diff variant_effect_predictor/Bio/DB/GFF/Homol.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/GFF/Homol.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,102 @@
+=head1 NAME
+
+Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another
+
+=head1 SYNOPSIS
+
+See L<Bio::DB::GFF>.
+
+=head1 DESCRIPTION
+
+Bio::DB::GFF::Homol is a named subtype of Bio::DB::GFF::Segment.  It
+inherits all the methods of its parent, and was created primarily to
+allow for isa() queries and for compatibility with
+Ace::Sequence::Homol.  
+
+A Homol object is typically returned as the method result of the
+Bio::DB::GFF::Feature-E<gt>target() method.
+
+=head1 METHODS
+
+=cut
+
+package Bio::DB::GFF::Homol;
+use strict;
+
+use Bio::DB::GFF::Segment;
+use vars qw(@ISA);
+@ISA = 'Bio::DB::GFF::Segment';
+
+=head2 name
+
+ Title   : name
+ Usage   : $name = $homol->name
+ Function: get the ID of the homology object
+ Returns : a string
+ Args    : none
+ Status  : Public
+
+=cut
+
+sub name     { shift->refseq }
+
+=head2 asString
+
+ Title   : asString
+ Usage   : $name = $homol->asString
+ Function: same as name(), for operator overloading
+ Returns : a string
+ Args    : none
+ Status  : Public
+
+=cut
+
+sub asString { shift->name }
+
+
+=head2 id
+
+ Title   : id
+ Usage   : $id = $homol->id
+ Function: get database ID in class:id format
+ Returns : a string
+ Args    : none
+ Status  : Public
+
+=cut
+
+sub id       {
+  my $self = shift;
+  return "$self->{class}:$self->{name}";
+}
+
+sub new_from_segment {
+  my $package   = shift;
+  $package      = ref $package if ref $package;
+  my $segment   = shift;
+  my $new = {};
+  @{$new}{qw(factory sourceseq start stop strand class ref refstart refstrand)}
+    = @{$segment}{qw(factory sourceseq start stop strand class ref refstart refstrand)};
+  return bless $new,__PACKAGE__;
+}
+
+=head1 BUGS
+
+This module is still under development.
+
+=head1 SEE ALSO
+
+L<bioperl>, L<Bio::DB::GFF>, L<Bio::DB::RelSegment>
+
+=head1 AUTHOR
+
+Lincoln Stein E<lt>[e-mail]<gt>.
+
+Copyright (c) 2001 Cold Spring Harbor Laboratory.
+
+This library is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+1;