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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Coordinate/MapperI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,193 @@
+# $Id: MapperI.pm,v 1.5 2002/11/08 09:28:24 heikki Exp $
+#
+# bioperl module for Bio::Coordinate::MapperI
+#
+# 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::MapperI - Interface describing coordinate mappers
+
+=head1 SYNOPSIS
+
+  # not to be used directly
+
+=head1 DESCRIPTION
+
+MapperI defines methods for classes capable for mapping locations
+between coordinate systems.
+
+=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://bugzilla.bioperl.org/
+
+=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
+
+Additional contributors names and emails here
+
+=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::MapperI;
+use vars qw(@ISA );
+use strict;
+
+# Object preamble - inherits from Bio::Root::RootI
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+
+
+=head2 in
+
+ Title   : in
+ Usage   : $obj->in('peptide');
+ Function: Set and read the input coordinate system.
+ Example :
+ Returns : value of input system
+ Args    : new value (optional), Bio::LocationI
+
+=cut
+
+sub in {
+   my ($self,$value) = @_;
+
+   $self->throw_not_implemented();
+
+}
+
+
+=head2 out
+
+ Title   : out
+ Usage   : $obj->out('peptide');
+ Function: Set and read the output coordinate system.
+ Example :
+ Returns : value of output system
+ Args    : new value (optional), Bio::LocationI
+
+=cut
+
+sub out {
+   my ($self,$value) = @_;
+
+   $self->throw_not_implemented();
+}
+
+=head2 swap
+
+ Title   : swap
+ Usage   : $obj->swap;
+ Function: Swap the direction of mapping: input <-> output)
+ Example :
+ Returns : 1
+ Args    : 
+
+=cut
+
+sub swap {
+   my ($self) = @_;
+
+   $self->throw_not_implemented();
+
+}
+
+=head2 test
+
+ Title   : test
+ Usage   : $obj->test;
+ Function: test that both components are of same length
+ Example :
+ Returns : ( 1 | undef )
+ Args    :
+
+=cut
+
+sub test {
+   my ($self) = @_;
+
+   $self->throw_not_implemented();
+}
+
+
+=head2 map
+
+ Title   : map
+ Usage   : $newpos = $obj->map($loc);
+ Function: Map the location from the input coordinate system
+           to a new value in the output coordinate system.
+ Example :
+ Returns : new value in the output coordiante system
+ Args    : Bio::LocationI
+
+=cut
+
+sub map {
+   my ($self,$value) = @_;
+
+   $self->throw_not_implemented();
+
+}
+
+=head2 return_match
+
+ Title   : return_match
+ Usage   : $obj->return_match(1);
+ Function: A flag to turn on the simplified mode of
+           returning only one joined Match object or undef
+ Example :
+ Returns : boolean
+ Args    : boolean (optional)
+
+=cut
+
+sub return_match {
+   my ($self,$value) = @_;
+   if( defined $value) {
+       $value ? ( $self->{'_return_match'} = 1 ) :
+                ( $self->{'_return_match'} = 0 );
+   }
+   return $self->{'_return_match'} || 0 ;
+}
+
+1;
+