Provided by: libbio-perl-perl_1.7.2-2_all bug


       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 = {
                 '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 'Unpublished (2003)'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

       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).


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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 _

        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.

        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

        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)

        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

        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

        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