From e329941817da9a516f4cb315eae989e96823800e Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 20 Mar 2012 11:54:27 +0000
Subject: [PATCH] Fixing to use SUPER::seq() on the subsequence slice and then
using the block fetched repeats
---
modules/Bio/EnsEMBL/RepeatMaskedSlice.pm | 50 +++++++++++++-----------
1 file changed, 27 insertions(+), 23 deletions(-)
diff --git a/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm b/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
index 6ae8e12eb2..e75fac1296 100644
--- a/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
+++ b/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
@@ -210,19 +210,14 @@ sub not_default_masking_cases {
sub seq {
my $self = shift;
+
#
# get all the features
#
- my $logic_names = $self->repeat_mask_logic_names();
+ my $repeats = $self->_get_repeat_features($self);
my $soft_mask = $self->soft_mask();
- my $not_default_masking_cases = $self->not_default_masking_cases;
-
- my @repeats;
-
- foreach my $l (@$logic_names) {
- push @repeats, @{$self->get_all_RepeatFeatures($l)};
- }
-
+ my $not_default_masking_cases = $self->not_default_masking_cases();
+
#
# get the dna
#
@@ -231,7 +226,7 @@ sub seq {
#
# mask the dna
#
- $self->_mask_features(\$dna,\@repeats,$soft_mask,$not_default_masking_cases);
+ $self->_mask_features(\$dna,$repeats,$soft_mask,$not_default_masking_cases);
return $dna;
}
@@ -282,23 +277,32 @@ sub subseq {
$subslice = $subsequence_slice;
}
- #
- # get all the features
- #
- my $logic_names = $self->repeat_mask_logic_names();
+ my $repeats = $self->_get_repeat_features($subslice);
my $soft_mask = $self->soft_mask();
- my $not_default_masking_cases = $self->not_default_masking_cases;
-
- my @repeats;
+ my $not_default_masking_cases = $self->not_default_masking_cases();
+ my $dna = $subsequence_slice->SUPER::seq();
+ $subsequence_slice->_mask_features(\$dna,$repeats,$soft_mask,$not_default_masking_cases);
+ return $dna;
+}
+
+=head2 _get_repeat_features
+
+ Args [1] : Bio::EnsEMBL::Slice to fetch features for
+ Description : Gets repeat features for the given slice
+ Returntype : ArrayRef[Bio::EnsEMBL::RepeatFeature] array of repeats
+
+=cut
+
+
+sub _get_repeat_features {
+ my ($self, $slice) = @_;
+ my $logic_names = $self->repeat_mask_logic_names();
+ my @repeats;
foreach my $l (@$logic_names) {
- push @repeats, @{$subslice->get_all_RepeatFeatures($l)};
+ push @repeats, @{$slice->get_all_RepeatFeatures($l)};
}
-
- #
- # No need to mask sequence, seq() already does it for the new subsequence_slice
- #
- return $subsequence_slice->seq();
+ return \@repeats;
}
1;
--
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