From 294957fc0f6d9805903878a0e58cc88b81b89203 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 27 Aug 2010 16:08:47 +0000
Subject: [PATCH] In new(): Document TRANSLATION_ID. In translation_id():
Update for this method.
All from Michael S.
---
modules/Bio/EnsEMBL/ProteinFeature.pm | 48 +++++++++++++++------------
1 file changed, 27 insertions(+), 21 deletions(-)
diff --git a/modules/Bio/EnsEMBL/ProteinFeature.pm b/modules/Bio/EnsEMBL/ProteinFeature.pm
index 30b8fbabbf..d9b5368c34 100755
--- a/modules/Bio/EnsEMBL/ProteinFeature.pm
+++ b/modules/Bio/EnsEMBL/ProteinFeature.pm
@@ -55,12 +55,17 @@ use vars qw(@ISA);
=head2 new
- Arg [IDESC] : (optional) string An interpro description
- Arg [INTERPRO_AC] : (optional) string An interpro accession
- Arg [...] : named arguments to FeaturePair superclass
- Example : $pf = Bio::EnsEMBL::ProteinFeature->new(-IDESC => $idesc,
- -INTERPRO_AC => $iac,
- @fp_args);
+ 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
@@ -70,18 +75,19 @@ use vars qw(@ISA);
=cut
sub new {
- my $caller = shift;
+ my $proto = shift;
- my $class = ref($caller) || $caller;
+ my $class = ref($proto) || $proto;
- my ($idesc, $interpro_ac, $translation_id) = rearrange(['IDESC', 'INTERPRO_AC', 'TRANSLATION_ID'], @_);
+ 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 || '';
+ # 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;
@@ -110,7 +116,7 @@ sub strand {
Arg [1] : (optional) string The interpro description
Example : print $protein_feature->idesc();
- Description: Getter/Setter for the interpro description of this protein
+ Description: Getter/Setter for the interpro description of this protein
feature.
Returntype : string
Exceptions : none
@@ -131,7 +137,7 @@ sub idesc{
Arg [1] : (optional) string The interpro accession
Example : print $protein_feature->interpro_ac();
- Description: Getter/Setter for the interpro accession of this protein
+ Description: Getter/Setter for the interpro accession of this protein
feature.
Returntype : string
Exceptions : none
@@ -147,11 +153,11 @@ sub interpro_ac{
}
-=head2 idesc
+=head2 translation_id
- Arg [1] : (optional) string The interpro description
- Example : print $protein_feature->idesc();
- Description: Getter/Setter for the interpro description of this protein
+ 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
@@ -160,9 +166,9 @@ sub interpro_ac{
=cut
-sub translation_id{
+sub translation_id {
my $self = shift;
- $self->{'translation_id'} = shift if(@_);
+ $self->{'translation_id'} = shift if (@_);
return $self->{'translation_id'};
}
--
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