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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/Position.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,202 @@
+# $Id: Position.pm,v 1.9 2002/10/22 07:45:16 lapp Exp $
+#
+# BioPerl module for Bio::Map::Position
+#
+# 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::Position - A single position of a Marker in a Map
+
+=head1 SYNOPSIS
+
+    use Bio::Map::Position;
+    my $position = new Bio::Map::Position(-map => $map, 
+					  -marker => $marker
+					  -value => 100
+					  );
+
+=head1 DESCRIPTION
+
+This object is an implementation of the PositionI interface that
+handles the specific values of a position.  This allows an element
+(e.g. Marker) to have multiple positions within a map and still be
+treated as a single entity.  
+
+This does not directly handle the concept of a relative map in which
+no known exact positions exist but markers are just ordered relative
+to one another - in that case arbitrary values must be assigned for
+position values.
+
+No units are assumed here - units are handled by context of which Map
+a position is placed in or the subclass of this Position.
+
+=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]
+Chad Matsalla, [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::Position;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::Root::Root;
+use Bio::Map::PositionI;
+
+@ISA = qw(Bio::Root::Root Bio::Map::PositionI );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Map::Position();
+ Function: Builds a new Bio::Map::Position object 
+ Returns : Bio::Map::Position
+ Args    : -map     a <Bio::Map::MapI> object
+           -marker  a <Bio::Map::MarkerI> object
+           -value   string or number
+
+=cut
+
+sub new {
+    my($class,@args) = @_;
+    my $self = $class->SUPER::new(@args);
+  
+    my ($map, $marker, $value) = 
+	$self->_rearrange([qw( MAP 
+			       MARKER 
+			       VALUE
+			       )], @args);
+
+    $map     && $self->map($map);
+    $marker  && $self->marker($marker);
+    $value   && $self->value($value);
+
+    return $self;
+}
+
+=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 ($self,$map) = @_;
+   if( defined $map ) {
+       $self->throw("This is [$map], not a Bio::Map::MapI object")
+	   unless $map->isa('Bio::Map::MapI');
+       $self->{'_map'} = $map;
+   }
+   return $self->{'_map'};
+}
+
+=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 ($self,$marker) = @_;
+   if( defined $marker ) {
+       $self->thow("This is [$marker], not a Bio::Map::MarkerI object")
+	   unless $marker->isa('Bio::Map::MarkerI');
+       $self->{'_marker'} = $marker;
+   }
+   return $self->{'_marker'};
+}
+
+=head2 value
+
+ Title   : value
+ Usage   : my $pos = $position->value;
+ Function: Get/Set the value for this postion
+ Returns : scalar, value
+ Args    : [optional] new value to set
+
+=cut
+
+sub value {
+   my ($self,$value) = @_;
+   if( defined $value ) {
+       $self->{'_value'} = $value;
+   }
+   return $self->{'_value'};
+}
+
+=head2 numeric
+
+ Title   : numeric
+ Usage   : my $num = $position->numeric;
+ Function: Read-only method that is guarantied to return a numeric 
+           representation for this position. 
+ Returns : numeric (int or real) 
+ Args    : none
+
+=cut
+
+sub numeric {
+   my ($self) = @_;
+   my $num = $self->{'_value'} || 0;
+
+   # expand this to cover scientific notation, too!
+   $self->throw("This value [$num] is not numeric!")
+       unless $num && $num =~ /^[+-]?[\d.]+$/;
+   return $num;
+}
+
+1;