diff variant_effect_predictor/Bio/EnsEMBL/Variation/ReadCoverage.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/ReadCoverage.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,167 @@
+=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
+
+# Ensembl module for Bio::EnsEMBL::Variation::ReadCoverage
+#
+# Copyright (c) 2005 Ensembl
+#
+
+
+=head1 NAME
+
+Bio::EnsEMBL::Variation::ReadCoverage - A coverage reagion for a read.
+
+=head1 SYNOPSIS
+
+    # Read coverage feature representing a genomic region covered by 1 read
+
+    $rc = Bio::EnsEMBL::Variation::ReadCoverage->new
+       (-start   => 100,
+        -end     => 200,
+        -slice   => $slice,
+        -level   => 1.
+        -sample  => $individual);
+
+    $rc = $rc->transform('supercontig');
+
+    print $rc->start(), "-", $rc->end(), "\n";
+
+
+=head1 DESCRIPTION
+
+This is a class representing the read coverage information
+from the ensembl-variation database. A ReadCoverage behaves as any other Ensembl feature.
+
+See B<Bio::EnsEMBL::Feature>.
+
+=head1 METHODS
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Variation::ReadCoverage;
+
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::Argument  qw(rearrange);
+
+our @ISA = ('Bio::EnsEMBL::Feature');
+
+
+=head2 new
+
+  Arg [-ADAPTOR] :
+    see superclass constructor
+
+  Arg [-START] :
+    see superclass constructor
+  Arg [-END] :
+    see superclass constructor
+  Arg [-SLICE] :
+    see superclass constructor
+
+  Arg [-LEVEL] :
+    int - the number of times the region represented by start and end has been seen
+
+  Arg [-SAMPLE] :
+    Bio::EnsEMBL::Variation::Individual - the individual
+                     in which the allele was recorded
+    
+  Example    :
+    $rc = Bio::EnsEMBL::Variation::ReadCoverage->new
+       (-start   => 100,
+        -end     => 100,
+        -slice   => $slice,
+        -level  => 1,
+        -sample => $individual);
+
+  Description: Constructor. Instantiates a new ReadCoverage object.
+  Returntype : Bio::EnsEMBL::Variation::ReadCoverage
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+  my $class = ref($caller) || $caller;
+
+  my $self = $class->SUPER::new(@_);
+  my ($level, $individual) =
+    rearrange([qw(LEVEL SAMPLE)], @_);
+
+  $self->{'level'}    = $level;
+  $self->{'sample'}   = $individual;
+
+  return $self;
+}
+
+
+=head2 level
+
+    Arg[1]      : int $newval (optional)
+                  The new value to set the level attribute to
+    Example     : $depth = $obj->level();
+    Description : Getter/Setter for the level attribute. The level is
+                  the number of times this feature has been seen in the genome
+    ReturnType  : int 
+    Exceptions  : none
+    Caller      : general
+    Status      : At Risk
+
+=cut
+
+sub level{
+    my $self = shift;
+    return $self->{'level'} = shift if (@_);
+    return $self->{'level'};
+}
+
+
+=head2 sample
+
+  Arg [1]    : Bio::EnsEMBL::Variation::Individual $newval (optional)
+               The new value to set the sample attribute to
+  Example    : $individual = $rc->sample();
+  Description: Getter/Setter for the individual attribute
+  Returntype : Bio::EnsEMBL::Variation::Individual
+  Exceptions : throw on incorrect argument
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub sample{
+  my $self = shift;
+
+  if(@_) {
+    if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Individual')) {
+      throw('Bio::EnsEMBL::Variation::Individual argument expected.');
+    }
+    $self->{'sample'} = shift;
+  }
+
+  return $self->{'sample'};
+}
+
+1;