From c9f8ba632ab2edcbe81d6ec6eff0524cb9517034 Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Tue, 13 Feb 2007 16:31:08 +0000
Subject: [PATCH] modified method get_all_Slices
---
modules/Bio/EnsEMBL/AlignStrainSlice.pm | 26 ++++++-------------------
1 file changed, 6 insertions(+), 20 deletions(-)
diff --git a/modules/Bio/EnsEMBL/AlignStrainSlice.pm b/modules/Bio/EnsEMBL/AlignStrainSlice.pm
index 4ea9ecf69c..5699420b50 100644
--- a/modules/Bio/EnsEMBL/AlignStrainSlice.pm
+++ b/modules/Bio/EnsEMBL/AlignStrainSlice.pm
@@ -262,15 +262,9 @@ sub _get_indels{
return $range_registry->get_ranges(1);
}
-=head2 get_all_underlying_Slices
-
- Arg [1] : int $startBasePair
- relative to start of slice, which is 1.
- Arg [2] : int $endBasePair
- relative to start of slice.
- Arg [3] : (optional) int $strand
- The strand of the slice to obtain sequence from. Default
- value is 1.
+=head2 get_all_Slices
+
+ Args : none
Description: This Slice is made of several Bio::EnsEMBL::StrainSlices
sequence. This method returns these StrainSlices (or part of
them) with the original coordinates
@@ -280,18 +274,10 @@ sub _get_indels{
=cut
-sub get_all_underlying_Slices {
- my ($self, $start, $end, $strand) = @_;
- my $underlying_slices = [];
-
- $start = 1 if (!defined($start));
- $end ||= $self->Slice->length;
- $strand ||= 1;
+sub get_all_Slices {
+ my $self = shift;
- foreach my $strainSlice (@{$self->strains}){
- push @{$underlying_slices},$strainSlice->sub_Slice($start,$end,$strand);
- }
- return $underlying_slices;
+ return $self->strains
}
1;
--
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