NAME

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

DESCRIPTION

Superclass for all filter modules. Don't use this directly. Use this as interface for new filters (see Bio::Grep::Filter::MIRNAFilter for details). 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

$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 ist 1.

ABSTRACT METHODS

Every filter must implement this methods.

new()

This function constructs a filter object.

$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::Backends::BackendI takes care of that.

Internal method: Only Bio::Grep::Backends::BackendI should call this method.

$filter->reset()

Get/set reset. A flag needed by some Filters like FilterRemoveDuplicates to tell them, it is a new search, forget everything.

Internal method: Only Bio::Grep::Backends::BackendI should call this method.

$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::Backends::BackendI should call them directly.

$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::Container::SearchResult object.

SEE ALSO

Bio::Grep::Backends::BackendI Bio::Grep::Container::SearchResult

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENCE AND COPYRIGHT

Based on Weigel::Seach 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.

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