From 3365da5033a406104455e9bf7ddd829345cabfdd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 17 Oct 2007 10:01:45 +0000
Subject: [PATCH] Small optimization to coding_region_start() and
coding_region_end(): If the coding region does not start/end in this exon, it
also will not end/start here.
---
modules/Bio/EnsEMBL/Exon.pm | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index c9c5048610..607c711422 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -650,6 +650,7 @@ sub coding_region_start {
if ( $transcript->coding_region_end() < $start ) {
# ... and also ends upstream of this exon.
$self->{'coding_region_start'}->{$transcript_id} = undef;
+ $self->{'coding_region_end'}->{$transcript_id} = undef;
} else {
# ... and does not end upstream of this exon.
$self->{'coding_region_start'}->{$transcript_id} = $start;
@@ -665,6 +666,7 @@ sub coding_region_start {
} else {
# Coding region starts downstream of this exon.
$self->{'coding_region_start'}->{$transcript_id} = undef;
+ $self->{'coding_region_end'}->{$transcript_id} = undef;
}
}
} ## end else [ if ( !defined($transcript_coding_start...
@@ -723,7 +725,8 @@ sub coding_region_end {
if ( $transcript->coding_region_start() > $end ) {
# ... and also starts downstream of this exon.
- $self->{'coding_region_end'}->{$transcript_id} = undef;
+ $self->{'coding_region_start'}->{$transcript_id} = undef;
+ $self->{'coding_region_end'}->{$transcript_id} = undef;
} else {
# ... and does not start downstream of this exon.
$self->{'coding_region_end'}->{$transcript_id} = $end;
@@ -738,7 +741,8 @@ sub coding_region_end {
$transcript_coding_end;
} else {
# Coding region ends upstream of this exon.
- $self->{'coding_region_end'}->{$transcript_id} = undef;
+ $self->{'coding_region_start'}->{$transcript_id} = undef;
+ $self->{'coding_region_end'}->{$transcript_id} = undef;
}
}
} ## end else [ if ( !defined($transcript_coding_end...
--
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