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#-----------------------------------------------------------------
# $Id: SearchWriterI.pm 15635 2009-04-14 19:11:13Z cjfields $
#
# BioPerl module Bio::SearchIO::SearchWriterI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Steve Chervitz <sac@bioperl.org>
#
# 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 L<Bio::Search::Result::ResultI>
objects.
=head1 AUTHOR
Steve Chervitz E<lt>sac-at-bioperl.orgE<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 base 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 start_report
Title : start_report
Usage : $self->start_report()
Function: The method to call when starting a report. You can override it
to make a custom header
Returns : string
Args : none
=cut
sub start_report { return '' }
=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 { 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 unless $method;
$method = uc($method);
if( $method ne 'HSP' &&
$method ne 'HIT' &&
$method ne 'RESULT' ) {
$self->warn("Unknown method $method");
return;
}
if( $code ) {
$self->throw("Must provide a valid code reference") unless ref($code) =~ /CODE/;
$self->{$method} = $code;
}
return $self->{$method};
}
1;
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