diff variant_effect_predictor/Bio/Factory/SeqAnalysisParserFactoryI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Factory/SeqAnalysisParserFactoryI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,113 @@
+# $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 <[e-mail]>,
+# and Hilmar Lapp <[e-mail]>
+#
+# 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.
+
+  [e-mail]                - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp, Jason Stajich
+
+Email Hilmar Lapp E<lt>[e-mail]<gt>, Jason Stajich E<lt>[e-mail]<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;