NAME

Bio::Grep::Filter::FilterI - Superclass for all filter modules

SYNOPSIS

   package MyFilter;
   
   use strict;
   use warnings;
   
   use Bio::Grep::Filter::FilterI;
   
   use base 'Bio::Grep::Filter::FilterI';
   
   use Class::MethodMaker
    [ new => [ qw / new2 / ],
      ... # here some local variables, see perldoc Class::MethodMaker
    ];
   
   sub new {
      my $self = shift->new2;
      $self->delete(1); # a filter that actually filters, not only adds
                        # remarks to $self->search_result->remark

      $self->supports_alphabet( dna => 1, protein => 1);
      $self;
   }
   
   sub filter {
      my $self = shift;
      # code that examines $self->search_result
      # and returns 0 (not passed) or 1 (passed)
      ...
      $self->message('passed');
      return 1;
   }   
   
   sub reset_filter {
      my $self = shift;
      # if you need local variables, you can clean up here
   }

   1;# Magic true value required at end of module

DESCRIPTION

Bio::Grep::Filter::FilterI is the superclass for all filter modules. Don't use this directly.

A Filter module implements a filter function that returns 1 if query and subject pass the filter, 0 otherwise. If the member variable "delete" is 1, then this subject won't be in the search results of the back-end.

METHODS

See Bio::Grep::Root for inherited methods.

ACCESSORS/MUTATORS

Following the Bioperl guidelines, accessors are also mutators:

  $filter->delete(1);
  if ($filter->delete) {
    ...
  }

$filter->delete()

Get/set delete. If this is 0, then the search result will not be deleted (but you will still have the filter message). Otherwise, this hit won't be included in the search results of the back-end. Default is 1.

ABSTRACT METHODS

Every filter must implement these methods:

new()

This function constructs a filter object.

$filter->supports_alphabet()

Get supported alphabets. Returns a hash. Keys are the supported alphabets.

    my $can_filter_proteins = $filter->supports_alphabet_exists('protein');

INTERNAL METHODS

Only Bio::Grep::Backend::BackendI should call them directly.

$filter->filter()

This function returns 1 if query and subject pass the filter, 0 otherwise. You have to set the search result with the function $filter->search_result before. Bio::Grep::Backend::BackendI takes care of that.

$filter->reset_filter()

Get/set reset_filter. A flag needed by some Filters like Bio::Grep::Filter::FilterRemoveDuplicates to tell them, it is a new search, forget everything.

$filter->message()

Get/set the message. This is a string with the reason for rejecting the search result.

$filter->search_result()

Get/set the search_result. A Bio::Grep::SearchResult object.

MOTIVATION

You might wonder why or when you should write a Filter object instead of filtering in the while loop:

Code reuse:

Is it likely that you need the code (or parts of it) in other projects? Do you think other people may find your code useful? Good candidates here are parsers for other programs (that perform thermodynamic calculations for example).

Debugging:

It is easier to debug and test modular code than whole scripts. Additionally, the code in your script is easier to understand and maintain.

SEE ALSO

Bio::Grep::Backend::BackendI Bio::Grep::SearchResult

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENSE AND COPYRIGHT

Copyright (C) 2007-2009 by M. Riester.

Based on Weigel::Search v0.13, Copyright (C) 2005-2006 by Max Planck Institute for Developmental Biology, Tuebingen.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

cpanm Bio::Grep

perl -MCPAN -e shell
install Bio::Grep