From af3a76a7db2740c255816ff16fff81875ab7f2e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 27 Aug 2010 10:45:17 +0000
Subject: [PATCH] In map_indel(): Fix documentation to mention right return
type. From Michael S.
Also, reformat method.
---
modules/Bio/EnsEMBL/Mapper.pm | 116 +++++++++++++++++-----------------
1 file changed, 57 insertions(+), 59 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index a60dc33cc8..426074fb43 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -641,83 +641,81 @@ sub add_indel_coordinates{
Arg [5] : string $type - the coordinate system name the coords are from.
Example : @coords = $mapper->map_indel();
Description: This is in internal function which handles the special mapping
- case for indels (start = end +1). It will be used to map from
+ case for indels (start = end +1). It will be used to map from
a coordinate system with a gap to another that contains an
insertion. It will be mainly used by the Variation API.
- Returntype : Bio::EnsEMBL::Mapper::IndelCoordinate objects
+ Returntype : Bio::EnsEMBL::Mapper::Unit objects
Exceptions : none
Caller : general
=cut
sub map_indel {
- my ($self, $id, $start, $end, $strand, $type) = @_;
+ my ( $self, $id, $start, $end, $strand, $type ) = @_;
-# swap start/end and map the resultant 2bp coordinate
- ($start, $end) =($end,$start);
+ # swap start/end and map the resultant 2bp coordinate
+ ( $start, $end ) = ( $end, $start );
- if( ! $self->{'_is_sorted'} ) { $self->_sort() }
+ if ( !$self->{'_is_sorted'} ) { $self->_sort() }
- my $hash = $self->{"_pair_$type"};
+ my $hash = $self->{"_pair_$type"};
- my ($from, $to, $cs);
+ my ( $from, $to, $cs );
- if($type eq $self->{'to'}) {
- $from = 'to';
- $to = 'from';
- $cs = $self->{'from_cs'};
- } else {
- $from = 'from';
- $to = 'to';
- $cs = $self->{'to_cs'};
- }
+ if ( $type eq $self->{'to'} ) {
+ $from = 'to';
+ $to = 'from';
+ $cs = $self->{'from_cs'};
+ } else {
+ $from = 'from';
+ $to = 'to';
+ $cs = $self->{'to_cs'};
+ }
- unless(defined $hash) {
- throw("Type $type is neither to or from coordinate systems");
- }
- my $last_used_pair;
- my @indel_coordinates;
-
- my ( $start_idx, $end_idx, $mid_idx, $pair, $self_coord );
- my $lr = $hash->{uc($id)};
-
- $start_idx = 0;
- $end_idx = $#$lr;
-
- # binary search the relevant pairs
- # helps if the list is big
- while(( $end_idx - $start_idx ) > 1 ) {
- $mid_idx = ($start_idx+$end_idx)>>1;
- $pair = $lr->[$mid_idx];
- $self_coord = $pair->{$from};
- if( $self_coord->{'end'} <= $start ) {
- $start_idx = $mid_idx;
- } else {
- $end_idx = $mid_idx;
- }
- }
+ unless ( defined $hash ) {
+ throw("Type $type is neither to or from coordinate systems");
+ }
+ my $last_used_pair;
+ my @indel_coordinates;
- for( my $i = $start_idx; $i<=$#$lr; $i++ ) {
- $pair = $lr->[$i];
- my $self_coord = $pair->{$from};
- my $target_coord = $pair->{$to};
+ my ( $start_idx, $end_idx, $mid_idx, $pair, $self_coord );
+ my $lr = $hash->{ uc($id) };
- if (exists $pair->{'indel'}){
- #need to return unit coordinate
- my $to =
- Bio::EnsEMBL::Mapper::Unit->new($target_coord->{'id'},
- $target_coord->{'start'},
- $target_coord->{'end'},
- );
- push @indel_coordinates, $to;
- last;
- }
- $last_used_pair = $pair;
- }
+ $start_idx = 0;
+ $end_idx = $#$lr;
+
+ # binary search the relevant pairs
+ # helps if the list is big
+ while ( ( $end_idx - $start_idx ) > 1 ) {
+ $mid_idx = ( $start_idx + $end_idx ) >> 1;
+ $pair = $lr->[$mid_idx];
+ $self_coord = $pair->{$from};
+ if ( $self_coord->{'end'} <= $start ) {
+ $start_idx = $mid_idx;
+ } else {
+ $end_idx = $mid_idx;
+ }
+ }
+ for ( my $i = $start_idx; $i <= $#$lr; $i++ ) {
+ $pair = $lr->[$i];
+ my $self_coord = $pair->{$from};
+ my $target_coord = $pair->{$to};
- return @indel_coordinates;
-}
+ if ( exists $pair->{'indel'} ) {
+ #need to return unit coordinate
+ my $to =
+ Bio::EnsEMBL::Mapper::Unit->new( $target_coord->{'id'},
+ $target_coord->{'start'},
+ $target_coord->{'end'}, );
+ push @indel_coordinates, $to;
+ last;
+ }
+ $last_used_pair = $pair;
+ }
+
+ return @indel_coordinates;
+} ## end sub map_indel
=head2 add_Mapper
--
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