Lincoln D. Stein > Bio-Das > Bio::Das::TypeHandler

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NAME ^

Bio::Das::TypeHandler -- Utilities for handling types

SYNOPSIS ^

This is to be replaced by ontology-based types very soon.

METHODS ^

new

 Title   : new
 Usage   : $typehandle = Bio::Das::TypeHandler->new;
 Function: create new typehandler
 Returns : a typehandler
 Args    : a verbose/debug flag (optional)

parse_types

 Title   : parse_types
 Usage   : $db->parse_types(@args)
 Function: parses list of types
 Returns : an array ref containing ['method','source'] pairs
 Args    : a list of types in 'method:source' form
 Status  : internal

This method takes an array of type names in the format "method:source" and returns an array reference of ['method','source'] pairs. It will also accept a single argument consisting of an array reference with the list of type names.

make_match_sub

 Title   : make_match_sub
 Usage   : $db->make_match_sub($types)
 Function: creates a subroutine used for filtering features
 Returns : a code reference
 Args    : a list of parsed type names
 Status  : protected

This method is used internally to generate a code subroutine that will accept or reject a feature based on its method and source. It takes an array of parsed type names in the format returned by parse_types(), and generates an anonymous subroutine. The subroutine takes a single Bio::DB::GFF::Feature object and returns true if the feature matches one of the desired feature types, and false otherwise.

SEE ALSO ^

Bio::Das

AUTHOR ^

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

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

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