Commit 7873b631 authored by David Barnwell's avatar David Barnwell
Browse files

Change static_golden_path_type to assembly_type (so as to work with

rev. 1.79 DBAdaptor.pm).
parent 1c2fe558
......@@ -215,7 +215,7 @@ sub get_chr_start_end_of_contig {
$self->throw("Must have contig id to fetch Slice of contig");
}
my $type = $self->db->static_golden_path_type()
my $type = $self->db->assembly_type()
or $self->throw("No assembly type defined");
my $sth = $self->db->prepare("SELECT c.name,
......@@ -266,7 +266,7 @@ sub fetch_Slice_by_chr_start_end {
&eprof_start('Slice: staticcontig build');
my $type = $self->db->static_golden_path_type();
my $type = $self->db->assembly_type();
eval {
$slice = Bio::EnsEMBL::Slice->new(
......@@ -332,7 +332,7 @@ sub fetch_Slice_by_clone{
}
if( !defined $size ) {$size=0;}
my $type = $self->db->static_golden_path_type()
my $type = $self->db->assembly_type()
or $self->throw("No assembly type defined");
my $sth = $self->db->prepare("SELECT c.name,
......@@ -388,7 +388,7 @@ sub fetch_Slice_by_clone{
sub get_Gene_chr_bp {
my ($self,$geneid) = @_;
my $type = $self->db->static_golden_path_type()
my $type = $self->db->assembly_type()
or $self->throw("No assembly type defined");
my $sth = $self->db->prepare("SELECT
......@@ -452,7 +452,7 @@ sub fetch_Slice_by_gene{
my ($chr_name,$start,$end) = $self->get_Gene_chr_bp($geneid);
if( !defined $start ) {
my $type = $self->adaptor->db->static_golden_path_type()
my $type = $self->adaptor->db->assembly_type()
or $self->throw("No assembly type defined");
$self->throw("Gene is not on the golden path '$type'. Cannot build Slice.");
}
......
......@@ -1151,7 +1151,7 @@ sub _missed_exon_Evidence{
-dbname => $dbname,
);
$db->static_golden_path_type($path);
$db->assembly_type($path);
my $sgp = $db->get_StaticGoldenPathAdaptor;
# get info of where we are sitting:
......
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