
#
# 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::Tools::HMMER::Domain - One particular domain hit from HMMER
=head1 SYNOPSIS
Read the Bio::Tools::HMMER::Results docs
=head1 DESCRIPTION
A particular domain score. We reuse the Homol SeqFeature system
here, so this inherits off Homol SeqFeature. As this code
originally came from a separate project, there are some backward
compatibility stuff provided to keep this working with old code.
Don't forget this inherits off Bio::SeqFeature, so all your usual
nice start/end/score stuff is ready for use.
=head1 CONTACT
Ewan Birney, birney@ebi.ac.uk
=head1 CONTRIBUTORS
Jason Stajich, jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#'
package Bio::Tools::HMMER::Domain;
use vars qw(@ISA);
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use strict;
@ISA = qw(Bio::SeqFeature::FeaturePair);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'alignlines'} = [];
my $hmmf1 = Bio::SeqFeature::Generic->new(@args);
my $hmmf2 = Bio::SeqFeature::Generic->new(@args);
$self->feature1($hmmf1);
$self->feature2($hmmf2);
return $self;
}
=head2 add_alignment_line
Title : add_alignment_line
Usage : $domain->add_alignment_line($line_from_hmmer_output);
Function: add an alignment line to this Domain object
Returns : Nothing
Args : scalar
Adds an alignment line, mainly for storing the HMMER alignments
as flat text which can be reguritated. You're right. This is *not
nice* and not the right way to do it. C'est la vie.
=cut
sub add_alignment_line {
my $self = shift;
my $line = shift;
push(@{$self->{'alignlines'}},$line);
}
=head2 each_alignment_line
Title : each_alignment_line
Usage : foreach $line ( $domain->each_alignment_line )
Function: reguritates the alignment lines as they were fed in.
only useful realistically for printing.
Example :
Returns :
Args : None
=cut
sub each_alignment_line {
my $self = shift;
return @{$self->{'alignlines'}};
}
=head2 get_nse
Title : get_nse
Usage : $domain->get_nse()
Function: Provides a seqname/start-end format, useful
for unique keys. nse stands for name-start-end
It is used alot in Pfam
Example :
Returns : A string
Args : Optional seperator 1 and seperator 2 (default / and -)
=cut
sub get_nse {
my $self = shift;
my $sep1 = shift;
my $sep2 = shift;
if( !defined $sep2 ) {
$sep2 = "-";
}
if( !defined $sep1 ) {
$sep1 = "/";
}
return sprintf("%s%s%d%s%d",$self->seq_id,$sep1,$self->start,$sep2,$self->end);
}
# =head2 start_seq
# Title : start_seq
# Usage : Backward compatibility with old HMMER modules.
# should use $domain->start
# Function:
# Example :
# Returns :
# Args :
# =cut
sub start_seq {
my $self = shift;
my $start = shift;
$self->warn("Using old domain->start_seq. Should use domain->start");
return $self->start($start);
}
# =head2 end_seq
# Title : end_seq
# Usage : Backward compatibility with old HMMER modules.
# should use $domain->end
# Function:
# Example :
# Returns :
# Args :
# =cut
sub end_seq {
my $self = shift;
my $end = shift;
$self->warn("Using old domain->end_seq. Should use domain->end");
return $self->end($end);
}
# =head2 start_hmm
# Title : start_hmm
# Usage : Backward compatibility with old HMMER modules, and
# for convience. Equivalent to $self->homol_SeqFeature->start
# Function:
# Example :
# Returns :
# Args :
# =cut
sub start_hmm {
my $self = shift;
my $start = shift;
$self->warn("Using old domain->start_hmm. Should use domain->hstart");
return $self->hstart($start);
}
# =head2 end_hmm
# Title : end_hmm
# Usage : Backward compatibility with old HMMER modules, and
# for convience. Equivalent to $self->homol_SeqFeature->start
# Function:
# Example :
# Returns :
# Args :
# =cut
sub end_hmm {
my $self = shift;
my $end = shift;
$self->warn("Using old domain->end_hmm. Should use domain->hend");
return $self->hend($end);
}
=head2 hmmacc
Title : hmmacc
Usage : $domain->hmmacc($newacc)
Function: set get for HMM accession number. This is placed in the homol
feature of the HMM
Example :
Returns :
Args :
=cut
sub hmmacc{
my ($self,$acc) = @_;
if( defined $acc ) {
$self->feature2->add_tag_value('accession',$acc);
}
my @vals = $self->feature2->each_tag_value('accession');
return shift @vals;
}
=head2 hmmname
Title : hmmname
Usage : $domain->hmmname($newname)
Function: set get for HMM accession number. This is placed in the homol
feature of the HMM
Example :
Returns :
Args :
=cut
sub hmmname {
my ($self,$hname) = @_;
if( defined $hname ) {
$self->hseqname($hname);
}
return $self->hseqname();
}
=head2 bits
Title : bits
Usage :
Function: backward compatibility. Same as score
Example :
Returns :
Args :
=cut
sub bits{
my ($self,$sc) = @_;
return $self->score($sc);
}
=head2 evalue
Title : evalue
Usage :
Function: $domain->evalue($value);
Example :
Returns :
Args :
=cut
sub evalue{
my ($self,$value) = @_;
if( defined $value ) {
$self->add_tag_value('evalue',$value);
}
my @vals = $self->each_tag_value('evalue');
return shift @vals;
}
=head2 seqbits
Title : seqbits
Usage :
Function: $domain->seqbits($value);
Example :
Returns :
Args :
=cut
sub seqbits {
my ($self,$value) = @_;
if( defined $value ) {
$self->add_tag_value('seqbits',$value);
}
my @vals = $self->each_tag_value('seqbits');
return shift @vals;
}
=head2 seq_range
Title : seq_range
Usage :
Function: Throws an exception to catch scripts which need to upgrade
Example :
Returns :
Args :
=cut
sub seq_range{
my ($self,@args) = @_;
$self->throw("You have accessed an old method. Please recode your script to the new bioperl HMMER module");
}
=head2 hmm_range
Title : hmm_range
Usage :
Function: Throws an exception to catch scripts which need to upgrade
Example :
Returns :
Args :
=cut
sub hmm_range{
my ($self,@args) = @_;
$self->throw("You have accessed an old method. Please recode your script to the new bioperl HMMER module");
}
1; # says use was ok
__END__
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