diff variant_effect_predictor/Bio/SeqIO/game/idHandler.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqIO/game/idHandler.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,177 @@
+# $Id: idHandler.pm,v 1.8 2001/11/20 02:09:38 lstein Exp $
+#
+# BioPerl module for Bio::SeqIO::game::idHandler
+#
+# Cared for by Brad Marshall <[e-mail]>
+#         
+# Copyright Brad Marshall
+#
+# You may distribute this module under the same terms as perl itself
+# _history
+# June 25, 2000     written by Brad Marshall
+#
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqIO::game::idHandler - GAME helper via PerlSAX helper.
+
+=head1 SYNOPSIS
+
+GAME helper for parsing new ID objects from GAME XML. Do not use directly
+
+=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]        - Bioperl list
+  [e-mail]        - Technical discussion - Moderate volume
+  [e-mail]   - General Announcements - Pretty dead
+  http://www.bioxml.org/MailingLists/         - About the mailing lists
+
+=head1 AUTHOR - Brad Marshall
+
+Email: [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# This template file is in the Public Domain.
+# You may do anything you want with this file.
+#
+
+package Bio::SeqIO::game::idHandler;
+use Bio::Root::Root;
+
+use vars qw{ $AUTOLOAD @ISA };
+use strict;
+@ISA = qw(Bio::Root::Root);
+sub new {
+    my ($class,@args) = @_;
+    my $self = $class->SUPER::new(@args);
+    
+    # initialize ids
+    $self->{'ids'} = [];
+
+    return $self;
+}
+
+=head2 start_document
+
+ Title   : start_document
+ Usage   : $obj->start_document
+ Function: PerlSAX method called when a new document is initialized
+ Returns : nothing
+ Args    : document name
+
+=cut
+
+# Basic PerlSAX
+sub start_document            {
+    my ($self, $document) = @_;
+}
+
+=head2 end_document
+
+ Title   : end_document
+ Usage   : $obj->end_document
+ Function: PerlSAX method called when a document is finished for cleaning up
+ Returns : list of ids seen
+ Args    : document name
+
+=cut
+
+sub end_document              {
+    my ($self, $document) = @_;
+    return $self->{'ids'};
+}
+
+=head2 start_element
+
+ Title   : start_element
+ Usage   : $obj->start_element
+ Function: PerlSAX method called when a new element is reached
+ Returns : nothing
+ Args    : element object
+
+=cut
+
+sub start_element             {
+    my ($self, $element) = @_;
+
+    if ($element->{'Name'} eq 'bx-seq:seq') {
+	if ($element->{'Attributes'}->{'bx-seq:id'}) {
+	    push @{$self->{'ids'}}, $element->{'Attributes'}->{'bx-seq:id'};
+	} else {
+	    if ($self->can('warn')) {
+		$self->warn('WARNING: Attribute bx-seq:id is required on bx-seq:seq. Sequence will not be parsed.');
+	    } else {
+		warn('WARNING: Attribute bx-seq:id is required on bx-seq:seq. Sequence will not be parsed.');
+	    }
+	}
+    }
+    return 0;
+}
+
+=head2 end_element
+
+ Title   : end_element
+ Usage   : $obj->end_element
+ Function: PerlSAX method called when an element is finished
+ Returns : nothing
+ Args    : element object
+
+=cut
+
+sub end_element               {
+    my ($self, $element) = @_;
+
+}
+
+=head2 characters
+
+ Title   : characters
+ Usage   : $obj->end_element
+ Function: PerlSAX method called when text between XML tags is reached
+ Returns : nothing
+ Args    : text
+
+=cut
+
+sub characters   {
+    my ($self, $text) = @_;
+}
+
+
+=head2 AUTOLOAD
+
+ Title   : AUTOLOAD
+ Usage   : do not use directly
+ Function: autoload handling of missing DESTROY method
+ Returns : nothing
+ Args    : text
+
+=cut
+
+# Others
+sub AUTOLOAD {
+    my $self = shift;
+
+    my $method = $AUTOLOAD;
+    $method =~ s/.*:://;
+    return if $method eq 'DESTROY';
+
+    print "UNRECOGNIZED $method\n";
+}
+
+1;
+
+__END__