From 4492f88fac49a6cfe9c2e2fe73d26f4c9e4048c0 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 6 Feb 2004 14:46:47 +0000
Subject: [PATCH] name changes to follow naming conventions
---
modules/Bio/EnsEMBL/Intron.pm | 12 +++++-----
modules/t/intron.t | 43 +++++++++++++++++++++++++++++++++++
2 files changed, 49 insertions(+), 6 deletions(-)
create mode 100644 modules/t/intron.t
diff --git a/modules/Bio/EnsEMBL/Intron.pm b/modules/Bio/EnsEMBL/Intron.pm
index ae2a85dcbe..ad74848349 100644
--- a/modules/Bio/EnsEMBL/Intron.pm
+++ b/modules/Bio/EnsEMBL/Intron.pm
@@ -81,10 +81,10 @@ sub new {
}
-=head2 prev_exon
+=head2 prev_Exon
Args : none
- Example : $exon = $intron->prev_exon
+ Example : $exon = $intron->prev_Exon
Description: Returns the exon before this Intron
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
@@ -92,17 +92,17 @@ sub new {
=cut
-sub prev_exon {
+sub prev_Exon {
my ($self) = shift;
return $self->{'prev'};
}
-=head2 next_exon
+=head2 next_Exon
Args : none
- Example : $exon = $intron->next_exon
+ Example : $exon = $intron->next_Exon
Description: Returns the exon after this Intron
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
@@ -110,7 +110,7 @@ sub prev_exon {
=cut
-sub next_exon {
+sub next_Exon {
my ($self) = shift;
return $self->{'next'};
diff --git a/modules/t/intron.t b/modules/t/intron.t
new file mode 100644
index 0000000000..666a574289
--- /dev/null
+++ b/modules/t/intron.t
@@ -0,0 +1,43 @@
+use lib 't';
+use strict;
+
+BEGIN { $| = 1;
+ use Test ;
+ plan tests => 14;
+}
+
+my $loaded = 0;
+END {print "not ok 1\n" unless $loaded;}
+
+use MultiTestDB;
+use TestUtils qw(debug test_getter_setter);
+
+our $verbose = 0; #set to 1 to turn on debug printouts
+
+$loaded = 1;
+my $multi = MultiTestDB->new();
+
+ok(1);
+
+my $db = $multi->get_DBAdaptor( 'core' );
+
+ok($db);
+
+my $stable_id = 'ENST00000217347';
+my $transcript_adaptor = $db->get_TranscriptAdaptor();
+my $transcript =
+ $transcript_adaptor->fetch_by_stable_id($stable_id);
+
+
+my @exons = (@{$transcript->get_all_Exons()});
+my @introns = (@{$transcript->get_all_Introns()});
+
+my $i=0;
+foreach my $intron (@introns){
+ ok($intron->prev_Exon->end == $intron->start-1);
+ ok($intron->next_Exon->start == $intron->end+1);
+}
+
+
+$multi->restore();
+
--
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