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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Mapper/Coordinate.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,208 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::Mapper::Coordinate
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Representation of a mapped region in a sequence; returned from Mapper.pm
+when the target region maps on to valid sequence.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Mapper::Coordinate;
+
+use strict;
+
+=head2 new
+
+  Arg [1]     char|int id of object in mapped region
+  Arg [2]     int start of region   
+  Arg [3]     int end of region
+  Arg [4]     int strand if region
+  Arg [5]     Bio::EnsEMBL::CoordSystem  coordsytem of the region
+  Function    creates a new Coordinate object
+  Returntype  Bio::EnsEMBL::Mapper::Coordinate
+  Exceptions  none
+  Status      Stable
+
+=cut
+
+sub new {
+  my ( $proto, $id, $start, $end, $strand, $coord_system, $rank ) = @_;
+
+  my $class = ref($proto) || $proto;
+
+  return
+    bless( { 'id'           => $id,
+             'start'        => $start,
+             'end'          => $end,
+             'strand'       => $strand,
+             'coord_system' => $coord_system,
+             'rank'         => $rank || 0
+           },
+           $class );
+}
+
+
+=head2 start
+
+  Arg  1      int $start
+              start coordinate of object in mapped region
+  Function    getter/setter method
+  Returntype  int
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Coordinate
+  Status      Stable
+
+=cut
+
+sub start {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'start'} = $value;
+  }
+
+  return $self->{'start'};
+}
+
+
+=head2 end
+
+  Arg  1      int $end
+              end coordinate of object in mapped region
+  Function    getter/setter method
+  Returntype  int
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Coordinate
+  Status      Stable
+
+=cut
+
+sub end {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'end'} = $value;
+  }
+
+  return $self->{'end'};
+}
+
+=head2 strand
+
+  Arg  1      int $strand
+              strand of object in mapped region
+  Function    getter/setter method
+  Returntype  int
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Coordinate
+  Status      Stable
+
+=cut
+
+sub strand {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'strand'} = $value;
+  }
+
+  return $self->{'strand'};
+}
+
+=head2 id
+
+  Arg  1      char|int $id
+              id of object in mapped region
+	      e.g. seq_region_id / seq_region_name
+  Function    getter/setter method
+  Returntype  char|int
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Coordinate
+  Status      Stable
+
+=cut
+
+sub id {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'id'} = $value;
+  }
+
+  return $self->{'id'};
+}
+
+=head2 coord_system
+
+  Arg  1      Bio::EnsEMBL::CoordSystem
+  Function    getter/setter method
+  Returntype  Bio::EnsEMBL::CoordSystem
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Coordinate
+  Status      Stable
+
+=cut
+
+sub coord_system {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'coord_system'} = $value;
+  }
+
+  return $self->{'coord_system'};
+}
+
+=head2 length
+
+  Function    getter method
+  Returntype  int
+  Exceptions  none
+  Caller      ?
+  Status      Stable
+
+=cut
+
+sub length {
+  my ($self) = @_;
+
+  return $self->{'end'} - $self->{'start'} + 1;
+}
+
+sub rank {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'rank'} = $value;
+  }
+
+  return $self->{'rank'};
+}
+
+1;