Commit 790ef9b8 authored by Andy Yates's avatar Andy Yates
Browse files

[ENSCORESW-584] Reverting back to 1.188 version and re-introducing the bug.

We have decided to revert this change. GeneBuilder code has a link to the
existing functionality manifesting itself as subtle silent breakages. The
old functionality has been brought back. Warning added about how possibly
bad using the array from this function is.
parent cad24ffa
......@@ -959,6 +959,14 @@ sub add_Transcript {
Example : my @transcripts = @{ $gene->get_all_Transcripts };
Description: Returns the Transcripts in this gene.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Warning : This method returns the internal transcript array
used by this object. Avoid any modification
of this array. We class use of shift and
reassignment of the loop variable when iterating
this array as modification.
Dereferencing the structure as shown in the example is
a safe way of using this data structure.
Exceptions : none
Caller : general
Status : Stable
......@@ -975,18 +983,7 @@ sub get_all_Transcripts {
$self->{'_transcript_array'} = $transcripts;
# copy of cache references needed to protect Gene cache
if (exists($self->{'_transcript_array'})) {
my @transcripts = @{$self->{'_transcript_array'}};
return \@transcripts;
else {
# Original implementation returned the Gene's cache. If there was no cache
# it returned undef, rather than an empty array reference.
# Code should read: return [];
# Not fixed to retain legacy support.
return $self->{'_transcript_array'};
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