Commit e595a961 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Method optimisation removing multiple calls to the same method with no apparent reason

parent 3ca76e1a
......@@ -69,7 +69,6 @@ sub print_feature {
my @endcs = $self->_make_stop_codon_features($transcript);
my ($hasstart, $hasend) = $self->_check_start_and_stop($transcript);
# TODO: ask Andy if this is safe
my $dbname = $transcript->adaptor()->dbc()->dbname();
my $vegadb = $dbname =~ /vega/;
my $gene = $transcript->get_Gene();
......@@ -165,7 +164,7 @@ sub print_feature {
$exon == $transcript->translation->start_Exon && $hasstart) {
my $tmpcnt = $count;
foreach my $startc (@startcs) {
# here we should check the start codon covers 3 bases
# here we should check the start codon covers 3 bases
print $fh $idstr . "\t" .
$transcript_biotype . "\t" .
'start_codon' . "\t" .
......@@ -272,8 +271,6 @@ sub _make_start_codon_features {
return (()) unless $trans->translation;
my @translateable = @{$trans->get_all_translateable_Exons};
my @pepgencoords = $trans->pep2genomic(1,1);
# cdna can come padded these days so allow gap at the start
......@@ -292,7 +289,7 @@ sub _make_start_codon_features {
throw(sprintf "Pep start (end of) for transcript %s maps to gap", $trans->display_id);
}
@translateable = @{$trans->get_all_translateable_Exons};
my @translateable = @{$trans->get_all_translateable_Exons};
my @startc_feat;
my $phase = 0;
foreach my $pepgencoord (@pepgencoords) {
......
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