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

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

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

 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   : 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

Methods code

sub bits {

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

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

1;

}

sub hit {

    my ($self, @args) = @_;
    my $f = $self->feature2();
    if(! @args || (!ref($args[0]) && $args[0] eq 'null') ) {
	if( ! defined( $f) ) {
	    @args = Bio::SeqFeature::Similarity->new();
	} elsif( ! $f->isa('Bio::SeqFeature::Similarity') && 
		 $f->isa('Bio::SeqFeatureI')) {
	    # a Bio::SeqFeature::Generic was placeholder for feature2	    
	    my $newf = new 
	      Bio::SeqFeature::Similarity( -start   => $f->start(),
					   -end     => $f->end(),
					   -strand  => $f->strand(),
					   -primary => $f->primary_tag(),
					   -source  => $f->source_tag(),
					   -seq_id  => $f->seq_id(),
					   -score   => $f->score(),
					   -frame   => $f->frame(),
					   );
	    foreach my $tag ( $newf->all_tags ) {
		$tag->add_tag($tag, $newf->each_tag($tag));
	    }
	    @args = $newf;
	}
    }
    return $self->feature2(@args);

}

sub new {

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

    my $self = $class->SUPER::new(@args);

    # Hack to deal with the fact that SimilarityPair calls strand()
    # which will lead to an error in Bio::Search::HSP::BlastHSP 
    # because parsing hasn't yet occurred.
    # TODO: Remove this when BlastHSP doesn't do lazy parsing.
    $self->{'_initializing'} = 1;

    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");
	}
    }

    # make sure at least the query feature exists -- this refers to feature1
    if($query && ! $fea1) { $self->query( $query);  } 
    else { $self->query('null'); } # call with no args sets a default value for query
    
    $hit && $self->hit($hit);
    # the following refer to feature1, which has been ensured to exist
    if( defined $primary || ! defined $self->primary_tag) { 
	$primary = 'similarity' unless defined $primary;
	$self->primary_tag($primary);
    } 

    $source && $self->source_tag($source);
    $self->strand(0) unless( defined $self->strand() );

    $self->{'_initializing'} = 0;  # See "Hack" note above
    return $self;
}

#
# Everything else is just inherited from SeqFeature::FeaturePair.
#

}

sub query {

    my ($self, @args) = @_;
    my $f = $self->feature1();
    if( ! @args || ( !ref($args[0]) && $args[0] eq 'null') ) {
	if( ! defined( $f) ) {
	    @args = Bio::SeqFeature::Similarity->new();
	} elsif( ! $f->isa('Bio::SeqFeature::Similarity') && 
		 $f->isa('Bio::SeqFeatureI') ) {
	    # a Bio::SeqFeature::Generic was placeholder for feature1	    
	    my $newf = new 
	      Bio::SeqFeature::Similarity( -start   => $f->start(),
					   -end     => $f->end(),
					   -strand  => $f->strand(),
					   -primary => $f->primary_tag(),
					   -source  => $f->source_tag(),
					   -seq_id  => $f->seq_id(),
					   -score   => $f->score(),
					   -frame   => $f->frame(),
					   );
	    foreach my $tag ( $newf->all_tags ) {
		$tag->add_tag($tag, $newf->each_tag($tag));
	    }
	    @args = $newf;	   
	} else {
	    @args = ();
	}
    }
    return $self->feature1(@args);

}

sub score {

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

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

}

sub significance {

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

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

}

sub source_tag {

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

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

}

sub subject {

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

*sbjct =\& subject;

}

General documentation

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