From 90160e7e4c93e69ad8d0a3b56b61fba277d07885 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Tue, 14 May 2013 16:22:34 +0000
Subject: [PATCH] Swapped the count_by_slice_constraint constraint triggers, as
they were the wrong way round. Test suite was passing by luck. Rewrote
adjoining comments.
---
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 137 ++++++++++--------
1 file changed, 75 insertions(+), 62 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index ef815242c8..aa29abd669 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -584,77 +584,90 @@ sub _create_feature_fast {
Arg [2] : String Custom SQL constraint
Arg [3] : String Logic name to search by
Description : Finds all features with at least partial overlap to the given
- slice and sums them up
+ slice and sums them up.
+ Explanation of workings with projections:
+
+ |-------------------------Constraint Slice---------------------------------|
+ | | | |
+ |--Segment 1--| | |
+ | |--Segment 2, on desired Coordinate System--| |
+ | | |---Segment 3----|
+ #Feature 1# #Feature 2# #Feature 3# |
+ | #####################Feature 4#################### |
+ | #Feature 5# | | |
+
+ Feature 1 is overlapping the original constraint. Counted in Segment 1
+ Feature 2,3 and 4 are counted when inspecting Segment 2
+ Feature 5 is counted in Segment 1
+
Returntype : Integer
=cut
sub count_by_Slice_constraint {
- my ($self, $slice, $constraint, $logic_name) = @_;
-
- assert_ref($slice, 'Bio::EnsEMBL::Slice', 'slice');
-
- my $count = 0;
-
- #Remember the bind params
- my $bind_params = $self->bind_param_generic_fetch();
-
- #Table synonym
- my @tables = $self->_tables;
- my ($table_name, $table_synonym) = @{ $tables[0] };
-
- #Constraints
- $constraint ||= '';
- $constraint = $self->_logic_name_to_constraint( $constraint, $logic_name );
- # If the logic name was invalid, undef was returned
- return $count if ! defined $constraint;
+ my ($self, $slice, $constraint, $logic_name) = @_;
+
+ assert_ref($slice, 'Bio::EnsEMBL::Slice', 'slice');
+
+ my $count = 0;
+
+ #Remember the bind params
+ my $bind_params = $self->bind_param_generic_fetch();
+
+ #Table synonym
+ my @tables = $self->_tables;
+ my ($table_name, $table_synonym) = @{ $tables[0] };
+
+ # Basic constraints limit the feature hits to the starting Slice constraint
+ $constraint ||= '';
+ $constraint = $self->_logic_name_to_constraint( $constraint, $logic_name );
- #Query logic
- my $sa = $slice->adaptor();
- my $proj_ref = $self->_get_and_filter_Slice_projections($slice);
-
- my $proj_ref_length = @{$proj_ref};
- #Manual loop to support look-ahead/behind
- for (my $i = 0; $i < $proj_ref_length; $i++) {
- my $seg = $proj_ref->[$i];
- my $seg_slice = $seg->to_Slice();
- $self->_bind_param_generic_fetch($bind_params);
+ return $count if ! defined $constraint;
+
+ #Query logic
+ my $sa = $slice->adaptor();
+ my $projections = $self->_get_and_filter_Slice_projections($slice);
+
+ my $segment_count = @{$projections};
+ #Manual loop to support look-ahead/behind
+ for (my $i = 0; $i < $segment_count; $i++) {
+ my $seg = $projections->[$i];
+ my $seg_slice = $seg->to_Slice();
+ $self->_bind_param_generic_fetch($bind_params);
- # Because we cannot filter boundary crossing features in code we need to
- # do it in SQL. So we detect when we are not on the original query Slice
- # we do manual filtering by the seg_Slice's start and end. If we are on
- # the *1st* section we only limit by the *end* and when we are on the *last*
- # we filter by the *start*
- #
- # This is the same as fetch_all_by_Slice_constraint()'s in-memory filtering
- # except we need to alter projected features in that code with an offset
- my $local_constraint = $constraint;
- if ( $seg_slice->name() ne $slice->name() ) {
- my ($limit_start, $limit_end) = (1,1); #limit both by default, flags are reset every iteration
- if($i == 0) {
- $limit_start = 0; #don't check start as we are on the final projection
- }
- elsif($i == ($proj_ref_length - 1)) {
- $limit_end = 0; #don't check end as we are on the final projection
- }
- $local_constraint .= ' AND ' if $local_constraint;
- my @conditionals;
+ # We cannot filter boundary crossing features in code, so we constrain the
+ # SQL. We detect when we are not on the original query Slice and manually
+ # filter by the segment Slice's start and end. If we are on "earlier" (5')
+ # projection segments, we only limit by the *end* and when we are on the later
+ # projection segments, we filter by the *start*.
+
+ # This is the same as fetch_all_by_Slice_constraint()'s in-memory filtering
+ # except we need to alter projected features in that code with an offset
+ my $local_constraint = $constraint;
+ if ( $seg_slice->name() ne $slice->name() ) {
+ my ($limit_start, $limit_end) = (1,1); #fully constrained by default, flags are reset every iteration
+ if($i == 0) {
+ $limit_start = 0;
+ } elsif ($i == ($segment_count - 1)) {
+ $limit_end = 0; #don't check end as we are on the final projection
+ }
+ $local_constraint .= ' AND ' if $local_constraint;
+ my @conditionals;
- #Do not cross the start boundary so our feature must be less than slice end on all counts
- if($limit_start) {
- push(@conditionals, sprintf('%1$s.seq_region_start <= %2$d AND %1$s.seq_region_end <= %2$d', $table_synonym, $seg_slice->end));
- }
- #Do not cross the start boundary so our feature must be larger than slice start on all counts
- if($limit_end) {
- push(@conditionals, sprintf('%1$s.seq_region_start >= %2$d AND %1$s.seq_region_end >= %2$d', $table_synonym, $seg_slice->start));
- }
+ if($limit_end) {
+ # Restrict features to the end of this projection segment when after the named segment
+ push(@conditionals, sprintf('%1$s.seq_region_end <= %2$d', $table_synonym, $seg_slice->end));
+ }
+ if($limit_start) {
+ #Do not cross the start boundary on this projection segment
+ push(@conditionals, sprintf('%1$s.seq_region_start >= %2$d', $table_synonym, $seg_slice->start));
+ }
- $local_constraint .= join(q{ AND }, @conditionals);
- }
+ $local_constraint .= join(q{ AND }, @conditionals);
+ }
- my $count_array = $self->_get_by_Slice($seg_slice, $local_constraint, 'count');
- #Data comes out as an array
- $count += $_ for @$count_array;
- }
+ my $count_array = $self->_get_by_Slice($seg_slice, $local_constraint, 'count');
+ $count += $_ for @$count_array;
+ }
return $count;
}
--
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