view variant_effect_predictor/Bio/SeqFeature/SimilarityPair.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

# $Id: SimilarityPair.pm,v 1.21 2002/12/24 15:15:32 jason Exp $
#
# BioPerl module for Bio::SeqFeature::SimilarityPair
#
# Cared for by Hilmar Lapp <[e-mail]>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

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

=head1 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";

=head1 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.

=head1 FEEDBACK

=head2 Mailing Lists

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.

  [e-mail]              - General discussion
  http://bio.perl.org/MailList.html  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 email or the web:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Hilmar Lapp

Email [e-mail] or [e-mail]

Describe contact details here

=head1 APPENDIX

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

=cut


# Let the code begin...


package Bio::SeqFeature::SimilarityPair;
use vars qw(@ISA);
use strict;

use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Similarity;
use Bio::SearchIO;

@ISA = qw(Bio::SeqFeature::FeaturePair);

=head2 new

 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


=cut

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.
#

=head2 query

 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 L<Bio::SeqFeature::Similarity>, L<Bio::SeqFeature::FeaturePair>

=cut

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);
}




=head2 subject

 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

=cut

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

*sbjct = \&subject;

=head2 hit

 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


=cut

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);
}

=head2 source_tag

 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


=cut

sub source_tag {
    my ($self, @args) = @_;

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

=head2 significance

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


=cut

sub significance {
    my ($self, @args) = @_;

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

=head2 score

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


=cut

sub score {
    my ($self, @args) = @_;

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

=head2 bits

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


=cut

sub bits {
    my ($self, @args) = @_;

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

1;