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Bio::HandlerBaseI(3)  User Contributed Perl Documentation Bio::HandlerBaseI(3)

NAME
       Bio::HandlerBaseI - Interface class for handler methods which interact
       with any	event-driven parsers (drivers).

SYNOPSIS
	 # 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...

	 $hobj->data_handler($data);

	 # 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
	     $hobj->$mth($data);
	 }

DESCRIPTION
       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 = {
		 'NAME'	=> 'REFERENCE',
		 '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 'Unpublished (2003)'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',
		 'NAME'	=> 'FEATURES',
		 '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
       Bio::SeqIO::embldriver).

FEEDBACK
   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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Fields
       Email cjfields at bioperl dot org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   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.

   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

   format
	Title	:  format
	Usage	:  $handler->format('GenBank')
		   $handler->format('BLAST')
	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)

   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

   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

   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

perl v5.24.1			  2017-07-08		  Bio::HandlerBaseI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chris Fields | APPENDIX

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