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Summary

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

Package variables

Inherit

Bio::SeqFeature::Generic

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";

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 Bio::SeqFeature::Generic.

Methods

Methods description

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

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

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

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

 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    :

Methods code

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;

}

General documentation

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

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.

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/

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

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