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Commit bbb81025 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Use a row cache and fetchall_arrayref() instead of single calls to 

fetchrow_arrayref().
parent 4e00396a
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Showing with 31 additions and 29 deletions
modules/Bio/EnsEMBL/Collection.pm
View file @ bbb81025
......@@ -1275,40 +1275,42 @@ sub _objs_from_sth {
my $slice_name = $this->slice()->name();
my $slice_start = $this->slice()->start();
while ( my $entry = $sth->fetchrow_arrayref() ) {
if ( !defined($segment)
|| $segment !=
$SEQ_REG_MAP{$slice_name}{ $entry->[ENTRY_SEQREGIONID] } )
{
$segment =
$SEQ_REG_MAP{$slice_name}{ $entry->[ENTRY_SEQREGIONID] };
$segment_slice = $segment->to_Slice();
$segment_slice_start = $segment_slice->start();
$segment_slice_strand = $segment_slice->strand();
if ( $segment_slice_strand == -1 ) {
$segment_offset = $segment->from_end();
} else {
$segment_offset = $segment->from_start();
while ( my $rowcache = $sth->fetchall_arrayref( undef, 1000 ) ) {
while ( my $entry = shift( @{$rowcache} ) ) {
if ( !defined($segment)
|| $segment !=
$SEQ_REG_MAP{$slice_name}{ $entry->[ENTRY_SEQREGIONID] } )
{
$segment =
$SEQ_REG_MAP{$slice_name}{ $entry->[ENTRY_SEQREGIONID] };
$segment_slice = $segment->to_Slice();
$segment_slice_start = $segment_slice->start();
$segment_slice_strand = $segment_slice->strand();
if ( $segment_slice_strand == -1 ) {
$segment_offset = $segment->from_end();
} else {
$segment_offset = $segment->from_start();
}
}
}
my $start = $slice_start + $segment_offset;
my $end = $start;
my $start = $slice_start + $segment_offset;
my $end = $start;
if ( $segment_slice_strand == -1 ) {
$start -= $entry->[ENTRY_SEQREGIONEND] - $segment_slice_start;
$end -= $entry->[ENTRY_SEQREGIONSTART] - $segment_slice_start;
} else { # Assumes '0' is really the positive strand.
$start += $entry->[ENTRY_SEQREGIONSTART] - $segment_slice_start;
$end += $entry->[ENTRY_SEQREGIONEND] - $segment_slice_start;
}
if ( $segment_slice_strand == -1 ) {
$start -= $entry->[ENTRY_SEQREGIONEND] - $segment_slice_start;
$end -= $entry->[ENTRY_SEQREGIONSTART] - $segment_slice_start;
} else { # Assumes '0' is really the positive strand.
$start += $entry->[ENTRY_SEQREGIONSTART] - $segment_slice_start;
$end += $entry->[ENTRY_SEQREGIONEND] - $segment_slice_start;
}
$entry->[ENTRY_SEQREGIONSTART] = $start - 1;
$entry->[ENTRY_SEQREGIONEND] = $end - 1;
$entry->[ENTRY_SEQREGIONSTART] = $start - 1;
$entry->[ENTRY_SEQREGIONEND] = $end - 1;
push( @features, [ @{$entry} ] );
} ## end while ( my $entry = $sth->fetchrow_arrayref...
push( @features, [ @{$entry} ] );
} ## end while ( my $entry = shift...
} ## end while ( my $rowcache = $sth...
$sth->finish();
return \@features;
......
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