From 335232027e6670682f996cb90e60914ad0408c31 Mon Sep 17 00:00:00 2001
From: James Gilbert <jgrg@sanger.ac.uk>
Date: Thu, 30 Oct 2003 13:40:22 +0000
Subject: [PATCH] fixed CORE::length warnings in Transcript added TYPE
parameter to DBAdaptor constructor
---
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm | 6 +++++-
modules/Bio/EnsEMBL/Transcript.pm | 4 ++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 7cc96fb25e..357341a58e 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -57,6 +57,7 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
Arg [-DNADB]: (optional) Bio::EnsEMBL::DBSQL::DBAdaptor DNADB
All sequence, assembly, contig information etc, will be
retrieved from this database instead.
+ Arg [-TYPE]: (optional) An assembly_type
Arg [..] : Other args are passed to superclass
Bio::EnsEMBL::DBSQL::DBConnection
Example : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
@@ -77,11 +78,14 @@ sub new {
#call superclass constructor
my $self = $class->SUPER::new(@args);
- my ( $dnadb ) = $self->_rearrange([qw(DNADB)],@args);
+ my ( $dnadb, $assembly_type ) = $self->_rearrange([qw(DNADB TYPE)],@args);
if(defined $dnadb) {
$self->dnadb($dnadb);
}
+ if ($assembly_type) {
+ $self->assembly_type($assembly_type);
+ }
# $self here is actually a Container object
# so need to call _obj to get the DBAdaptor
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index ca55a82ded..4b01b092cd 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1156,7 +1156,7 @@ sub five_prime_utr {
my $self = shift;
my $seq = substr($self->spliced_seq, 0, $self->cdna_coding_start - 1);
- length $seq or return;
+ CORE::length($seq) or return;
return Bio::Seq->new(
-DISPLAY_ID => $self->stable_id,
@@ -1169,7 +1169,7 @@ sub three_prime_utr {
my $self = shift;
my $seq = substr($self->spliced_seq, $self->cdna_coding_end);
- length $seq or return;
+ CORE::length($seq) or return;
return Bio::Seq->new(
-DISPLAY_ID => $self->stable_id,
--
GitLab