From 0bfeb666fcfc61186abc964007e84eb7ca2ff4e4 Mon Sep 17 00:00:00 2001
From: ens-bwalts <bwalts@ebi.ac.uk>
Date: Wed, 20 Nov 2019 10:53:25 +0000
Subject: [PATCH] factor interval tree construction out into a separate method
---
modules/Bio/EnsEMBL/Mapper.pm | 110 ++++++++++++++--------------------
1 file changed, 44 insertions(+), 66 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 699dca486c..5f3d03cbc0 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -305,42 +305,11 @@ sub map_coordinates {
my $last_used_pair;
- # my best guess is that lr stands for "list of regions"
- my $lr = $hash->{ uc($id) };
-
# if we don't already have an interval tree built for this id,
# build one now
if ( !defined( $self->{"_tree_$type"}->{ uc($id) } )) {
- # create set of intervals to be checked for overlap
- my $from_intervals;
-
- foreach my $i (@{$lr}) {
- my $start = $i->{$from}{start};
- my $end = $i->{$from}{end};
-
- if ($end < $start) {
- my $tmp = $start;
- $start = $end;
- $end = $tmp;
- }
-
- push @{$from_intervals}, Bio::EnsEMBL::Utils::Interval->new($start, $end, $i);
- }
-
- #
- # Create the interval tree defined on the above set of intervals
- #
- # Two options:
- #
- # 1. Use immutable interval tree implementation
- # 2. Use mutable interval tree implementation
- #
- # As of release/99, we have more experience with the immutable
- # interval tree, so we will stick with this one. A future
- # refactoring effort may wish to replace this with a dynamically
- # maintained mutable interval tree, rather than simply throwing
- # trees away and rebuilding when the underlying interval set changes
- $self->{"_tree_$type"}->{ uc($id) } = Bio::EnsEMBL::Utils::Tree::Interval::Immutable->new($from_intervals);
+ $self->{"_tree_$type"}->{ uc($id) } = _build_immutable_tree($from,
+ $hash->{ uc($id) });
}
# query the interval tree (either cached or created new) for overlapping intervals
my $overlap = $self->{"_tree_$type"}->{ uc($id) }->query($start, $end);
@@ -828,42 +797,12 @@ sub map_indel {
}
my @indel_coordinates;
- my $lr = $hash->{ uc($id) };
-
# if we don't already have an interval tree built for this id,
# build one now
if ( !defined $self->{"_tree_$type"}->{ uc($id) } ) {
- # create set of intervals to be checked for overlap
- my $from_intervals;
-
- foreach my $i (@{$lr}) {
- my $start = $i->{$from}{start};
- my $end = $i->{$from}{end};
-
- if ($end < $start) {
- my $tmp = $start;
- $start = $end;
- $end = $tmp;
- }
-
- push @{$from_intervals}, Bio::EnsEMBL::Utils::Interval->new($start, $end, $i);
- }
-
- #
- # Create the interval tree defined on the above set of intervals
- #
- # Two options:
- #
- # 1. Use immutable interval tree implementation
- # 2. Use mutable interval tree implementation
- #
- # As of release/99, we have more experience with the immutable
- # interval tree, so we will stick with this one. A future
- # refactoring effort may wish to replace this with a dynamically
- # maintained mutable interval tree, rather than simply throwing
- # trees away and rebuilding when the underlying interval set changes
- $self->{"_tree_$type"}->{ uc($id) } = Bio::EnsEMBL::Utils::Tree::Interval::Immutable->new($from_intervals);
-}
+ $self->{"_tree_$type"}->{ uc($id) } = _build_immutable_tree($from,
+ $hash->{ uc($id) });
+ }
# query the interval tree (either cached or created new) for overlapping intervals
my $overlap = $self->{"_tree_$type"}->{ uc($id) }->query($start, $end);
@@ -1240,5 +1179,44 @@ sub _is_sorted {
return $self->{'_is_sorted'};
}
+# _build_immutable_tree
+#
+# Arg 1 string $pair_side - the from or to half of each pair to be
+# the source of intervals
+# Arg 2 listref $pair_list - a list of Bio::EnsEMBL::Mapper::Pair
+# Function builds a Bio::EnsEMBL::Utils::Tree::Interval::Immutable with
+# intervals corresponding to the chosen side (from or to) of
+# each Pair in $pair_list and a pointer to each Pair
+# Returntype Bio::EnsEMBL::Utils::Tree::Interval::Immutable
+# Exceptions none
+# Caller internal
+
+sub _build_immutable_tree {
+ my ($pair_side, $pair_list) = @_;
+ # create set of intervals for the tree
+ my $from_intervals;
+
+ foreach my $i (@{$pair_list}) {
+ my $start = $i->{$pair_side}{start};
+ my $end = $i->{$pair_side}{end};
+
+ if ($end < $start) {
+ my $tmp = $start;
+ $start = $end;
+ $end = $tmp;
+ }
+
+ push @{$from_intervals}, Bio::EnsEMBL::Utils::Interval->new($start, $end, $i);
+ }
+
+ # Create the interval tree defined on the above set of intervals
+ #
+ # As of release/99, we have more experience with the immutable
+ # interval tree, so we will stick with this one. A future
+ # refactoring effort may wish to replace this with a dynamically
+ # maintained mutable interval tree, rather than simply throwing
+ # trees away and rebuilding when the underlying interval set changes
+ return Bio::EnsEMBL::Utils::Tree::Interval::Immutable->new($from_intervals);
+}
1;
--
GitLab