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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/OrderedPosition.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,248 @@
+# BioPerl module for Bio::Map::OrderedPosition
+#
+# 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::OrderedPosition - Abstracts the notion of a member
+	of an ordered list of markers. Each marker is a certain distance
+	from the one in the ordered list before it.
+
+=head1 SYNOPSIS
+
+    use Bio::Map::OrderedPosition;
+	# the first marker in the sequence
+    my $position = new Bio::Map::OrderedPosition(-order => 1,
+			-positions => [ [ $map, 22.3] ] );
+	# the second marker in the sequence, 15.6 units from the fist one
+    my $position2 = new Bio::Map::OrderedPosition(-order => 2,
+			-positions => [ [ $map, 37.9] ] );
+	# the third marker in the sequence, coincidental with the second
+	# marker
+    my $position3 = new Bio::Map::OrderedPosition(-order => 3,
+                        -posititions => [ [ $map, 37.9]] );
+
+=head1 DESCRIPTION
+
+This object is an implementation of the PositionI interface and the
+Position object handles the specific values of a position.
+OrderedPosition is intended to be slightly more specific then Position
+but only specific enough for a parser from the MarkerIO subsystem to
+create and then pass to a client application to bless into the proper
+type. For an example of how this is intended to work, see the
+Mapmaker.pm.
+
+No units are assumed here - units are handled by context of which Map
+a position is placed in.
+
+Se Bio::Map::Position for additional information.
+
+=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::OrderedPosition;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Map::Position;
+
+@ISA = qw(Bio::Map::Position);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Map::OrderedPosition();
+ Function: Builds a new Bio::Map::OrderedPosition object 
+ Returns : Bio::Map::OrderedPosition
+ Args    : -order - The order of this position
+
+=cut
+
+sub new {
+    my($class,@args) = @_;
+    my $self = $class->SUPER::new(@args);
+#    $self->{'_order'} = [];
+  
+    my ($map, $marker, $value, $order) = 
+	$self->_rearrange([qw( MAP 
+			       MARKER 
+			       VALUE
+			       ORDER
+			       )], @args);
+#    print join ("|-|", ($map, $marker, $value, $order)), "\n";
+    $map     && $self->map($map);
+    $marker  && $self->marker($marker);
+    $value   && $self->value($value);
+    $order   && $self->order($order);
+
+    return $self;
+}
+
+=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 $new_position.
+
+=cut
+
+sub order {
+    my ($self,$order) = @_;
+    if ($order) {
+	# no point in keeping the old ones
+	$self->{'_order'} = $order;
+    }
+    return $self->{'_order'};
+}
+
+=head2 Bio::Map::Position functions
+
+=cut
+
+=head2 known_maps
+
+ Title   : known_maps
+ Usage   : my @maps = $position->known_maps
+ Function: Returns the list of maps that this position has values for
+ Returns : list of Bio::Map::MapI unique ids
+ Args    : none
+
+=head2 in_map
+
+ Title   : in_map
+ Usage   : if ( $position->in_map($map) ) {}
+ Function: Tests if a position has values in a specific map
+ Returns : boolean
+ Args    : a map unique id OR Bio::Map::MapI
+
+=head2 each_position_value
+
+ Title   : positions
+ Usage   : my @positions = $position->each_position_value($map);
+ Function: Retrieve a list of positions coded as strings or ints 
+ Returns : Array of position values for a Map
+ Args    : Bio::Map::MapI object to get positions for
+
+=head2 add_position_value
+
+ Title   : add_position_value
+ Usage   : $position->add_position_value($map,'100');
+ Function: Add a numeric or string position to the PositionI container 
+           and assoiciate it with a Bio::Map::MapI
+ Returns : none
+ Args    : $map - Bio::Map::MapI
+           String or Numeric coding for a position on a map
+
+=head2 purge_position_values
+
+ Title   : purge_position_values
+ Usage   : $position->purge_position_values
+ Function: Remove all the position values stored for a position
+ Returns : none
+ Args    : [optional] only purge values for a given map
+
+=head2 equals
+
+ Title   : equals
+ Usage   : if( $mappable->equals($mapable2)) ...
+ Function: Test if a position is equal to another position.
+ Returns : boolean
+ Args    : Bio::Map::PositionI
+
+=cut
+
+sub equals{
+   my ($self,$compare) = @_;
+   return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
+   return ( $compare->order == $self->order);
+}
+
+# admittedly these are really the best comparisons in the world
+# but it is a first pass we'll need to refine the algorithm or not 
+# provide general comparisions and require these to be implemented
+# by objects closer to the specific type of data
+
+=head2 less_than
+
+ Title   : less_than
+ Usage   : if( $mappable->less_than($m2) ) ...
+ Function: Tests if a position is less than another position
+           It is assumed that 2 positions are in the same map.
+ Returns : boolean
+ Args    : Bio::Map::PositionI
+
+=cut
+
+
+sub less_than{
+   my ($self,$compare) = @_;
+   return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
+   return ( $compare->order < $self->order);
+}
+
+=head2 greater_than
+
+ Title   : greater_than
+ Usage   : if( $mappable->greater_than($m2) ) ...
+ Function: Tests if position is greater than another position.
+           It is assumed that 2 positions are in the same map.
+ Returns : boolean
+ Args    : Bio::Map::PositionI
+
+=cut
+
+sub greater_than{
+   my ($self,$compare) = @_;
+   return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
+   return ( $compare->order > $self->order);
+}
+
+1;