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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/LinkagePosition.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,110 @@
+# BioPerl module for Bio::Map::LinkagePosition
+#
+# Cared for by Chad Matsalla <[e-mail]>
+#
+# Copyright Chad Matsalla
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed
+	on a Bio::Map::LinkageMap
+
+=head1 SYNOPSIS
+
+    use Bio::Map::Position;
+    my $position = new Bio::Map::LinkagePosition(-positions => 1,
+						 -distance => 22.1 );
+
+	    # can get listing of positions
+    my @positions = $position->each_position;
+
+
+=head1 DESCRIPTION
+
+Position for a Bio::Map::MarkerI compliant object that will be
+placed on a Bio::Map::LinkageMap. See L<Bio::Map::MarkerI> and
+L<Bio::Map::LinkageMap> for details
+
+=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 - Chad Matsalla
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+Lincoln Stein, [e-mail]
+Heikki Lehvaslaiho, [e-mail]
+Jason Stajich [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::LinkagePosition;
+use vars qw(@ISA);
+use strict;
+require 'dumpvar.pl';
+
+use Bio::Map::OrderedPosition;
+
+@ISA = qw(Bio::Map::OrderedPosition);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Map::LinkagePosition(-positions => $position,
+				-distance => $distance );
+ Function: Builds a new Bio::Map::LinkagePosition object
+ Returns : Bio::Map::LinkagePosition
+ Args    : -order => the relative order of this marker on a linkage map
+ 	   -positions => positions on a map
+=cut
+
+=head2 Bio::Map::PositionI methods
+
+=cut
+
+=head2 order
+
+ Title   : order
+ Usage   : $o_position->order($new_position) _or_
+           $o_position->order()
+ Function: get/set the order position of this position in a map
+ Returns :
+ Args    : If $new_position is provided, the current position of this Position
+           will be set to $new_position.
+
+=cut
+
+
+1;