From edacc15e1065484113c48ff59391b646f7ef6d4d Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 16 Jan 2004 12:05:27 +0000
Subject: [PATCH] reduced number of function calls in add_map_coordinates,
probably a little bit faster now in some situations
---
modules/Bio/EnsEMBL/Mapper.pm | 26 ++++++++------------------
1 file changed, 8 insertions(+), 18 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 6e451553c2..cea829dba5 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -371,7 +371,7 @@ sub fastmap {
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)) {
@@ -382,30 +382,20 @@ sub add_map_coordinates{
throw("Cannot deal with mis-lengthed mappings so far");
}
- my $pair = Bio::EnsEMBL::Mapper::Pair->new();
-
- my $from = Bio::EnsEMBL::Mapper::Unit->new();
- $from->start($contig_start);
- $from->end($contig_end);
- $from->id($contig_id);
-
- my $to = Bio::EnsEMBL::Mapper::Unit->new();
- $to->start($chr_start);
- $to->end($chr_end);
- $to->id($chr_name);
-
- $pair->to($to);
- $pair->from($from);
+ 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);
- $pair->ori($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_from = $self->{'from'};
-
+
push( @{$self->{"_pair_$map_to"}->{uc($chr_name)}}, $pair );
push( @{$self->{"_pair_$map_from"}->{uc($contig_id)}}, $pair );
-
+
$self->{'pair_count'}++;
$self->{'_is_sorted'} = 0;
--
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