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# BioPerl module for Bio::HandlerI
# Please direct questions and support issues to <>
# Cared for by Chris Fields
# Copyright Chris Fields
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::HandlerBaseI - Interface class for handler methods which interact with any
event-driven parsers (drivers).
# MyHandler is a Bio::HandlerBaseI-derived class for dealing with GenBank
# sequence data, derived from a GenBank event-driven parser
# inside a parser (driver) constructor
$self->seqhandler($handler || MyHandler->new(-format => 'genbank'));
# in the driver parsing method ( such as next_seq() ) ...
$handler = $self->seqhandler();
# roll data up into hashref chunks, pass off into Handler for processing...
# or retrieve Handler methods and pass data directly to Handler methods
my $hmeth = $hobj->handler_methods;
if ($hmeth->{ $data->{NAME} }) {
my $mth = $hmeth->{ $data->{NAME} }; # code ref
This interface describes simple class methods used for processing data from an
event-based parser (a driver). This is similar in theme to an XML SAX-based
driver but differs in that one can optionally pass related data
semi-intelligently as chunks (defined in a hash reference) vs. passing as single
data elements in a stream. For instance, any reference-related and
species-related data as well as individual sequence features could be passed as
chunks of data to be processed in part or as a whole (from Data::Dumper output):
Annotation Data (References):
$VAR1 = {
'DATA' => '1 (bases 1 to 10001)'
'AUTHORS' => 'International Human Genome Sequencing Consortium.'
'TITLE' => 'The DNA sequence of Homo sapiens'
'JOURNAL' => 'Unpublished (2003)'
Sequence features (source seqfeature):
$VAR1 = {
'mol_type' => 'genomic DNA',
'LOCATION' => '<1..>10001',
'FEATURE_KEY' => 'source',
'note' => 'Accession AL451081 sequenced by The Sanger Centre',
'db_xref' => 'taxon:9606',
'clone' => 'RP11-302I18',
'organism' => 'Homo sapiens'
These would be 'handled' accordingly by methods specified in a
HandlerI-based class. The data in a chunk is intentionally left vague
here since this may vary from implementation to implementation and can
be somewhat open to interpretation. A data chunk in a sequence record,
for instance, will be different than a data chunk in a BLAST
report. This also allows one the flexibility to pass data as more
XML-like small bits, as huge chunks, or even as indexed locations in a
file (such as when using a "pull" parser, like a Bio::PullParserI).
For an sequence-based implementation see
Bio::SeqIO::RichSeq::GenericRichSeqHandler, which handles any GenBank,
UniProt, and EMBL data from their respective driver modules
(Bio::SeqIO::gbdriver, Bio::SeqIO::swissdriver, and
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated. - General discussion - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
=head1 AUTHOR - Chris Fields
Email cjfields at bioperl dot org
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
# Let the code begin...
package Bio::HandlerBaseI;
use strict;
use warnings;
use base qw(Bio::Root::RootI);
my %HANDLERS = ('foo' => \&noop);
=head2 data_handler
Title : data_handler
Usage : $handler->data_handler($data)
Function: Centralized method which accepts all data chunks, then distributes
to the appropriate methods for processing based on the chunk name
from within the HandlerBaseI object.
One can also use
Returns : None
Args : an hash ref containing a data chunk.
sub data_handler {
=head2 handler_methods
Title : handler_methods
Usage : $handler->handler_methods('GenBank')
%handlers = $handler->handler_methods();
Function: Retrieve the handler methods used for the current format() in
the handler. This assumes the handler methods are already
described in the HandlerI-implementing class.
Returns : a hash reference with the data type handled and the code ref
associated with it.
Args : [optional] String representing the sequence format. If set here
this will also set sequence_format()
Throws : On unimplemented sequence format in %HANDLERS
sub handler_methods {
=head2 format
Title : format
Usage : $handler->format('GenBank')
Function: Get/Set the format for the report/record being parsed. This can be
used to set handlers in classes which are capable of processing
similar data chunks from multiple driver modules.
Returns : String with the sequence format
Args : [optional] String with the sequence format
Note : The format may be used to set the handlers (as in the
current GenericRichSeqHandler implementation)
sub format {
=head2 get_params
Title : get_params
Usage : $handler->get_params('-species')
Function: Convenience method used to retrieve the specified
parameters from the internal parameter cache
Returns : Hash ref containing parameters requested and data as
key-value pairs. Note that some parameter values may be
objects, arrays, etc.
Args : List (array) representing the parameters requested
sub get_params {
=head2 set_params
Title : set_params
Usage : $handler->set_params({
'-species' => $species,
'-accession_number' => $acc
Function: Convenience method used to set specific parameters
Returns : None
Args : Hash ref containing the data to be passed as key-value pairs
sub set_params {
=head2 reset_parameters
Title : reset_parameters
Usage : $handler->reset_parameters()
Function: Resets the internal cache of data (normally object parameters for
a builder or factory)
Returns : None
Args : None
sub reset_parameters {
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