Commit 571f28ab authored by Monika Komorowska's avatar Monika Komorowska
Browse files

Internal method _build_circular_slice_cache added

parent 3c8204c8
......@@ -120,7 +120,6 @@ sub new {
$self->{'sr_name_cache'} = $seq_region_cache->{'name_cache'};
$self->{'sr_id_cache'} = $seq_region_cache->{'id_cache'};
$self->{'lrg_region_test'} = undef;
my $meta_container = $self->db->get_MetaContainer();
my @values = $meta_container->list_value_by_key("LRG");
......@@ -499,6 +498,7 @@ sub fetch_by_region_unique {
my @out = ();
my $slice = $self->fetch_by_region(@_);
if ( !exists( $self->{'asm_exc_cache'} ) ) {
$self->_build_exception_cache();
}
......@@ -602,6 +602,7 @@ sub fetch_by_seq_region_id {
my $arr = $self->{'sr_id_cache'}->{$seq_region_id};
my ( $name, $length, $cs, $cs_id );
if ( $arr && defined( $arr->[2] ) ) {
( $name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
$cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
......@@ -778,6 +779,7 @@ sub fetch_all {
my %bad_vals=();
#
# Get a hash of non reference seq regions
#
......@@ -1241,6 +1243,7 @@ sub fetch_by_Feature{
throw('Feature must be attached to a valid slice.');
}
my $fstart = $feature->start();
my $fend = $feature->end();
if(!defined($fstart) || !defined($fend)) {
......@@ -1864,6 +1867,36 @@ LSQL
} ## end sub cache_toplevel_seq_mappings
sub _build_circular_slice_cache {
my $self = shift;
# build up a cache of circular sequence region ids
my $sth =
$self->prepare( "SELECT sra.seq_region_id FROM seq_region_attrib sra "
. "INNER JOIN attrib_type at ON sra.attrib_type_id = at.attrib_type_id "
. "INNER JOIN seq_region sr ON sra.seq_region_id = sr.seq_region_id "
. "INNER JOIN coord_system cs ON sr.coord_system_id = cs.coord_system_id "
. "WHERE code = 'circular_seq' and cs.species_id = ?");
$sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
$sth->execute();
my $id;
my %hash;
if ( ($id) = $sth->fetchrow_array() ) {
$self->{'circular_sr_id_cache'} = \%hash;
$self->{'is_circular'} = 1;
$hash{ $id } = $id;
while ( ($id) = $sth->fetchrow_array() ) {
$hash{ $id } = $id;
}
} else {
$self->{'is_circular'} = 0;
}
$sth->finish();
} ## end _build_circular_slice_cache
#####################################
# sub DEPRECATED METHODs
#####################################
......@@ -2077,4 +2110,8 @@ sub fetch_by_chr_name{
}
1;
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