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Commit 90160e7e authored by Kieron Taylor's avatar Kieron Taylor :angry:
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Swapped the count_by_slice_constraint constraint triggers, as they were the... 

Swapped the count_by_slice_constraint constraint triggers, as they were the wrong way round. Test suite was passing by luck. Rewrote adjoining comments.
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modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+ 75
− 62
View file @ 90160e7e
......@@ -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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