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

NAME

       Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI
       compliant parsers

SYNOPSIS

           # initialize an object implementing this interface, e.g.
           $factory = Bio::Factory::SeqAnalysisParserFactory->new();
           # find out the methods it knows about
           print "registered methods: ",
                 join(', ', keys %{$factory->driver_table}), "\n";
           # obtain a parser object
           $parser = $factory->get_parser(-input=>$inputobj,
                                          -params=>[@params],
                                          -method => $method);
           # $parser is an object implementing Bio::SeqAnalysisParserI
           # annotate sequence with features produced by parser
           while(my $feat = $parser->next_feature()) {
               $seq->add_SeqFeature($feat);
           }

DESCRIPTION

       This is a factory class capable of instantiating SeqAnalysisParserI implementing parsers.

       The concept behind this class and the interface it implements
       (Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing in high-
       throughput automated sequence annotation pipelines. See Bio::SeqAnalysisParserI for more
       documentation of this concept.

       You can always find out the methods an instance of this class knows about by the way given
       in the SYNOPSIS section. By default, and assuming that the documentation is up-to-date,
       this will comprise of genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all case-
       insensitive).

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 - Hilmar Lapp, Jason Stajich

       Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   get_parser
        Title   : get_parser
        Usage   : $factory->get_parser(-input=>$inputobj,
                                       [ -params=>[@params] ],
                                       -method => $method)
        Function: Creates and returns a parser object for the given input and method.
                  Both file names and streams (filehandles) are allowed.

                  Parameters (-params argument) are passed on to the parser object
                  and therefore are specific to the parser to be created.
        Example :
        Returns : A Bio::SeqAnalysisParserI implementing object. Exception if
                  creation of the parser object fails.
        Args    : B<input>  - object/file where analysis results are coming from,
                  B<params> - parameter to use when parsing/running analysis
                  B<method> - method of analysis

   register_driver
        Title   : register_driver
        Usage   : $factory->register_driver("genscan", "Bio::Tools::Genscan");
        Function: Registers a driver a factory class should be able to instantiate.

                  This method can be called both as an instance and as a
                  class method.

        Returns :
        Args    : Key of the driver (string) and the module implementing the driver
                  (string).

   driver_table
        Title   : driver_table
        Usage   : $table = $factory->driver_table();
        Function: Returns a reference to the hash table storing associations of
                  methods with drivers.

                  You use this table to look up registered methods (keys) and
                  drivers (values).

                  In this implementation the table is class-specific and
                  therefore shared by all instances. You can override this in
                  a derived class, but note that this method can be called
                  both as an instance and a class method.

                  This will be the table used by the object internally. You
                  should definitely know what you're doing if you modify the
                  table's contents.  Modifications are shared by _all_
                  instances, those present and those yet to be created.

        Returns : A reference to a hash table.
        Args    :