From 17c888b4e04ed6c29f96345afa85be553c0d1b3d Mon Sep 17 00:00:00 2001
From: Stephen Searle <searle@sanger.ac.uk>
Date: Tue, 5 Apr 2005 18:41:21 +0000
Subject: [PATCH] Added supporting feature lazy loading
---
modules/Bio/EnsEMBL/Transcript.pm | 34 ++++++++++++++++++++++++++++++-
1 file changed, 33 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 4c3bb36d1b..05b5d5c34a 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -243,6 +243,14 @@ sub add_DBEntry {
sub get_all_supporting_features {
my $self = shift;
+
+ if( !exists $self->{_supporting_evidence} ) {
+ if($self->adaptor) {
+ my $tsfa = $self->adaptor->db->get_TranscriptSupportingFeatureAdaptor();
+ $self->{_supporting_evidence} = $tsfa->fetch_all_by_Transcript($self);
+ }
+ }
+
return $self->{_supporting_evidence} || [];
}
@@ -273,7 +281,11 @@ sub add_supporting_features {
# check whether this feature object has been added already
FEATURE: foreach my $feature (@features) {
- unless($feature && $feature->isa("Bio::EnsEMBL::FeaturePair")) {
+ if (!defined($feature) || ref($feature) eq "ARRAY") {
+ throw("Element in transcript supporting features array is undefined or is an ARRAY for " . $self->dbID);
+ }
+ if (!$feature || !$feature->isa("Bio::EnsEMBL::FeaturePair")) {
+ print "feature = " . $feature . "\n";
throw("Supporting feat [$feature] not a " .
"Bio::EnsEMBL::FeaturePair");
}
@@ -1603,6 +1615,16 @@ sub transform {
$new_transcript->{'_trans_exon_array'} = \@new_exons;
}
+ if( exists $self->{'_supporting_evidence'} ) {
+ my @new_features;
+ for my $old_feature ( @{$self->{'_supporting_evidence'}} ) {
+ my $new_feature = $old_feature->transform( @_ );
+ push( @new_features, $new_feature );
+ }
+ $new_transcript->{'_supporting_evidence'} = \@new_features;
+ }
+
+
# flush cached internal values that depend on the exon coords
$new_transcript->{'transcript_mapper'} = undef;
$new_transcript->{'coding_region_start'} = undef;
@@ -1658,6 +1680,16 @@ sub transfer {
$new_transcript->{'_trans_exon_array'} = \@new_exons;
}
+ if( exists $self->{'_supporting_evidence'} ) {
+ my @new_features;
+ for my $old_feature ( @{$self->{'_supporting_evidence'}} ) {
+ my $new_feature = $old_feature->transfer( @_ );
+ push( @new_features, $new_feature );
+ }
+ $new_transcript->{'_supporting_evidence'} = \@new_features;
+ }
+
+
# flush cached internal values that depend on the exon coords
$new_transcript->{'transcript_mapper'} = undef;
$new_transcript->{'coding_region_start'} = undef;
--
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