Bio::SeqFeature::Similarity - A sequence feature based on similarity

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::SeqFeature::Similarity - A sequence feature based on similarity

SYNOPSIS

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    # 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";

DESCRIPTION

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This module is basically a sequence features based on similarity, and therefore has support for measures assessing the similarity.

Everything else is inherited from Bio::SeqFeature::Generic.

FEEDBACK

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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

Support

Please direct usage questions or support issues to the mailing list:

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.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp

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Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

significance

 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: 
 Returns : 
 Args    :

bits

 Title   : bits
 Usage   : $bits = $obj->bits();
           $obj->bits($value);
 Function: 
 Returns : 
 Args    :

frac_identical

 Title   : frac_identical
 Usage   : $fracid = $obj->frac_identical();
           $obj->frac_identical($value);
 Function: 
 Returns : 
 Args    :

seqlength

 Title   : seqlength
 Usage   : $len = $obj->seqlength();
           $obj->seqlength($len);
 Function: 
 Returns : 
 Args    :

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    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# 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



# Let the code begin...


package Bio::SeqFeature::Similarity;
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;
}


sub significance {
    return shift->_tag_value('signif', @_);
}


sub bits {
    return shift->_tag_value('Bits', @_);
}


sub frac_identical {
    return shift->_tag_value('FracId', @_);
}


sub seqlength {
    return shift->_tag_value('SeqLength', @_);
}


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;