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Summary

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

Package variables

Included modules

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   : 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   : 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    :

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

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

Methods code

sub bits {

    my ($self, $value) = @_;

    return $self->_tag_value('Bits', $value);

}

sub frac_identical {

    my ($self, $value) = @_;

    return $self->_tag_value('FracId', $value);

}

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;

}

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;

}

sub seqlength {

    my ($self, $value) = @_;

    return $self->_tag_value('SeqLength', $value);

}

sub significance {

    my ($self, $value) = @_;

    return $self->_tag_value('signif', $value);

}

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://bio.perl.org/MailList.html             - About the mailing lists

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/

Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
Describe contact details here

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