Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers # 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); } 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).

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org> 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 :