Summary

Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.

Package variables

Included modules

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

Methods description

 Title   : new
 Usage   : my $similarityPair = new Bio::SeqFeature::SimilarityPair
                                 (-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

 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

 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

 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

 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

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

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

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

Methods code

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;

}

sub query {

    return shift->feature1(@_);

}

sub subject {

     my $self = shift;
#    $self->deprecated("Method subject deprecated: use hit() instead");
    $self->hit(@_);

}

sub hit {

    return shift->feature2(@_);

}

sub source_tag {

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

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

}

sub significance {

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

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

}

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);

}

sub bits {

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

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

}

General documentation

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Bioperl modules. Send your comments and suggestions preferably to one
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  bioperl-bugs@bio.perl.org
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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 _