diff variant_effect_predictor/Bio/SeqAnalysisParserI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqAnalysisParserI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,104 @@
+# $Id: SeqAnalysisParserI.pm,v 1.12 2002/12/01 00:05:19 jason Exp $
+#
+# BioPerl module for Bio::SeqAnalysisParserI
+#
+# 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::SeqAnalysisParserI - Sequence analysis output parser interface  
+
+=head1 SYNOPSIS
+
+    # get a SeqAnalysisParserI somehow, e.g. by
+    my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
+                            '-input' => 'inputfile', '-method' => 'genscan');
+    while( my $feature = $parser->next_feature() ) {
+	print "Feature from ", $feature->start, " to ", $feature->end, "\n";
+    }
+
+=head1 DESCRIPTION
+
+SeqAnalysisParserI is a generic interface for describing sequence analysis
+result parsers. Sequence analysis in this sense is a search for similarities
+or the identification of features on the sequence, like a databank search or a
+a gene prediction result.
+
+The concept behind this interface is to have a generic interface in sequence
+annotation pipelines (as used e.g. in high-throughput automated
+sequence annotation). This interface enables plug-and-play for new analysis
+methods and their corresponding parsers without the necessity for modifying
+the core of the annotation pipeline. In this concept the annotation pipeline
+has to rely on only a list of methods for which to process the results, and a
+factory from which it can obtain the corresponding parser implementing this
+interface.
+
+See Bio::Factory::SeqAnalysisParserFactoryI and
+Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
+of the corresponding factory.
+
+=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::SeqAnalysisParserI;
+use strict;
+use vars qw(@ISA);
+use Bio::Root::RootI;
+use Carp;
+@ISA = qw(Bio::Root::RootI);
+
+=head2 next_feature
+
+ Title   : next_feature
+ Usage   : $seqfeature = $obj->next_feature();
+ Function: Returns the next feature available in the analysis result, or
+           undef if there are no more features.
+ Example :
+ Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
+           more features.
+ Args    : none    
+
+=cut
+
+sub next_feature {
+    my ($self) = shift;
+    $self->throw_not_implemented();
+}
+
+1;