From a032c47caf9933b8ea7f2365c5e5f6c88d5723a5 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 13 Aug 2004 15:30:14 +0000
Subject: [PATCH] max feature length can be overridden, allows optimization for
misc feature retrieval
---
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 19 +++++++++++++++++--
.../Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm | 11 ++++++++++-
2 files changed, 27 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index a76129a17d..87a7fa896c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -492,7 +492,7 @@ sub _slice_fetch {
if($feat_cs->equals($slice_cs)) {
# no mapping is required if this is the same coord system
- my $max_len =
+ my $max_len = $self->_max_feature_length() ||
$mcc->fetch_max_length_by_CoordSystem_feature_type($feat_cs,$tab_name);
my $constraint = $orig_constraint;
@@ -552,7 +552,7 @@ sub _slice_fetch {
} else {
# do multiple split queries using start / end constraints
- my $max_len =
+ my $max_len = $self->_max_feature_length() ||
$mcc->fetch_max_length_by_CoordSystem_feature_type($feat_cs,
$tab_name);
my $len = @coords;
@@ -1044,6 +1044,21 @@ sub _objs_from_sth {
}
+
+#
+# Internal function. Allows the max feature length which is normally
+# retrieved from the meta_coord table to be overridden. This allows
+# for some significant optimizations to be put in when it is known
+# that requested features will not be over a certain size.
+#
+sub _max_feature_length {
+ my $self = shift;
+ return $self->{'_max_feature_length'} = shift if(@_);
+ return $self->{'_max_feature_length'};
+}
+
+
+
=head1 DEPRECATED METHODS
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
index ea1baf56de..c62ad8a902 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
@@ -87,8 +87,10 @@ sub fetch_all_by_Slice_and_set_code {
my $msa = $self->db->get_MiscSetAdaptor();
my @sets = ();
+ my $max_len = 0;
foreach my $set_code (@_) {
my $set = $msa->fetch_by_code($set_code);
+ $max_len = $set->longest_feature() if($set->longest_feature > $max_len);
if(!$set) { warning("No misc_set with code [$set_code] exists") }
else { push @sets, $set->dbID; }
}
@@ -100,7 +102,14 @@ sub fetch_all_by_Slice_and_set_code {
} else {
return [];
}
- return $self->fetch_all_by_Slice_constraint($slice, $constraint);
+
+ $self->_max_feature_length($max_len);
+
+ my $results = $self->fetch_all_by_Slice_constraint($slice, $constraint);
+
+ $self->_max_feature_length(undef);
+
+ return $results;
}
--
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