Raw content of Bio::SeqFeature::Similarity
<![CDATA[# $Id: Similarity.pm,v 1.10 2002/11/01 21:39:05 jason Exp $
#
# BioPerl module for Bio::SeqFeature::Similarity
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::Similarity - A sequence feature based on similarity
=head1 SYNOPSIS
# obtain a similarity feature somehow
print "significance: ", $sim_fea->significance(), "\n";
print "bit score: ", $sim_fea->bits(), "\n";
print "score: ", $sim_fea->score(), "\n";
print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";
=head1 DESCRIPTION
This module is basically a sequence features based on similarity, and therefore
has support for measures assessing the similarity.
Everything else is inherited from L<Bio::SeqFeature::Generic>.
=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 - Hilmar Lapp
Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
Describe contact details here
=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::Similarity;
use vars qw(@ISA);
use strict;
use Bio::SeqFeature::Generic;
@ISA = qw(Bio::SeqFeature::Generic);
sub new {
my ( $caller, @args) = @_;
my ($self) = $caller->SUPER::new(@args);
my ($primary,$evalue, $bits, $frac,$seqlen,$seqdesc) =
$self->_rearrange([qw(PRIMARY
EXPECT
BITS
FRAC
SEQDESC
SEQLENGTH
)],@args);
defined $evalue && $self->significance($evalue);
defined $bits && $self->bits($bits);
defined $frac && $self->frac_identical($frac);
defined $seqlen && $self->seqlength($seqlen);
defined $seqdesc && $self->seqdesc($seqdesc);
$primary = 'similarity' unless defined $primary;
$self->primary_tag($primary) unless( defined $self->primary_tag() );
$self->strand(0) unless( defined $self->strand() );
return $self;
}
=head2 significance
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
=cut
sub significance {
my ($self, $value) = @_;
return $self->_tag_value('signif', $value);
}
=head2 bits
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
=cut
sub bits {
my ($self, $value) = @_;
return $self->_tag_value('Bits', $value);
}
=head2 frac_identical
Title : frac_identical
Usage : $fracid = $obj->frac_identical();
$obj->frac_identical($value);
Function:
Returns :
Args :
=cut
sub frac_identical {
my ($self, $value) = @_;
return $self->_tag_value('FracId', $value);
}
=head2 seqlength
Title : seqlength
Usage : $len = $obj->seqlength();
$obj->seqlength($len);
Function:
Returns :
Args :
=cut
sub seqlength {
my ($self, $value) = @_;
return $self->_tag_value('SeqLength', $value);
}
=head2 seqdesc
Title : seqdesc
Usage : $desc = $obj->seqdesc();
$obj->seqdesc($desc);
Function: At present this method is a shorthand for
$obj->annotation()->description().
Note that this is not stored in the tag system and hence will
not be included in the return value of gff_string().
Returns :
Args :
=cut
sub seqdesc {
my ($self, $value) = @_;
if( defined $value ) {
my $v = Bio::Annotation::SimpleValue->new();
$v->value($value);
$self->annotation->add_Annotation('description',$v);
}
my ($v) = $self->annotation()->get_Annotations('description');
return $v ? $v->value : undef;
}
#
# Everything else is just inherited from SeqFeature::Generic.
#
1;
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