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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Mapper/Gap.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,135 @@
+=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::Gap
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Representation of a gap in a sequence; returned from Mapper.pm when the
+target region is in a gap.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Mapper::Gap;
+
+use strict;
+
+=head2 new
+
+  Arg [1]    : int $start
+  Arg [2]    : int $end
+  Example    : $gap = Bio::EnsEMBL::Mapper::Gap($start, $end);
+  Description: Creates a new Gap object.
+  Returntype : Bio::EnsEMBL::Mapper::Gap
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::Mapper
+  Status     : Stable
+
+=cut
+
+sub new {
+  my ( $proto, $start, $end, $rank ) = @_;
+
+  my $class = ref($proto) || $proto;
+
+  return bless( { 'start' => $start, 'end' => $end, 'rank' => $rank  || 0 }, $class );
+}
+
+=head2 start
+
+  Arg [1]    : (optional) int $start
+               start coordinate of gap region
+  Example    : $start = $gap->start();
+  Description: Getter/Setter for the start attribute
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub start {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'start'} = $value;
+  }
+
+  return $self->{'start'};
+}
+
+=head2 end
+
+  Arg [1]    : (optional) int $newval
+               The new value to set the end coordinate to
+  Example    : $end = $gap->end()
+  Description: Getter/Setter for the end coordinate of the gap region
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub end {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'end'} = $value;
+  }
+
+  return $self->{'end'};
+}
+
+=head2 length
+
+  Arg [1]    : none
+  Example    : $len = $gap->length();
+  Description: Getter for the length of this gap region
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub length {
+  my ($self) = @_;
+
+  return $self->{'end'} - $self->{'start'} + 1;
+}
+
+sub rank {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'rank'} = $value;
+  }
+
+  return $self->{'rank'};
+}
+
+1;