diff variant_effect_predictor/Bio/Search/Hit/HitFactory.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/Hit/HitFactory.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,149 @@
+# $Id: HitFactory.pm,v 1.3 2002/10/22 07:45:17 lapp Exp $
+#
+# BioPerl module for Bio::Search::Hit::HitFactory
+#
+# 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::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects 
+
+=head1 SYNOPSIS
+
+    use Bio::Search::Hit::HitFactory;
+    my $factory = new Bio::Search::Hit::HitFactory();
+    my $resultobj = $factory->create(@args);
+
+=head1 DESCRIPTION
+
+This is a general way of hiding the object creation process so that we
+can dynamically change the objects that are created by the SearchIO
+parser depending on what format report we are parsing.
+
+This object is for creating new Hits.
+
+=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::Search::Hit::HitFactory;
+use vars qw(@ISA $DEFAULT_TYPE);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Factory::ObjectFactoryI;
+
+@ISA = qw(Bio::Root::Root Bio::Factory::ObjectFactoryI );
+
+BEGIN { 
+    $DEFAULT_TYPE = 'Bio::Search::Hit::GenericHit'; 
+}
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Search::Hit::HitFactory();
+ Function: Builds a new Bio::Search::Hit::HitFactory object 
+ Returns : Bio::Search::Hit::HitFactory
+ Args    :
+
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  my ($type) = $self->_rearrange([qw(TYPE)],@args);
+  $self->type($type) if defined $type;
+  return $self;
+}
+
+=head2 create
+
+ Title   : create
+ Usage   : $factory->create(%args)
+ Function: Create a new L<Bio::Search::Hit::HitI> object  
+ Returns : L<Bio::Search::Hit::HitI>
+ Args    : hash of initialization parameters
+
+
+=cut
+
+sub create{
+   my ($self,@args) = @_;
+   my $type = $self->type;
+   eval { $self->_load_module($type) };   
+   if( $@ ) { $self->throw("Unable to load module $type"); }
+   return $type->new(@args);
+}
+
+
+=head2 type
+
+ Title   : type
+ Usage   : $factory->type('Bio::Search::Hit::GenericHit');
+ Function: Get/Set the Hit creation type
+ Returns : string
+ Args    : [optional] string to set 
+
+
+=cut
+
+sub type{
+    my ($self,$type) = @_;
+   if( defined $type ) { 
+       # redundancy with the create method which also calls _load_module
+       # I know - but this is not a highly called object so I am going 
+       # to leave it in
+       eval {$self->_load_module($type) };
+       if( $@ ){ $self->warn("Cannot find module $type, unable to set type"); }
+       else { $self->{'_type'} = $type; }
+   } 
+    return $self->{'_type'} || $DEFAULT_TYPE;
+}
+
+1;