From a0077393ed25c9f07fbe01ec754d60bd7ed88284 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 10:32:27 +0000
Subject: [PATCH] In add_map_coordinates(): Correct spelling in documentation
and remove mentioning of return values as none are returned (and the rest of
the API is not expecting anything). From Michael S.
Also, reformat method.
---
modules/Bio/EnsEMBL/Mapper.pm | 56 ++++++++++++++++++-----------------
1 file changed, 29 insertions(+), 27 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 93c6a51bea..2b07b5b4bd 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -528,54 +528,56 @@ sub fastmap {
Arg 4 int $strand
relative orientation of source and target (+/- 1)
Arg 5 int $id
- id of 'targe' sequence
+ id of 'target' sequence
Arg 6 int $start
- start coordinate of 'targe' sequence
+ start coordinate of 'target' sequence
Arg 7 int $end
- end coordinate of 'targe' sequence
- Function stores details of mapping between two regions:
- 'source' and 'target'. Returns 1 if the pair was added, 0 if it
- was already in.
- Returntype int 0,1
+ end coordinate of 'target' sequence
+ Function Stores details of mapping between
+ 'source' and 'target' regions.
+ Returntype none
Exceptions none
Caller Bio::EnsEMBL::Mapper
=cut
-sub add_map_coordinates{
- my ($self, $contig_id, $contig_start, $contig_end,
- $contig_ori, $chr_name, $chr_start, $chr_end) = @_;
-
- unless(defined($contig_id) && defined($contig_start) && defined($contig_end)
- && defined($contig_ori) && defined($chr_name) && defined($chr_start)
- && defined($chr_end)) {
+sub add_map_coordinates {
+ my ( $self, $contig_id, $contig_start, $contig_end, $contig_ori,
+ $chr_name, $chr_start, $chr_end )
+ = @_;
+
+ unless ( defined($contig_id)
+ && defined($contig_start)
+ && defined($contig_end)
+ && defined($contig_ori)
+ && defined($chr_name)
+ && defined($chr_start)
+ && defined($chr_end) )
+ {
throw("7 arguments expected");
}
- if( ($contig_end - $contig_start) != ($chr_end - $chr_start) ) {
+ if ( ( $contig_end - $contig_start ) != ( $chr_end - $chr_start ) ) {
throw("Cannot deal with mis-lengthed mappings so far");
}
+ my $from = Bio::EnsEMBL::Mapper::Unit->new( $contig_id, $contig_start,
+ $contig_end );
+ my $to =
+ Bio::EnsEMBL::Mapper::Unit->new( $chr_name, $chr_start, $chr_end );
- my $from =
- Bio::EnsEMBL::Mapper::Unit->new($contig_id, $contig_start, $contig_end);
- my $to =
- Bio::EnsEMBL::Mapper::Unit->new($chr_name, $chr_start, $chr_end);
-
- my $pair = Bio::EnsEMBL::Mapper::Pair->new($from, $to, $contig_ori);
+ my $pair = Bio::EnsEMBL::Mapper::Pair->new( $from, $to, $contig_ori );
# place into hash on both ids
- my $map_to = $self->{'to'};
+ my $map_to = $self->{'to'};
my $map_from = $self->{'from'};
- push( @{$self->{"_pair_$map_to"}->{uc($chr_name)}}, $pair );
- push( @{$self->{"_pair_$map_from"}->{uc($contig_id)}}, $pair );
+ push( @{ $self->{"_pair_$map_to"}->{ uc($chr_name) } }, $pair );
+ push( @{ $self->{"_pair_$map_from"}->{ uc($contig_id) } }, $pair );
$self->{'pair_count'}++;
-
$self->{'_is_sorted'} = 0;
-
-}
+} ## end sub add_map_coordinates
=head2 add_indel_coordinates
--
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