Bio::Factory::SeqAnalyUseraContributeBio::Factory::SeqAnalysisParserFactory(3)

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:

	 http://bugzilla.open-bio.org/

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	:

perl v5.14.1			  201Bio::Factory::SeqAnalysisParserFactory(3)

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