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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/MappableI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,145 @@
+# $Id: MappableI.pm,v 1.9 2002/10/22 07:45:15 lapp Exp $
+#
+# BioPerl module for Bio::Map::MappableI
+#
+# 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::MappableI - An object that can be placed in a map
+
+=head1 SYNOPSIS
+
+    # get a Bio::Map::MappableI somehow
+    my $position = $element->map_position();
+    # these methods will be important for building sorted lists
+    if( $position->equals($p2) ) {
+	# do something
+    } elsif( $position->less_tha($p2) ) {} 
+      elsif( $position->greater_than($p2) ) { }    
+
+
+=head1 DESCRIPTION
+
+This object handles the generic notion of an element placed on a
+(linear) Map.  Elements can have multiple positions in a map such as
+is the case of Restriction enzyme cut sites on a sequence map.  For
+exact information about an element's position in a map one must query
+the associate PositionI object which is accessible through the
+position() method.
+
+=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]
+
+=head1 CONTRIBUTORS
+
+Heikki Lehvaslaiho [e-mail]
+Lincoln Stein      [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::MappableI;
+use vars qw(@ISA);
+use strict;
+use Bio::Root::RootI;
+use Carp;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 position
+
+ Title   : position
+ Usage   : my $position = $mappable->position(); 
+ Function: Get/Set the Bio::Map::PositionI for a mappable element
+ Returns : Bio::Map::PositionI
+ Args    : (optional) Bio::Map::PositionI
+
+=cut
+
+sub position{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 equals
+
+ Title   : equals
+ Usage   : if( $mappable->equals($mapable2)) ...
+ Function: Test if a position is equal to another position
+ Returns : boolean
+ Args    : Bio::Map::MappableI or Bio::Map::PositionI
+
+=cut
+
+sub equals{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 less_than
+
+ Title   : less_than
+ Usage   : if( $mappable->less_than($m2) ) ...
+ Function: Tests if a position is less than another position
+ Returns : boolean
+ Args    : Bio::Map::MappableI or Bio::Map::PositionI
+
+=cut
+
+sub less_than{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 greater_than
+
+ Title   : greater_than
+ Usage   : if( $mappable->greater_than($m2) ) ...
+ Function: Tests if position is greater than another position
+ Returns : boolean
+ Args    : Bio::Map::MappableI or Bio::Map::PositionI
+
+=cut
+
+sub greater_than{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+1;