diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/ExternalFeature.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/ExternalFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,160 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::ExternalFeature
+#
+
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 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]>.
+
+
+=head1 NAME
+
+Bio::EnsEMBL::ExternalFeature - A module to represent an externally curated feature 
+mapping from an external_db.
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::ExternalFeature;
+
+my $feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new(
+	-SLICE         => $chr_1_slice,
+	-START         => 1_000_000,
+	-END           => 1_000_024,
+	-STRAND        => -1,
+    -DISPLAY_LABEL => $text,
+    -FEATURE_SET   => $fset,
+    -FEATURE_TYPE  => $ftype,
+);
+
+
+
+=head1 DESCRIPTION
+
+An ExternalFeature object represents the genomic placement of an externally curated
+feature from and DB external to Ensembl.
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::ExternalFeature;
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw );
+use Bio::EnsEMBL::Funcgen::SetFeature;
+use Bio::EnsEMBL::Funcgen::FeatureType;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::SetFeature);
+
+
+=head2 new
+
+ 
+  Arg [-FEATURE_SET]  : Bio::EnsEMBL::Funcgen::FeatureSet
+  Arg [-FEATURE_TYPE] : Bio::EnsEMBL::Funcgen::FeatureType
+  Arg [-ANALYSIS]     : Bio::EnsEMBL::Analysis 
+  Arg [-SLICE]        : Bio::EnsEMBL::Slice - The slice on which this feature is.
+  Arg [-START]        : int - The start coordinate of this feature relative to the start of the slice
+		                it is sitting on. Coordinates start at 1 and are inclusive.
+  Arg [-END]          : int -The end coordinate of this feature relative to the start of the slice
+	                    it is sitting on. Coordinates start at 1 and are inclusive.
+  Arg [-DISPLAY_LABEL]: string - Display label for this feature
+  Arg [-STRAND]       : int - The orientation of this feature. Valid values are 1, -1 and 0.
+  Arg [-dbID]         : (optional) int - Internal database ID.
+  Arg [-ADAPTOR]      : (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor - Database adaptor.
+  Example             : my $feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new(
+										                                  -SLICE         => $chr_1_slice,
+									                                      -START         => 1_000_000,
+                      				                                      -END           => 1_000_024,
+									                                      -STRAND        => -1,
+									                                      -DISPLAY_LABEL => $text,
+									                                      -FEATURE_SET   => $fset,
+                                                                          -FEATURE_TYPE  => $ftpe,
+                                                                         );
+
+
+  Description: Constructor for ExternalFeature objects.
+  Returntype : Bio::EnsEMBL::Funcgen::ExternalFeature
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+	
+  my $class = ref($caller) || $caller;
+  my $self = $class->SUPER::new(@_);
+
+  #Remove this method if we interdb_stable_id to SetFeature
+  ($self->{'interdb_stable_id'}) = rearrange(['INTERDB_STABLE_ID'], @_);
+ 		
+  return $self;
+}
+
+=head2 interdb_stable_id
+
+  Arg [1]    : (optional) int - stable_id e.g 1
+  Example    : my $idb_sid = $feature->interdb_stable_id();
+  Description: Getter for the interdb_stable_id attribute for this feature.
+               This is simply to avoid using internal db IDs for inter DB linking
+  Returntype : int
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub interdb_stable_id {
+  return $_[0]->{'interdb_stable_id'};
+}
+
+
+
+
+=head2 display_label
+
+  Example    : my $label = $feature->display_label();
+  Description: Getter for the display label of this feature.
+  Returntype : String
+  Exceptions : None
+  Caller     : General
+  Status     : Medium risk
+
+=cut
+
+sub display_label {
+  my $self = shift;
+	    
+  if(! $self->{'display_label'}  && $self->adaptor){
+	
+	$self->{'display_label'} = $self->feature_set->feature_type->name().' - ';
+	$self->{'display_label'} .= $self->cell_type->name() if $self->cell_type();
+	$self->{'display_label'} .= $self->feature_type->name() if(defined $self->{'feature_type'});
+  }
+	
+  return $self->{'display_label'};
+}
+
+
+
+1;
+