From 810d00595777f91fb81a404b5632e8fa8a69f1e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 4 Jan 2011 15:34:52 +0000
Subject: [PATCH] Sort out formatting of add_Exon() and use assert_ref() too,
before fixing problem reported by Mark McDowall.
---
modules/Bio/EnsEMBL/Transcript.pm | 58 +++++++++++++++++--------------
1 file changed, 31 insertions(+), 27 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index b6bb691f86..47d8699cd4 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1212,33 +1212,31 @@ sub add_Attributes {
=cut
-sub add_Exon{
- my ($self,$exon, $rank) = @_;
+sub add_Exon {
+ my ( $self, $exon, $rank ) = @_;
- #yup - we are going to be picky here...
- unless(defined $exon && ref $exon && $exon->isa("Bio::EnsEMBL::Exon") ) {
- throw("[$exon] is not a Bio::EnsEMBL::Exon!");
- }
+ assert_ref( $exon, 'Bio::EnsEMBL::Exon' );
$self->{'_trans_exon_array'} ||= [];
- if(defined($rank)) {
- $self->{'_trans_exon_array'}->[$rank-1] = $exon;
+ if ( defined($rank) ) {
+ $self->{'_trans_exon_array'}->[ $rank - 1 ] = $exon;
return;
}
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'}},$exon);
+
+ if ( @{$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() ) {
+ for ( my $i = 0; $i <= $#$ea; $i++ ) {
+ if ( $exon->end() < $ea->[$i]->start() ) {
splice( @$ea, $i, 0, $exon );
$was_added = 1;
last;
@@ -1246,13 +1244,13 @@ sub add_Exon{
}
}
} else {
- if( $exon->end() < $ea->[$#$ea]->start() ) {
- push(@{$self->{'_trans_exon_array'}},$exon);
+ 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() ) {
+ for ( my $i = 0; $i <= $#$ea; $i++ ) {
+ if ( $exon->start() > $ea->[$i]->end() ) {
splice( @$ea, $i, 0, $exon );
$was_added = 1;
last;
@@ -1266,24 +1264,30 @@ sub add_Exon{
}
# sanity check:
- if(!$was_added) {
+ 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";
+ $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");
+ 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" );
}
# recalculate start, end, slice, strand
$self->recalculate_coordinates();
-}
+} ## end sub add_Exon
=head2 get_all_Exons
--
GitLab