From 8b6666d7f564c29bf323483004dca1e99388ba8f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 1 Sep 2010 13:51:27 +0000
Subject: [PATCH] Michael S. noticed that we're blowing away the exon sequence
cache unneccesarily in add_Attributes(). Transcript attributes do not affect
exon sequences. Also, the code tried to fiddle with the internals of the
exon object, which is a no-no (especially since those particular internals
did not exist!).
While at it, I changed a few of "$hash->{'key'} = undef" into
"delete($hash->{'key'})".
---
modules/Bio/EnsEMBL/Transcript.pm | 31 +++++++++++++------------------
1 file changed, 13 insertions(+), 18 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index c645e09fa1..83fc4c91b1 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1137,39 +1137,34 @@ sub get_all_Attributes {
=cut
sub add_Attributes {
- my $self = shift;
- my @attribs = @_;
+ my ( $self, @attribs ) = @_;
- if ( !exists $self->{'attributes'} ) {
+ if ( !exists( $self->{'attributes'} ) ) {
$self->{'attributes'} = [];
}
my $seq_change = 0;
- for my $attrib (@attribs) {
- if ( !$attrib->isa("Bio::EnsEMBL::Attribute") ) {
- throw("Argument to add_Attribute "
- . "has to be an Bio::EnsEMBL::Attribute" );
- }
+ foreach my $attrib (@attribs) {
+ assert_ref( $attrib, 'Bio::EnsEMBL::Attribute' );
+
push( @{ $self->{'attributes'} }, $attrib );
- if ( $attrib->code eq "_rna_edit" ) {
+
+ if ( $attrib->code() eq "_rna_edit" ) {
$seq_change = 1;
}
}
+
if ($seq_change) {
- foreach my $ex ( @{ $self->get_all_Exons() } ) {
- $ex->{'_trans_exon_array'} = undef;
- $ex->{'_seq_cache'} = undef;
- }
- my $translation = $self->translation;
+ my $translation = $self->translation();
if ( defined($translation) ) {
- $translation->{seq} = undef;
+ delete( $translation->{'seq'} );
}
}
# flush cdna coord cache b/c we may have added a SeqEdit
- $self->{'cdna_coding_start'} = undef;
- $self->{'cdna_coding_end'} = undef;
- $self->{'transcript_mapper'} = undef;
+ delete( $self->{'cdna_coding_start'} );
+ delete( $self->{'cdna_coding_end'} );
+ delete( $self->{'transcript_mapper'} );
} ## end sub add_Attributes
--
GitLab