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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/ProteinFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,175 @@
+=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::ProteinFeature
+
+=head1 SYNOPSIS
+
+  my $feature = Bio::EnsEMBL::ProteinFeature->new(
+    -start    => $start,
+    -end      => $end,
+    -hstart   => $hit_start,
+    -hend     => $hit_end,
+    -hseqname => $hit_name
+  );
+
+=head1 DESCRIPTION
+
+ProteinFeature objects represent domains or other features of interest
+on a peptide sequence.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::ProteinFeature;
+
+use strict;
+
+use Bio::EnsEMBL::FeaturePair;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::FeaturePair);
+
+
+
+=head2 new
+
+  Arg [IDESC]           : (optional) string An interpro description
+  Arg [INTERPRO_AC]     : (optional) string An interpro accession
+  Arg [TRANSLATION_ID]  : (optional) integer A translation dbID
+  Arg [...]             : named arguments to FeaturePair superclass
+  Example    :
+
+    $pf =
+      Bio::EnsEMBL::ProteinFeature->new( -IDESC       => $idesc,
+                                         -INTERPRO_AC => $iac,
+                                         @fp_args );
+
+  Description: Instantiates a Bio::EnsEMBL::ProteinFeature
+  Returntype : Bio::EnsEMBL::FeaturePair
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub new {
+  my $proto = shift;
+
+  my $class = ref($proto) || $proto;
+
+  my ( $idesc, $interpro_ac, $translation_id ) =
+    rearrange( [ 'IDESC', 'INTERPRO_AC', 'TRANSLATION_ID' ], @_ );
+
+  my $self = $class->SUPER::new(@_);
+
+  # the strand of protein features is always 0
+  $self->{'strand'}         = 0;
+  $self->{'idesc'}          = $idesc || '';
+  $self->{'interpro_ac'}    = $interpro_ac || '';
+  $self->{'translation_id'} = $translation_id || '';
+
+  return $self;
+}
+
+
+=head2 strand
+
+  Arg [1]    : Ignored
+  Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
+             : the strand to be set.
+  Returntype : int
+  Status     : Stable
+
+=cut
+
+#do not allow the strand to be set
+sub strand {
+  my $self = shift;
+  return $self->{'strand'};
+}
+
+
+
+=head2 idesc
+
+  Arg [1]    : (optional) string The interpro description
+  Example    : print $protein_feature->idesc();
+  Description: Getter/Setter for the interpro description of this protein
+               feature.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub idesc{
+  my $self = shift;
+  $self->{'idesc'} = shift if(@_);
+  return $self->{'idesc'};
+}
+
+
+
+=head2 interpro_ac
+
+  Arg [1]    : (optional) string The interpro accession
+  Example    : print $protein_feature->interpro_ac();
+  Description: Getter/Setter for the interpro accession of this protein
+               feature.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub interpro_ac{
+  my $self = shift;
+  $self->{'interpro_ac'} = shift if(@_);
+  return $self->{'interpro_ac'};
+}
+
+
+=head2 translation_id
+
+  Arg [1]    : (optional) integer The dbID of the translation
+  Example    : print $protein_feature->translation_id();
+  Description: Getter/Setter for the translation dbID of this protein
+               feature.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub translation_id {
+  my $self = shift;
+  $self->{'translation_id'} = shift if (@_);
+  return $self->{'translation_id'};
+}
+
+1;