From c14e1a2a7ef043a0c6fd0b3c158758f38f8efaba Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Thu, 25 Mar 2004 13:17:29 +0000
Subject: [PATCH] Transcript::add_Exon now throws if exon could not be added
b/c of overlap with other exon, rather than silently doing nothing
---
modules/Bio/EnsEMBL/Transcript.pm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 838bb1145e..d4d6f2cee7 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -647,16 +647,20 @@ sub add_Exon{
$self->{'_trans_exon_array'} ||= [];
+ my $was_added = 0;
+
my $ea = $self->{'_trans_exon_array'};
if( @$ea ) {
if( $exon->strand() == 1 ) {
if( $exon->start() > $ea->[$#$ea]->end() ) {
push(@{$self->{'_trans_exon_array'}},$exon);
+ $was_added = 1;
} else {
# insert it at correct place
for( my $i=0; $i <= $#$ea; $i++ ) {
if( $exon->end() < $ea->[$i]->start() ) {
splice( @$ea, $i, 0, $exon );
+ $was_added = 1;
last;
}
}
@@ -664,11 +668,13 @@ sub add_Exon{
} else {
if( $exon->end() < $ea->[$#$ea]->start() ) {
push(@{$self->{'_trans_exon_array'}},$exon);
+ $was_added = 1;
} else {
# insert it at correct place
for( my $i=0; $i <= $#$ea; $i++ ) {
if( $exon->start() > $ea->[$i]->end() ) {
splice( @$ea, $i, 0, $exon );
+ $was_added = 1;
last;
}
}
@@ -676,7 +682,26 @@ sub add_Exon{
}
} else {
push( @$ea, $exon );
+ $was_added = 1;
}
+
+ # sanity check:
+ if(!$was_added) {
+ # exon was not added because it has same end coord as start
+ # of another exon
+ my $all_str = '';
+ foreach my $e (@$ea) {
+ $all_str .= ' '.$e->start .'-'.$e->end.' ('.$e->strand.') ' .
+ ($e->stable_id || '') . "\n";
+ }
+ my $cur_str = ' '.$exon->start.'-'.$exon->end. ' ('.$exon->strand.') '.
+ ($exon->stable_id || '')."\n";
+ throw("Exon overlaps with other exon in same transcript.\n" .
+ "Transcript Exons:\n$all_str\n" .
+ "This Exon:\n$cur_str");
+ throw("Exon overlaps with other exon in same transcript.");
+ }
+
# recalculate start, end, slice, strand
$self->recalculate_coordinates();
}
--
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