diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index bf09e81ec7d3912e67fcd3bd56d69cb23fbbf412..d823bd09632dc60330ae2991dd6036f39c2b7b0c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -69,6 +69,7 @@ use Bio::EnsEMBL::TopLevelAssemblyMapper;
use Bio::EnsEMBL::Utils::Cache; #CPAN LRU cache
use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);
+use Bio::EnsEMBL::Utils::SeqRegionCache;
use integer; #do proper arithmetic bitshifts
@@ -79,8 +80,6 @@ my $CHUNKFACTOR = 20; # 2^20 = approx. 10^6
# if the mapper is bigger than that its flushed before registering new stuff:
my $MAX_PAIR_COUNT = 1000;
-#number of seq regions to remember ids fo
-my $SEQ_REGION_CACHE_SIZE = 2500;
=head2 new
@@ -101,10 +100,6 @@ sub new {
$self->{'_asm_mapper_cache'} = {};
- my %cache;
- tie(%cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
- $self->{'_sr_id_cache'} = \%cache;
-
return $self;
}
@@ -319,6 +314,7 @@ sub register_assembled {
asm.cmp_end,
asm.cmp_seq_region_id,
sr.name,
+ sr.length,
asm.ori,
asm.asm_start,
asm.asm_end
@@ -339,10 +335,11 @@ sub register_assembled {
$sth->execute($asm_seq_region_id, $region_start, $region_end, $cmp_cs_id);
my($cmp_start, $cmp_end, $cmp_seq_region_id, $cmp_seq_region, $ori,
- $asm_start, $asm_end);
+ $asm_start, $asm_end, $cmp_seq_region_length);
$sth->bind_columns(\$cmp_start, \$cmp_end, \$cmp_seq_region_id,
- \$cmp_seq_region, \$ori, \$asm_start, \$asm_end);
+ \$cmp_seq_region, \$cmp_seq_region_length, \$ori,
+ \$asm_start, \$asm_end);
#
# Load the unregistered regions of the mapper
@@ -354,8 +351,12 @@ sub register_assembled {
$asm_seq_region, $asm_start, $asm_end,
$ori,
$cmp_seq_region, $cmp_start, $cmp_end);
- $self->{'_sr_id_cache'}->{"$cmp_seq_region:$cmp_cs_id"} =
- $cmp_seq_region_id;
+ my $arr = [ $cmp_seq_region_id, $cmp_seq_region, $cmp_cs_id, $cmp_seq_region_length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$cmp_seq_region:$cmp_cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$cmp_seq_region_id"} =
+ $arr;
}
}
@@ -372,15 +373,16 @@ sub _seq_region_name_to_id {
($sr_name && $cs_id) || throw('seq_region_name and coord_system_id args ' .
'are required');
- my $sr_id = $self->{'_sr_id_cache'}->{"$sr_name:$cs_id"};
-
- return $sr_id if($sr_id);
+ my $arr = $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$sr_name:$cs_id"};
+ if( $arr ) {
+ return $arr->[0];
+ }
# Get the seq_region_id via the name. This would be quicker if we just
# used internal ids instead but stored but then we lose the ability
# the transform accross databases with different internal ids
- my $sth = $self->prepare("SELECT seq_region_id " .
+ my $sth = $self->prepare("SELECT seq_region_id, length " .
"FROM seq_region " .
"WHERE name = ? AND coord_system_id = ?");
@@ -391,10 +393,15 @@ sub _seq_region_name_to_id {
"in coord system $cs_id");
}
- ($sr_id) = $sth->fetchrow_array();
+ my ($sr_id, $sr_length) = $sth->fetchrow_array();
$sth->finish();
- $self->{'_sr_id_cache'}->{"$sr_name:$cs_id"} = $sr_id;
+ $arr = [ $sr_id, $sr_name, $cs_id, $sr_length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$sr_name:$cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$sr_id"} =
+ $arr;
return $sr_id;
}
@@ -442,7 +449,8 @@ sub register_component {
asm.asm_start,
asm.asm_end,
asm.asm_seq_region_id,
- sr.name
+ sr.name,
+ sr.length
FROM
assembly asm, seq_region sr
WHERE
@@ -466,10 +474,15 @@ sub register_component {
"component region cmp_seq_region_id=[$cmp_seq_region_id]");
}
- my ($asm_start, $asm_end, $asm_seq_region_id, $asm_seq_region) =
+ my ($asm_start, $asm_end, $asm_seq_region_id, $asm_seq_region, $asm_seq_region_length) =
$sth->fetchrow_array();
- $self->{'_sr_id_cache'}->{"$asm_seq_region:$asm_cs_id"} = $asm_seq_region_id;
+ my $arr = [ $asm_seq_region_id, $asm_seq_region, $asm_cs_id, $asm_seq_region_length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$asm_seq_region:$asm_cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$asm_seq_region_id"} =
+ $arr;
$sth->finish();
@@ -574,6 +587,7 @@ sub register_chained {
asm.cmp_end,
asm.cmp_seq_region_id,
sr.name,
+ sr.length,
asm.ori,
asm.asm_start,
asm.asm_end
@@ -593,6 +607,7 @@ sub register_chained {
asm.asm_end,
asm.asm_seq_region_id,
sr.name,
+ sr.length,
asm.ori,
asm.cmp_start,
asm.cmp_end
@@ -655,11 +670,11 @@ sub register_chained {
#load the start <-> mid mapper with the results and record the mid cs
#ranges we just added to the mapper
- my ($mid_start, $mid_end, $mid_seq_region_id, $mid_seq_region,
+ my ($mid_start, $mid_end, $mid_seq_region_id, $mid_seq_region, $mid_length,
$ori, $start_start, $start_end);
$sth->bind_columns(\$mid_start, \$mid_end, \$mid_seq_region_id,
- \$mid_seq_region, \$ori, \$start_start,
+ \$mid_seq_region, \$mid_length, \$ori, \$start_start,
\$start_end);
while($sth->fetch()) {
@@ -686,8 +701,12 @@ sub register_chained {
}
#update sr_name cache
- $self->{'_sr_id_cache'}->{"$mid_seq_region:$mid_cs_id"} =
- $mid_seq_region_id;
+ my $arr = [ $mid_seq_region_id, $mid_seq_region, $mid_cs_id, $mid_length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$mid_seq_region:$mid_cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$mid_seq_region_id"} =
+ $arr;
push @mid_ranges,[$mid_seq_region_id,$mid_seq_region,
$mid_start,$mid_end];
@@ -748,11 +767,11 @@ sub register_chained {
#load the end <-> mid mapper with the results and record the mid cs
#ranges we just added to the mapper
- my ($end_start, $end_end, $end_seq_region_id, $end_seq_region,
+ my ($end_start, $end_end, $end_seq_region_id, $end_seq_region, $end_length,
$ori, $mid_start, $mid_end);
$sth->bind_columns(\$end_start, \$end_end, \$end_seq_region_id,
- \$end_seq_region, \$ori, \$mid_start,
+ \$end_seq_region, \$end_length, \$ori, \$mid_start,
\$mid_end);
while($sth->fetch()) {
@@ -766,8 +785,12 @@ sub register_chained {
);
#update sr_name cache
- $self->{'_sr_id_cache'}->{"$end_seq_region:$end_cs_id"} =
- $end_seq_region_id;
+ my $arr = [ $end_seq_region_id, $end_seq_region, $end_cs_id, $end_length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$end_seq_region:$end_cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$end_seq_region_id"} =
+ $arr;
#register this region on the end coord system
$end_registry->check_and_register($end_seq_region, $end_start, $end_end);
@@ -852,7 +875,6 @@ sub register_chained {
sub deleteObj {
my $self = shift;
- delete $self->{'_asm_mapper_cache'};
$self->SUPER::deleteObj();
}
@@ -884,9 +906,12 @@ sub seq_regions_to_ids {
my @out;
foreach my $sr (@$seq_regions) {
- my $id = $self->{'_sr_id_cache'}->{"$sr:$cs_id"};
- $id = $self->_seq_region_name_to_id($sr,$cs_id) if(!$id);
- push @out, $id;
+ my $arr = $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$sr:$cs_id"};
+ if( $arr ) {
+ push( @out, $arr->[0] );
+ } else {
+ push @out, $self->_seq_region_name_to_id($sr,$cs_id);
+ }
}
return \@out;
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 2da06e01fb329f3c0ef324c1f97fd08055da9efd..d313fc02ac25c816795afda53b587cd96d9b8f77 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -95,10 +95,10 @@ use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use Bio::EnsEMBL::Utils::Cache; #CPAN LRU cache
+use Bio::EnsEMBL::Utils::SeqRegionCache;
-@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
-my $SEQ_REGION_CACHE_SIZE = 1000;
+@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
sub new {
my $caller = shift;
@@ -107,14 +107,6 @@ sub new {
my $self = $class->SUPER::new(@_);
- my %name_cache;
- my %id_cache;
-
- tie(%name_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
- tie(%id_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
-
- $self->{'_name_cache'} = \%name_cache;
- $self->{'_id_cache'} = \%id_cache;
return $self;
}
@@ -170,6 +162,10 @@ sub new {
=cut
+
+#
+# ARNE: This subroutine needs simplification!!
+#
sub fetch_by_region {
my ($self, $coord_system_name, $seq_region_name,
$start, $end, $strand, $version) = @_;
@@ -209,7 +205,7 @@ sub fetch_by_region {
$constraint = "sr.coord_system_id = ?";
- $key = lc(join(':',$seq_region_name,$cs->name(), $cs->version));
+ $key = "$seq_region_name:".$cs->dbID();
} else {
$sql = "SELECT sr.name, sr.seq_region_id, sr.length, " .
" cs.coord_system_id " .
@@ -225,10 +221,13 @@ sub fetch_by_region {
#check the cache so we only go to the db if necessary
my $length;
- my $name_cache = $self->{'_name_cache'};
+ my $arr;
+ if( $key ) {
+ $arr = $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{$key};
+ }
- if($key && exists($name_cache->{$key})) {
- $length = $name_cache->{$key}->[1];
+ if( $arr ) {
+ $length = $arr->[3];
} else {
my $sth = $self->prepare($sql . " WHERE sr.name = ? AND " .
$constraint);
@@ -261,9 +260,11 @@ sub fetch_by_region {
my $tmp_cs = ($cs) ? $cs : $csa->fetch_by_dbID($cs_id);
# cache values for future reference
- $key = lc(join(':',$tmp_name,$tmp_cs->name(),$tmp_cs->version));
- $name_cache->{$key} = [$id,$tmp_length];
- $self->{'_id_cache'}->{$id} = [$tmp_name,$tmp_length,$high_cs];
+ my $arr = [ $id, $tmp_name, $cs_id, $tmp_length ];
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$tmp_name:$cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$id"} =
+ $arr;
my $tmp_ver = substr($tmp_name, $prefix_len);
@@ -291,15 +292,15 @@ sub fetch_by_region {
my ($id, $cs_id);
($seq_region_name, $id, $length, $cs_id) = $sth->fetchrow_array();
$sth->finish();
-
- if(!$cs) {
- $cs = $csa->fetch_by_dbID($cs_id);
- $key = lc(join(':',$seq_region_name,$cs->name(), $cs->version));
- }
-
- #cache results to speed up future queries
- $name_cache->{$key} = [$id,$length];
- $self->{'_id_cache'}->{$id} = [$seq_region_name, $length, $cs];
+
+ # cahce to speed up for future queries
+ my $arr = [ $id, $seq_region_name, $cs_id, $length ];
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$seq_region_name:$cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$id"} =
+ $arr;
+
+ $cs = $csa->fetch_by_dbID( $cs_id );
}
}
@@ -384,12 +385,13 @@ sub fetch_by_name {
sub fetch_by_seq_region_id {
my ($self, $seq_region_id) = @_;
- my $id_cache = $self->{'_id_cache'};
-
+ my $arr = $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{ $seq_region_id };
my ($name, $length, $cs);
- if(exists $id_cache->{$seq_region_id}) {
- ($name, $length, $cs) = @{$id_cache->{$seq_region_id}};
+ if( $arr ) {
+ my $cs_id;
+ ($name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
+ $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
} else {
my $sth = $self->prepare("SELECT name, length, coord_system_id " .
"FROM seq_region " .
@@ -406,9 +408,12 @@ sub fetch_by_seq_region_id {
$cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
#cache results to speed up repeated queries
- $id_cache->{$seq_region_id} = [$name, $length, $cs];
- my $key = lc(join(':', $name, $cs->name, $cs->version));
- $self->{'_name_cache'}->{$key} = [$seq_region_id, $length];
+ my $arr = [ $seq_region_id, $name, $cs_id, $length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$name:$cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$seq_region_id"} =
+ $arr;
}
return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM => $cs,
@@ -445,44 +450,42 @@ sub get_seq_region_id {
if(!$slice || !ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
throw('Slice argument is required');
}
-
- my $cs_name = $slice->coord_system->name();
- my $cs_version = $slice->coord_system->version();
+
my $seq_region_name = $slice->seq_region_name();
+ my $key = $seq_region_name.":".$slice->coord_system->dbID();
+ my $arr = $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$key"};
- my $key = lc(join(':', $seq_region_name,$cs_name,$cs_version));
-
- my $name_cache = $self->{'_name_cache'};
-
- if(exists($name_cache->{$key})) {
- return $name_cache->{$key}->[0];
+ if( $arr ) {
+ return $arr->[0];
}
- my $csa = $self->db()->get_CoordSystemAdaptor();
- my $coord_system = $csa->fetch_by_name($cs_name,$cs_version);
+ my $cs_id = $slice->coord_system->dbID();
my $sth = $self->prepare("SELECT seq_region_id, length " .
"FROM seq_region " .
"WHERE name = ? AND coord_system_id = ?");
#force seq_region_name cast to string so mysql cannot treat as int
- $sth->execute("$seq_region_name", $coord_system->dbID());
+ $sth->execute("$seq_region_name", $cs_id );
if($sth->rows() != 1) {
throw("Non existant or ambigous seq_region:\n" .
- " coord_system=[$cs_name],\n" .
- " name=[$seq_region_name],\n" .
- " version=[$cs_version]");
+ " coord_system=[$cs_id],\n" .
+ " name=[$seq_region_name],\n");
+
}
my($seq_region_id, $length) = $sth->fetchrow_array();
$sth->finish();
#cache information for future requests
- $name_cache->{$key} = [$seq_region_id, $length];
- $self->{'_id_cache'}->{$seq_region_id} =
- [$seq_region_name, $length, $coord_system];
-
+ $arr = [ $seq_region_id, $seq_region_name, $cs_id, $length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$seq_region_name:$cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$seq_region_id"} =
+ $arr;
+
return $seq_region_id;
}
@@ -592,8 +595,6 @@ sub fetch_all {
my ($seq_region_id, $name, $length, $cs_id);
$sth->bind_columns(\$seq_region_id, \$name, \$length, \$cs_id);
- my $name_cache = $self->{'_name_cache'};
- my $id_cache = $self->{'_id_cache'};
my $cache_count = 0;
my @out;
@@ -605,14 +606,16 @@ sub fetch_all {
throw("seq_region $name references non-existent coord_system $cs_id.");
}
- my $cs_key = lc($cs->name().':'.$cs_version);
-
#cache values for future reference, but stop adding to the cache once we
#we know we have filled it up
- if($cache_count < $SEQ_REGION_CACHE_SIZE) {
- my $key = lc($name) . ':'. $cs_key;
- $name_cache->{$key} = [$seq_region_id, $length];
- $id_cache->{$seq_region_id} = [$name, $length, $cs];
+ if($cache_count < $Bio::EnsEMBL::Utils::SEQ_REGION_CACHE_SIZE) {
+ my $arr = [ $seq_region_id, $name, $cs_id, $length ];
+
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_name_cache{"$name:$cs_id"} =
+ $arr;
+ $Bio::EnsEMBL::Utils::SeqRegionCache::sr_id_cache{"$seq_region_id"} =
+ $arr;
+
$cache_count++;
}
@@ -655,17 +658,6 @@ sub fetch_all {
}
-sub deleteObj {
- my $self = shift;
-
- $self->SUPER::deleteObj;
-
- $self->{'_id_cache'} = {};
- $self->{'_name_cache'} = {};
- $self->{'_exc_cache'} = {};
-}
-
-
=head2 fetch_by_band
diff --git a/modules/Bio/EnsEMBL/Utils/SeqRegionCache.pm b/modules/Bio/EnsEMBL/Utils/SeqRegionCache.pm
new file mode 100644
index 0000000000000000000000000000000000000000..703af8507fa6e4e865f7d20ac0f3004ea89720cc
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/SeqRegionCache.pm
@@ -0,0 +1,25 @@
+use strict;
+use Bio::EnsEMBL::Utils::Cache;
+
+
+package Bio::EnsEMBL::Utils::SeqRegionCache;
+
+my $SEQ_REGION_CACHE_SIZE = 4000;
+
+my %sr_id_cache;
+my %sr_name_cache;
+
+tie(%sr_name_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
+tie(%sr_name_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
+
+1;
+
+
+#
+# the items to cache should be listrefs to
+# [ sr_id, sr_name, cs_id, sr_length ]
+#
+# The name cache key is "sr_name:cs_id"
+# The id cache is keyed on "sr_id"
+#
+