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

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

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:

  http://bugzilla.open-bio.org/

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 _