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 'Unpublished (2003)'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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq