diff variant_effect_predictor/Bio/Coordinate/Chain.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Coordinate/Chain.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,214 @@
+# $Id: Chain.pm,v 1.1 2002/10/24 17:35:30 heikki Exp $
+#
+# bioperl module for Bio::Coordinate::Chain
+#
+# Cared for by Heikki Lehvaslaiho <[e-mail]>
+#
+# Copyright Heikki Lehvaslaiho
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Coordinate::Chain - Mapping locations through a chain of  coordinate mappers
+
+=head1 SYNOPSIS
+
+  # create Bio::Coordinate::Pairs, or any MapperIs, somehow
+  $pair1; $pair2;
+
+  # add them into a Chain
+  $collection = Bio::Coordinate::Chain->new;
+  $collection->add_mapper($pair1);
+  $collection->add_mapper($pair2);
+
+  # create a position and map it
+  $pos = Bio::Location::Simple->new (-start => 5, -end => 9 );
+  $match = $collection->map($pos);
+  if ($match) {
+      sprintf "Matches at %d-%d\n", $match->start, $match->end,
+  } else {
+      print "No match\n";
+  }
+
+=head1 DESCRIPTION
+
+This class assumes that you have built several mappers and want to
+link them together so that output from the previous mapper is the next
+mappers input. This way you can build arbitrarily complex mappers from
+simpler components.
+
+Note that Chain does not do any sanity checking on its mappers. You
+are solely responsible that input and output coordinate systems,
+direction of mapping and parameters internal to mappers make sense
+when chained together.
+
+To put it bluntly, the present class is just a glorified foreach loop
+over an array of mappers calling the map method.
+
+It would be neat to an internal function that would generate a new
+single step mapper from those included in the chain. It should speed
+things up considerably. Any volunteers?
+
+=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 lists  Your participation is much appreciated.
+
+  [e-mail]                         - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 Reporting Bugs
+
+report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.  Bug reports can be submitted via
+ email or the web:
+
+  [e-mail]
+  http://bio.perl.org/bioperl-bugs/
+
+=head1 AUTHOR - Heikki Lehvaslaiho
+
+Email:  [e-mail]
+Address:
+
+     EMBL Outstation, European Bioinformatics Institute
+     Wellcome Trust Genome Campus, Hinxton
+     Cambs. CB10 1SD, United Kingdom
+
+=head1 CONTRIBUTORS
+
+Ewan Birney, [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::Coordinate::Chain;
+use vars qw(@ISA );
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+use Bio::Root::Root;
+use Bio::Coordinate::MapperI;
+use Bio::Coordinate::Result;
+use Bio::Coordinate::Collection;
+
+@ISA = qw(Bio::Coordinate::Collection Bio::Coordinate::MapperI);
+
+
+=head2 map
+
+ Title   : map
+ Usage   : $newpos = $obj->map($pos);
+ Function: Map the location through all the mappers in the chain.
+ Example :
+ Returns : new Location in the output coordiante system
+ Args    : a Bio::Location::Simple object
+
+=cut
+
+sub map {
+    my ($self,$value) = @_;
+
+    $self->throw("Need to pass me a value.")
+	unless defined $value;
+    $self->throw("I need a Bio::Location, not [$value]")
+	unless $value->isa('Bio::LocationI');
+    $self->throw("No coordinate mappers!")
+	unless $self->each_mapper;
+
+    my $res = new Bio::Coordinate::Result;
+
+    foreach my $mapper ($self->each_mapper) {
+
+	my $res = $mapper->map($value);
+	return undef unless $res->each_match;
+	$value = $res->match;
+    }
+
+   return $value;
+}
+
+
+=head2 Inherited methods
+
+=cut
+
+=head2 add_mapper
+
+ Title   : add_mapper
+ Usage   : $obj->add_mapper($mapper)
+ Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
+           Sets _is_sorted() to false.
+ Example : 
+ Returns : 1 when succeeds, 0 for failure.
+ Args    : mapper object
+
+=cut
+
+=head2 mappers
+
+ Title   : mappers
+ Usage   : $obj->mappers();
+ Function: Returns or sets a list of mappers.
+ Example : 
+ Returns : array of mappers
+ Args    : array of mappers
+
+=cut
+
+=head2 each_mapper
+
+ Title   : each_mapper
+ Usage   : $obj->each_mapper();
+ Function: Returns a list of mappers.
+ Example : 
+ Returns : array of mappers
+ Args    : none
+
+=cut
+
+=head2 swap
+
+ Title   : swap
+ Usage   : $obj->swap;
+ Function: Swap the direction of mapping;input <-> output
+ Example :
+ Returns : 1
+ Args    : 
+
+=cut
+
+=head2 test
+
+ Title   : test
+ Usage   : $obj->test;
+ Function: test that both components of all pairs are of the same length.
+           Ran automatically.
+ Example :
+ Returns : boolean
+ Args    :
+
+=cut
+
+
+
+sub sort{
+   my ($self) = @_;
+   $self->warn("You do not really want to sort your chain, do you!\nDoing nothing.");
+}
+
+1;
+