Commit 9c9a1ce1 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Changes in store() to quieten the unit tests.

parent 8f65f33e
......@@ -790,11 +790,9 @@ sub store {
# store translation
#
my @translations =
@{ $db->get_TranslationAdaptor()
->fetch_all_by_Transcript($transcript) };
my $translation = shift(@translations);
my $alt_translations =
$transcript->get_all_alternative_translations();
my $translation = $transcript->translation();
if ( defined($translation) ) {
#make sure that the start and end exon are set correctly
......@@ -865,42 +863,45 @@ sub store {
# Store the alternative translations, if there are any.
#
foreach my $alt_translation (@translations) {
my $start_exon = $alt_translation->start_Exon();
my $end_exon = $alt_translation->end_Exon();
if ( defined($alt_translations) ) {
foreach my $alt_translation ( @{$alt_translations} ) {
my $start_exon = $alt_translation->start_Exon();
my $end_exon = $alt_translation->end_Exon();
if ( !defined($start_exon) ) {
throw("Translation does not define a start exon.");
} elsif ( !defined($end_exon) ) {
throw("Translation does not defined an end exon.");
}
if ( !defined($start_exon) ) {
throw("Translation does not define a start exon.");
} elsif ( !defined($end_exon) ) {
throw("Translation does not defined an end exon.");
}
if ( !defined( $start_exon->dbID() ) ) {
my $key = $start_exon->hashkey();
($start_exon) = grep { $_->hashkey() eq $key } @{$exons};
if ( !defined( $start_exon->dbID() ) ) {
my $key = $start_exon->hashkey();
($start_exon) = grep { $_->hashkey() eq $key } @{$exons};
if ( defined($start_exon) ) {
$alt_translation->start_Exon($start_exon);
} else {
throw(
if ( defined($start_exon) ) {
$alt_translation->start_Exon($start_exon);
} else {
throw(
"Translation's start_Exon does not appear to be one of the "
. "exons in its associated Transcript" );
}
} elsif ( !defined( $end_exon->dbID() ) ) {
my $key = $end_exon->hashkey();
($end_exon) = grep { $_->hashkey() eq $key } @$exons;
}
} elsif ( !defined( $end_exon->dbID() ) ) {
my $key = $end_exon->hashkey();
($end_exon) = grep { $_->hashkey() eq $key } @$exons;
if ( defined($end_exon) ) {
$translation->end_Exon($end_exon);
} else {
throw("Translation's end_Exon does not appear to be one of the "
if ( defined($end_exon) ) {
$translation->end_Exon($end_exon);
} else {
throw(
"Translation's end_Exon does not appear to be one of the "
. "exons in its associated Transcript." );
}
}
}
$db->get_TranslationAdaptor()
->store( $alt_translation, $transc_dbID );
} ## end foreach my $alt_translation...
$db->get_TranslationAdaptor()
->store( $alt_translation, $transc_dbID );
} ## end foreach my $alt_translation...
} ## end if ( defined($alt_translations...))
#
# store the xrefs/object xref mapping
......
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