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#
# BioPerl module for Bio::SeqFeature::Similarity
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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
HideShow 61 lines of Pod
=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://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Support 
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
=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 the
web:
  https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Hilmar Lapp
Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
=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;
$Bio::SeqFeature::Similarity::VERSION = '1.7.8';
use strict;
use base 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
                              SEQLENGTH
                              SEQDESC
                              )],@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;
}
HideShow 12 lines of Pod
=head2 significance
 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: 
 Returns : 
 Args    : 
=cut
sub significance {
    return shift->_tag_value('signif', @_);
}
HideShow 12 lines of Pod
=head2 bits
 Title   : bits
 Usage   : $bits = $obj->bits();
           $obj->bits($value);
 Function: 
 Returns : 
 Args    : 
=cut
sub bits {
    return shift->_tag_value('Bits', @_);
}
HideShow 12 lines of Pod
=head2 frac_identical
 Title   : frac_identical
 Usage   : $fracid = $obj->frac_identical();
           $obj->frac_identical($value);
 Function: 
 Returns : 
 Args    : 
=cut
sub frac_identical {
    return shift->_tag_value('FracId', @_);
}
HideShow 12 lines of Pod
=head2 seqlength
 Title   : seqlength
 Usage   : $len = $obj->seqlength();
           $obj->seqlength($len);
 Function: 
 Returns : 
 Args    : 
=cut
sub seqlength {
    return shift->_tag_value('SeqLength', @_);
}
HideShow 16 lines of Pod
=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 defined $v ? $v->value : undef;
}
#
# Everything else is just inherited from SeqFeature::Generic.
#
1;