From db65301fb494625cfc5883a782929c2a3014009a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 27 Oct 2011 23:05:14 +0000
Subject: [PATCH] Make code do what its comments say.
---
modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
index e556f04987..6c6ca90e76 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
@@ -180,10 +180,10 @@ sub internal_id_rescore {
sort { $b <=> $a } @{ $matrix->get_Entries_for_source($source) };
# nothing to do if we only have one mapping
- next unless ( scalar(@entries) > 1 );
+ if ( scalar(@entries) == 1 ) { next }
# only penalise if mappings are ambiguous
- next unless ( $entries[0]->score == $entries[1]->score );
+ if ( $entries[0]->score != $entries[1]->score ) { next }
# only penalise if one source id == target id where score == best
# score
@@ -197,15 +197,15 @@ sub internal_id_rescore {
}
}
- next unless ($ambiguous);
+ if ( !$ambiguous ) { next }
# now penalise those where source id != target id and score == best
# score
foreach my $e (@entries) {
if ( $e->target != $source and $e->score == $entries[0]->score() )
{
- # PENALTY: This stable ID is not any longer on the same object.
- $matrix->set_score( $source, $e->target(), 0.8*$e->score() );
+ # PENALTY: Reduce score for ambiguous mappings.
+ $matrix->set_score( $source, $e->target(), 0.9*$e->score() );
$i++;
}
}
--
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