From 97ab2a62c8f4026b976d0cc5960a2ecccf183805 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 6 Nov 2008 10:40:31 +0000
Subject: [PATCH] Formatting in prep for changes to translate().
---
modules/Bio/EnsEMBL/Transcript.pm | 43 ++++++++++++++++---------------
1 file changed, 22 insertions(+), 21 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 032d674a14..ee7a7a37dd 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1406,26 +1406,24 @@ sub get_all_translateable_Exons {
sub translate {
my ($self) = @_;
- if(!$self->translation()) {
- return undef;
- }
-
+ if ( !defined( $self->translation() ) ) { return undef }
my $mrna = $self->translateable_seq();
- my $display_id = $self->translation->display_id || scalar($self->translation);
+ my $display_id = $self->translation->display_id()
+ || scalar( $self->translation() );
# remove final stop codon from the mrna if it is present
# produced peptides will not have '*' at end
# if terminal stop codon is desired call translatable_seq directly
# and produce a translation from it
- if( CORE::length( $mrna ) % 3 == 0 ) {
+ if ( CORE::length($mrna) % 3 == 0 ) {
$mrna =~ s/TAG$|TGA$|TAA$//i;
}
- if(CORE::length($mrna) <1){
- return undef;
+ if ( CORE::length($mrna) < 1 ) {
+ return undef;
}
my $peptide = Bio::Seq->new( -seq => $mrna,
@@ -1433,27 +1431,30 @@ sub translate {
-alphabet => 'dna',
-id => $display_id );
- # Alternative codon tables (such as the mitochondrial codon table) can
- # be sepcified for a sequence region via the seq_region_attrib table.
- # A list of codon tables and their codes is at:
+ # Alternative codon tables (such as the mitochondrial codon table)
+ # can be sepcified for a sequence region via the seq_region_attrib
+ # table. A list of codon tables and their codes is at:
# http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
- my $codon_table;
- if($self->slice()) {
- my ($attrib) = @{$self->slice()->get_all_Attributes('codon_table')};
- $codon_table = $attrib->value() if($attrib);
- }
+ my $codon_table = 1; # default vertebrate codon table
+ if ( defined( $self->slice() ) ) {
+ my ($attrib) =
+ @{ $self->slice()->get_all_Attributes('codon_table') };
- $codon_table ||= 1; # default vertebrate codon table
+ if ( defined($attrib) ) {
+ $codon_table = $attrib->value();
+ }
+ }
- my $translation = $peptide->translate(undef,undef,undef,$codon_table);
+ my $translation =
+ $peptide->translate( undef, undef, undef, $codon_table );
- if($self->edits_enabled()) {
- $self->translation()->modify_translation( $translation );
+ if ( $self->edits_enabled() ) {
+ $self->translation()->modify_translation($translation);
}
return $translation;
-}
+} ## end sub translate
=head2 seq
--
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