diff variant_effect_predictor/Bio/Search/Result/WABAResult.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/Result/WABAResult.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,129 @@
+# $Id: WABAResult.pm,v 1.2 2002/10/22 07:45:18 lapp Exp $
+#
+# BioPerl module for Bio::Search::Result::WABAResult
+#
+# 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::Result::WABAResult - Result object for WABA alignment output
+
+=head1 SYNOPSIS
+
+# use this object exactly as you would a GenericResult
+# the only extra method is query_database which is the 
+# name of the file where the query sequence came from
+
+=head1 DESCRIPTION
+
+This object is for WABA result output, there is little difference
+between this object and a GenericResult save the addition of one
+method query_database.  Expect many of the fields for GenericResult to
+be empty however as WABA was not intended to provide a lot of extra
+information other than the alignment.
+
+=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::Result::WABAResult;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Search::Result::GenericResult;
+
+@ISA = qw( Bio::Search::Result::GenericResult );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Search::Result::WABAResult();
+ Function: Builds a new Bio::Search::Result::WABAResult object 
+ Returns : Bio::Search::Result::WABAResult
+ Args    : -query_database => "name of the database where the query came from"
+
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args);
+  defined $db && $self->query_database($db);
+  return $self;
+}
+
+=head2 query_database
+
+ Title   : query_database
+ Usage   : $obj->query_database($newval)
+ Function: Data field for the database filename where the 
+           query sequence came from
+ Returns : value of query_database
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub query_database{
+    my ($self,$value) = @_;
+    if( defined $value) {
+	$self->{'query_database'} = $value;
+    }
+    return $self->{'query_database'};
+}
+
+
+=head2 All other methods are inherited from Bio::Search::Result::GenericResult
+
+See the L<Bio::Search::Result::GenericResult> for complete
+documentation of the rest of the methods that are available for this
+module.
+
+=cut
+
+1;