Bio::SeqFeature SimilarityPair
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Summary
Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.
Package variables
No package variables defined.
Included modules
Bio::Factory::ObjectFactory
Bio::SeqFeature::Similarity
Inherit
Bio::SeqFeature::FeaturePair
Synopsis
  $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);
$sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query $sim = $sim_pair->hit(); # dto - the hit. # some properties for the similarity pair $expect = $sim_pair->significance(); $score = $sim_pair->score(); $bitscore = $sim_pair->bits(); # this will not write the description for the sequence (only its name) print $sim_pair->query()->gff_string(), "\n";
Description
Lightweight similarity search result as a pair of Similarity
features. This class inherits off Bio::SeqFeature::FeaturePair and
therefore implements Bio::SeqFeatureI, whereas the two features of the
pair are descendants of Bio::SeqFeature::Generic, with better support
for representing similarity search results in a cleaner way.
Methods
newDescriptionCode
queryDescriptionCode
subjectDescriptionCode
hitDescriptionCode
source_tagDescriptionCode
significanceDescriptionCode
scoreDescriptionCode
bitsDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $similarityPair = Bio::SeqFeature::SimilarityPair->new
(-hit => $hit,
-query => $query,
-source => 'blastp');
Function: Initializes a new SimilarityPair object
Returns : Bio::SeqFeature::SimilarityPair
Args : -query => The query in a Feature pair
-hit => (formerly '-subject') the subject/hit in a Feature pair
querycodeprevnextTop
 Title   : query
Usage : $query_feature = $obj->query();
$obj->query($query_feature);
Function: The query object for this similarity pair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair
subjectcodeprevnextTop
 Title   : subject
Usage : $sbjct_feature = $obj->subject();
$obj->subject($sbjct_feature);
Function: Get/Set Subject for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
Notes : Deprecated. Use the method 'hit' instead
hitcodeprevnextTop
 Title   : hit
Usage : $sbjct_feature = $obj->hit();
$obj->hit($sbjct_feature);
Function: Get/Set Hit for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
source_tagcodeprevnextTop
 Title   : source_tag
Usage : $source = $obj->source_tag(); # i.e., program
$obj->source_tag($evalue);
Function: Gets the source tag (program name typically) for a feature
Returns : string
Args : [optional] string
significancecodeprevnextTop
 Title   : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
scorecodeprevnextTop
 Title   : score
Usage : $score = $obj->score();
$obj->score($value);
Function:
Returns :
Args :
bitscodeprevnextTop
 Title   : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    if(! grep { lc($_) eq "-feature_factory"; } @args) {
	# if no overriding factory is provided, provide our preferred one
my $fact = Bio::Factory::ObjectFactory->new( -type => "Bio::SeqFeature::Similarity", -interface => "Bio::SeqFeatureI"); push(@args, '-feature_factory', $fact); } my $self = $class->SUPER::new(@args); my ($primary, $hit, $query, $fea1, $source,$sbjct) = $self->_rearrange([qw(PRIMARY HIT QUERY FEATURE1 SOURCE SUBJECT )],@args); if( $sbjct ) { # undeprecated by Jason before 1.1 release
# $self->deprecated("use of -subject deprecated: SimilarityPair now uses 'hit'");
if(! $hit) { $hit = $sbjct } else { $self->warn("-hit and -subject were specified, using -hit and ignoring -subject"); } } # set the query and subject feature if provided
$self->query( $query) if $query && ! $fea1; $hit && $self->hit($hit); # the following refer to feature1, which is guaranteed to exist
if( defined $primary || ! defined $self->primary_tag) { $primary = 'similarity' unless defined $primary; $self->primary_tag($primary); } $source && $self->source_tag($source); return $self; } #
# Everything else is just inherited from SeqFeature::FeaturePair.
#
}
querydescriptionprevnextTop
sub query {
    return shift->feature1(@_);
}
subjectdescriptionprevnextTop
sub subject {
     my $self = shift;
#    $self->deprecated("Method subject deprecated: use hit() instead");
$self->hit(@_);
}
hitdescriptionprevnextTop
sub hit {
    return shift->feature2(@_);
}
source_tagdescriptionprevnextTop
sub source_tag {
    my ($self, @args) = @_;

    if(@args) {
        $self->hit()->source_tag(@args);
    }
    return $self->query()->source_tag(@args);
}
significancedescriptionprevnextTop
sub significance {
    my ($self, @args) = @_;

    if(@args) {
        $self->hit()->significance(@args);
    }
    return $self->query()->significance(@args);
}
scoredescriptionprevnextTop
sub score {
    my ($self, @args) = @_;

    if(@args) {
        $self->hit()->score(@args);
    }
    # Note: You might think it's only getting set on the hit object.
# Actually, it's getting set on both hit and query.
return $self->query()->score(@args);
}
bitsdescriptionprevnextTop
sub bits {
    my ($self, @args) = @_;

    if(@args) {
        $self->hit()->bits(@args);
    }
    return $self->query()->bits(@args);
}

#################################################################
# aliases for backwards compatibility or convenience #
#################################################################
*sbjct =\& subject; 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 _