diff variant_effect_predictor/Bio/Map/PositionI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/PositionI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,144 @@
+# $Id: PositionI.pm,v 1.8 2002/10/22 07:45:16 lapp Exp $
+#
+# BioPerl module for Bio::Map::PositionI
+#
+# 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::Map::PositionI - Abstracts the notion of a position  having
+  a value in the context of a marker and a Map
+
+=head1 SYNOPSIS
+
+    # do not use directly
+
+=head1 DESCRIPTION
+
+This object stores one of the postions a that a mappable object
+(e.g. Marker) may have in a map (e.g. restriction enzymes or a SNP
+mapped to several chromosomes).
+
+The method numeric() returns the position in a form that can be
+compared between other positions of the same type.
+
+=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
+
+Lincoln Stein, [e-mail]
+Heikki Lehvaslaiho, [e-mail]
+
+=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::Map::PositionI;
+use vars qw(@ISA);
+use strict;
+use Bio::Root::RootI;
+use Carp;
+
+@ISA = qw(Bio::Root::RootI);
+
+
+=head2 map
+
+ Title   : map
+ Usage   : my $id = map->$map;
+ Function: Get/Set the map the position is in.
+ Returns : L<Bio::Map::MapI>
+ Args    : [optional] new L<Bio::Map::MapI>
+
+=cut
+
+sub map {
+   my ($self, $value) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 marker
+
+ Title   : marker
+ Usage   : my $id = marker->$marker;
+ Function: Get/Set the marker the position is in.
+ Returns : L<Bio::Map::MarkerI>
+ Args    : [optional] new L<Bio::Map::MarkerI>
+
+=cut
+
+sub marker {
+   my ($self, $value) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 value
+
+ Title   : value
+ Usage   : my $pos = $position->value;
+ Function: Get/Set the value for this position
+ Returns : scalar, value
+ Args    : [optional] new value to set
+
+=cut
+
+sub value {
+   my ($self, $value) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 numeric
+
+ Title   : numeric
+ Usage   : my $num = $position->numeric;
+ Function: Read-only method that is guarantied to return 
+           representation for this position that can be compared with others
+ Returns : numeric (int, real or range)
+ Args    : none
+
+=cut
+
+sub numeric {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+1;