Raw content of Bio::Factory::SeqAnalysisParserFactoryI # $Id: SeqAnalysisParserFactoryI.pm,v 1.8 2002/12/01 00:05:20 jason Exp $ # # BioPerl module for Bio::Factory::SeqAnalysisParserFactoryI # # Cared for by Jason Stajich <jason@bioperl.org>, # and Hilmar Lapp <hlapp@gmx.net> # # Copyright Jason Stajich, Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers =head1 SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # 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); } =head1 DESCRIPTION This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See L<Bio::SeqAnalysisParserI> for more documentation of this concept. =head1 FEEDBACK =head2 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 =head2 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/ =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Factory::SeqAnalysisParserFactoryI; use strict; use Bio::Root::RootI; use Carp; use vars qw(@ISA ); @ISA = qw(Bio::Root::RootI); =head2 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. The type of input which is suitable depends on the implementation, but a good-style implementation should allow both file names and streams (filehandles). A particular implementation may not be able to create a parser for the requested method. In this case it shall return undef. Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. An implementation of this interface should make this argument optional. Example : Returns : A Bio::SeqAnalysisParserI implementing object. 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 =cut sub get_parser { my ( $self, @args) = @_; $self->throw_not_implemented(); } 1;