diff variant_effect_predictor/Bio/Map/OrderedPositionWithDistance.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/OrderedPositionWithDistance.pm	Thu Apr 11 06:29:17 2013 -0400
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+# BioPerl module for Bio::Map::OrderedPositionWithDistance
+#
+# 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::OrderedPositionWithDistance - 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::OrderedPositionWithDistance;
+	# the first marker in the sequence
+    my $position = new Bio::Map::OrderedPositionWithDistance(-positions => 1,
+			-distance => 22.3 );
+	# the second marker in the sequence, 15.6 units from the fist one
+    my $position2 = new Bio::Map::OrderedPositionWithDistance(-positions => 2,
+			-distance => 15.6 );
+	# the third marker in the sequence, coincidental with the second
+	# marker
+    my $position3 = new Bio::Map::OrderedPositionWithDistance(-positions => 3,
+			-distance => 0 );
+
+
+=head1 DESCRIPTION
+
+This object is an implementation of the PositionI interface and the
+Position object handles the specific values of a position.
+OrderedPositionWithDistance 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]
+
+=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::OrderedPositionWithDistance;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Map::Position;
+
+@ISA = qw(Bio::Map::Position);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Map::OrderedPositionWithDistance();
+ Function: Builds a new Bio::Map::OrderedPositionWithDistance object 
+ Returns : Bio::Map::OrderedPositionWithDistance
+ Args    : -positions  - Should be a single value representing the order
+	of this marker within the list of markers
+	-distance - The distance this marker is from the marker before it.
+		0 reflects coincidentality.
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);
+  $self->{'_positions'} = [];
+  my ($positions,$distance) = $self->_rearrange([qw(POSITIONS DISTANCE)], @args);
+  if( ref($positions) =~ /array/i ) { 
+      foreach my $p ( @$positions ) {
+	  $self->add_position($p);
+      }
+  } else { 
+      $self->add_position($positions);
+  }
+	$distance && $self->distance($distance);
+	
+  return $self;
+
+}
+
+
+=head2 distance($new_distance)
+
+ Title   : distance($new_distance)
+ Usage   : $position->distance(new_distance) _or_
+        $position->distance()
+ Function: get/set the distance of this position from the previous marker
+ Returns : A scalar representing the current distance for this position.
+ Args    : If $new_distance is provided the distance of this Position will
+        be set to $new_distance
+
+=cut
+
+sub distance {
+        my ($self,$distance) = @_;
+        if ($distance) {
+           $self->{'_distance'} = $distance;
+        }
+        return $self->{'_distance'};
+}
+
+
+1;