view variant_effect_predictor/Bio/SearchIO/SearchWriterI.pm @ 3:d30fa12e4cc5 default tip

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

#-----------------------------------------------------------------
# $Id: SearchWriterI.pm,v 1.7 2002/12/01 00:05:01 jason Exp $
#
# BioPerl module Bio::SearchIO::SearchWriterI
#
# Cared for by Steve Chervitz <[e-mail]>
#
# You may distribute this module under the same terms as perl itself
#-----------------------------------------------------------------

=head1 NAME

Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results

=head1 SYNOPSIS

Bio::SearchIO::SearchWriterI objects cannot be instantiated since this
module defines a pure interface.

Given an object that implements the Bio::SearchIO::SearchWriterI interface,
you can do the following things with it:

    print $writer->to_string( $result_obj, @args );

=head1 DESCRIPTION

This module defines abstract methods that all subclasses must implement
to be used for outputting results from B<Bio::Search::Result::ResultI>
objects.

=head1 AUTHOR

Steve Chervitz E<lt>[e-mail]<gt>

=head1 DISCLAIMER

This software is provided "as is" without warranty of any kind.

=head1 APPENDIX

The rest of the documentation details each of the object methods.

=cut

package Bio::SearchIO::SearchWriterI;

use Bio::Root::RootI;

@ISA = qw( Bio::Root::RootI );

=head2 to_string

 Purpose   : Produces data for each Search::Result::ResultI in a string.
           : This is an abstract method. For some useful implementations,
           : see ResultTableWriter.pm, HitTableWriter.pm, 
           : and HSPTableWriter.pm.
 Usage     : print $writer->to_string( $result_obj, @args );
 Argument  : $result_obj = A Bio::Search::Result::ResultI object
           : @args = any additional arguments used by your implementation.
 Returns   : String containing data for each search Result or any of its
           : sub-objects (Hits and HSPs).
 Throws    : n/a

=cut

sub to_string {
    my ($self, $result, @args) = @_;
    $self->throw_not_implemented;
}

=head2 end_report

 Title   : end_report
 Usage   : $self->end_report()
 Function: The method to call when ending a report, this is
           mostly for cleanup for formats which require you to 
           have something at the end of the document (</BODY></HTML>)
           for HTML
 Returns : string
 Args    : none


=cut

sub end_report { 
    my $self = shift;
    return '';
}

=head2 filter

 Title   : filter
 Usage   : $writer->filter('hsp', \&hsp_filter);
 Function: Filter out either at HSP,Hit,or Result level
 Returns : none
 Args    : string => data type,
           CODE reference


=cut

# yes this is an implementation in the interface, 
# yes it assumes that the underlying class is hash-based
# yes that might not be a good idea, but until people
# start extending the SearchWriterI interface I think
# this is an okay way to go

sub filter {
    my ($self,$method,$code) = @_;    
    return undef unless $method;
    $method = uc($method);
    if( $method ne 'HSP' &&
	$method ne 'HIT' &&
	$method ne 'RESULT' ) {
	$self->warn("Unknown method $method");
	return undef;
    }
    if( $code )  {
	$self->throw("Must provide a valid code reference") unless ref($code) =~ /CODE/;
	$self->{$method} = $code;
    }
    return $self->{$method};
}

1;