Bio::SeqIO::Handler::GenericRichSeqHandler(3pm) 	User Contributed Perl Documentation	   Bio::SeqIO::Handler::GenericRichSeqHandler(3pm)

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://redmine.open-bio.org/projects/bioperl/

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 v5.14.2							    2012-03-02			   Bio::SeqIO::Handler::GenericRichSeqHandler(3pm)