diff variant_effect_predictor/Bio/EnsEMBL/SimpleFeature.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/SimpleFeature.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,187 @@
+=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::SimpleFeature - A simple feature with a location and label
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::SimpleFeature;
+
+  $feature = Bio::EnsEMBL::SimpleFeature->new(
+    -start         => 100,
+    -end           => 220,
+    -strand        => -1,
+    -slice         => $slice,
+    -analysis      => $analysis,
+    -score         => 58,
+    -display_label => 'EponineTSS',
+    -dbID          => 1230,
+    -adaptor       => $adaptor
+  );
+
+=head1 DESCRIPTION
+
+This is a simple feature which extends the Feature class to add
+display_label and score attributes.
+
+=head1 METHODS
+
+=cut
+
+use strict;
+
+package Bio::EnsEMBL::SimpleFeature;
+
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Scalar::Util qw(weaken isweak);
+
+@ISA = qw(Bio::EnsEMBL::Feature);
+
+
+=head2 new
+
+  Arg [DISPLAY_LABEL]: The label assigned to this simple feature
+  Arg [...]  : Named arguments passed to superclass
+  Example    : $feature = Bio::EnsEMBL::SimpleFeature->new
+                        (-start    => 1,
+                         -end      => 100,
+                         -strand   => 1,
+                         -slice    => $slice,
+                         -analysis => $analysis,
+                         -adaptor => $adaptor,
+                         -dbID    => 10,
+                         -display_label => 'EponineTSS',
+                         -score => 100);
+  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
+               of this method are instantiated, rather than this class itself.
+  Returntype : Bio::EnsEMBL::Feature
+  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
+  Caller     : general, subclass constructors
+  Status     : Stable
+
+=cut
+
+sub new {
+  my $caller = shift;
+
+  #allow this to be called as class or object method
+  my $class = ref($caller) || $caller;
+  my $self = $class->SUPER::new(@_);
+
+  my ($display_label, $score) = rearrange(['DISPLAY_LABEL','SCORE'],@_);
+
+  $self->{'display_label'} = $display_label;
+  $self->{'score'} = $score;
+
+  return $self;
+}
+
+
+=head2 new_fast
+
+  Arg [1]    : hashref to be blessed
+  Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
+  Exceptions : none
+  Returntype : Bio::EnsEMBL::Feature
+  Caller     : general, subclass constructors
+  Status     : Stable
+
+=cut
+
+
+sub new_fast {
+  my $class = shift;
+  my $hashref = shift;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
+}
+
+
+=head2 display_label
+
+  Arg [1]    : (optional) string $value
+  Example    : $label = $simple_feature->display_label();
+  Description: Getter/Setter for the display label associated with this
+               feature.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub display_label{
+  my $self = shift;
+
+  $self->{'display_label'} = shift if(@_);
+
+  return $self->{'display_label'};
+}
+
+
+=head2 display_id
+
+  Arg [1]    : none
+  Example    : print $rf->display_id();
+  Description: This method returns a string that is considered to be
+               the 'display' identifier.  For simple features this is the 
+               display_label if it is available otherwise it is an empty 
+               string.
+  Returntype : string
+  Exceptions : none
+  Caller     : web drawing code
+  Status     : Stable
+
+=cut
+
+sub display_id {
+  my $self = shift;
+  return $self->{'display_label'} || '';
+}
+
+
+
+=head2 score
+
+  Arg [1]    : (optional) string $value
+  Example    : $score = $simple_feature->score();
+  Description: Getter/Setter for the score associated with this
+               feature.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub score {
+  my $self = shift;
+  $self->{'score'} = shift if(@_);
+  return $self->{'score'};
+}
+
+
+1;