Bio::SeqFeature Similarity
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Summary
Bio::SeqFeature::Similarity - A sequence feature based on similarity
Package variables
No package variables defined.
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
new
No description
Code
significanceDescriptionCode
bitsDescriptionCode
frac_identicalDescriptionCode
seqlengthDescriptionCode
seqdescDescriptionCode
Methods description
significancecode    nextTop
 Title   : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
bitscodeprevnextTop
 Title   : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
frac_identicalcodeprevnextTop
 Title   : frac_identical
Usage : $fracid = $obj->frac_identical();
$obj->frac_identical($value);
Function:
Returns :
Args :
seqlengthcodeprevnextTop
 Title   : seqlength
Usage : $len = $obj->seqlength();
$obj->seqlength($len);
Function:
Returns :
Args :
seqdesccodeprevnextTop
 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
newdescriptionprevnextTop
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 $self;
}
significancedescriptionprevnextTop
sub significance {
    return shift->_tag_value('signif', @_);
}
bitsdescriptionprevnextTop
sub bits {
    return shift->_tag_value('Bits', @_);
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
    return shift->_tag_value('FracId', @_);
}
seqlengthdescriptionprevnextTop
sub seqlength {
    return shift->_tag_value('SeqLength', @_);
}
seqdescdescriptionprevnextTop
sub seqdesc {
    my ($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
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LappTop
Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _