diff variant_effect_predictor/Bio/SearchIO/EventHandlerI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SearchIO/EventHandlerI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,233 @@
+# $Id: EventHandlerI.pm,v 1.8 2002/10/22 07:45:18 lapp Exp $
+#
+# BioPerl module for Bio::SearchIO::EventHandlerI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
+
+=head1 SYNOPSIS
+
+# do not use this object directly it is an interface
+# See Bio::SearchIO::SearchResultEventBuilder for an implementation
+
+    use Bio::SearchIO::SearchResultEventBuilder;
+    my $handler = new Bio::SearchIO::SearchResultEventBuilder();
+
+=head1 DESCRIPTION
+
+This interface describes the basic methods needed to handle Events
+thrown from parsing a Search Result such as FASTA, BLAST, or HMMer.
+
+=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
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::SearchIO::EventHandlerI;
+use vars qw(@ISA);
+use strict;
+use Carp;
+
+use Bio::Event::EventHandlerI;
+
+@ISA = qw (Bio::Event::EventHandlerI);
+
+=head2 start_result
+
+ Title   : start_result
+ Usage   : $handler->start_result($data)
+ Function: Begins a result event cycle
+ Returns : none 
+ Args    : Type of Result
+
+=cut
+
+sub start_result {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 end_result
+
+ Title   : end_result
+ Usage   : $handler->end_result($data)
+ Function: Ends a result event cycle
+ Returns : Bio::Search::Result::ResultI object
+ Args    : none
+
+
+=cut
+
+sub end_result{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 start_hsp
+
+ Title   : start_hsp
+ Usage   : $handler->start_hsp($data)
+ Function: Start a HSP event cycle
+ Returns : none
+ Args    : type of element
+           associated hashref
+
+=cut
+
+sub start_hsp{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 end_hsp
+
+ Title   : end_hsp
+ Usage   : $handler->end_hsp()
+ Function: Ends a HSP event cycle
+ Returns : Bio::Search::HSP::HSPI object
+ Args    : type of event and associated hashref
+
+=cut
+
+sub end_hsp{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 start_hit
+
+ Title   : start_hit
+ Usage   : $handler->start_hit()
+ Function: Starts a Hit event cycle
+ Returns : none
+ Args    : type of event and associated hashref
+
+
+=cut
+
+sub start_hit {
+   my ($self,@args) = @_;
+   $self->throw_not_implemented
+}
+
+=head2 end_hit
+
+ Title   : end_hit
+ Usage   : $handler->end_hit()
+ Function: Ends a Hit event cycle
+ Returns : Bio::Search::Hit::HitI object
+ Args    : type of event and associated hashref
+
+
+=cut
+
+sub end_hit {
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 register_factory
+
+ Title   : register_factory
+ Usage   : $handler->register_factory('TYPE',$factory);
+ Function: Register a specific factory for a object type class
+ Returns : none
+ Args    : string representing the class and
+           Bio::Factory::ObjectFactoryI
+
+See L<Bio::Factory::ObjectFactoryI> for more information
+
+=cut
+
+sub register_factory{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 factory
+
+ Title   : factory
+ Usage   : my $f = $handler->factory('TYPE');
+ Function: Retrieves the associated factory for requested 'TYPE'
+ Returns : a Bio::Factory::ObjectFactoryI or undef if none registered
+ Args    : name of factory class to retrieve
+
+See L<Bio::Factory::ObjectFactoryI> for more information
+
+=cut
+
+sub factory{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 Bio::Event::EventHandlerI methods
+
+=cut
+
+=head2 will_handle
+
+ Title   : will_handle
+ Usage   : if( $handler->will_handle($event_type) ) { ... }
+ Function: Tests if this event builder knows how to process a specific event
+ Returns : boolean
+ Args    : event type name
+
+
+=cut
+
+=head2 SAX methods
+
+See L<Bio::Event::EventHandlerI> for the additional SAX methods.
+
+=cut
+
+
+1;