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Bio::SeqIO::Handler::GUseriContributedSPerl:DHandler::GenericRichSeqHandler(3)

NAME
       Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based	data
       handler for GenBank/EMBL/UniProt	(and other) sequence data

SYNOPSIS
	 # MyHandler is	a GenericRichSeqHandler	object.
	 # inside a parser (driver) constructor....

	 $self->seq_handler($handler ||	MyHandler->new(-format => 'genbank'));

	 # in next_seq() in driver...

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

DESCRIPTION
       This is an experimental implementation of a sequence-based HandlerBaseI
       parser and may change over time.	It is possible (nay, likely) that the
       way handler methods are set up will change over development to allow
       more flexibility.  Release pumpkins, please do not add this to a
       release until the API has settled.  It is also likely that write_seq()
       will not	work properly for some data.

       Standard	Developer caveats:

       Do not use for production purposes.  Not	responsible for	destroying
       (your data|computer|world).  Do not stare directly at
       GenericRichSeqHandler.  If GenericRichSeqHandler	glows, back slowly
       away and	call for help.

       Consider	yourself warned!

       This class acts as a demonstration on how to handle similar data	chunks
       derived from Bio::SeqIO::gbdriver, Bio::SeqIO::embldriver, and
       Bio::SeqIO::swissdriver using similar (or the same) handler methods.

       The modules currently pass all previous tests in	t/genbank.t, t/embl.t,
       and t/swiss.t yet all use the same handler methods (the collected tests
       for handlers can	be found in t/Handler.t). Some tweaking	of the methods
       themselves is probably in order over the	long run to ensure that	data
       is consistently handled for each	parser.	 Round-trip tests are probably
       in order	here...

       Though a	Bio::Seq::SeqBuilder is	employed for building sequence objects
       no bypassing of data based on builder slots has been implemented	(yet);
       this is planned in the near future.

       As a reminder: this is the current Annotation data chunk	(via
       Data::Dumper):

	 $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)'
		 };
	 ...

       This is the current SeqFeature data chunk (again	via Data::Dumper):

	 $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'
		 };

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 _

   new
	Title	:  new
	Usage	:
	Function:
	Returns	:
	Args	:  -format    Sequence format to be mapped for handler methods
		   -builder   Bio::Seq::SeqBuilder object (normally defined in
			      SequenceStreamI object implementation constructor)
	Throws	:  On undefined	'-format' sequence format parameter
	Note	:  Still under heavy development

Bio::HandlerBaseI implementing methods
   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

   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.

   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

   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)

   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_param({'-species')
	Function:  Convenience method used to set specific parameters
	Returns	:  None
	Args	:  Hash	ref containing the data	to be passed as	key-value pairs

Methods	unique to this implementation
   seqbuilder
	Title	:  seqbuilder
	Usage	:
	Function:
	Returns	:
	Args	:
	Throws	:
	Note	:

   build_sequence
	Title	:  build_sequence
	Usage	:
	Function:
	Returns	:
	Args	:
	Throws	:
	Note	:

   location_factory
	Title	:  location_factory
	Usage	:
	Function:
	Returns	:
	Args	:
	Throws	:
	Note	:

   annotation_collection
	Title	:  annotation_collection
	Usage	:
	Function:
	Returns	:
	Args	:
	Throws	:
	Note	:

perl v5.24.1			 Bio::SeqIO::Handler::GenericRichSeqHandler(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chris Fields | APPENDIX | Bio::HandlerBaseI implementing methods | Methods unique to this implementation

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