Provided by: libbio-perl-perl_1.7.2-3_all bug

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 'Unpublished (2003)'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