From d5e73c6ee6eda666d63a3951ddddc0f253321a1a Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Wed, 15 May 2013 16:27:48 +0000
Subject: [PATCH] Added a method that lists the species in available databases.
Ancestral_ are ignored, and the list is filtered to a group type, defaulting
to core dbs. Testcase is less than perfect, because the test db has so few
species in it.
---
modules/Bio/EnsEMBL/Registry.pm | 26 ++++++++++++++++++++++++++
modules/t/registry.t | 6 ++++++
2 files changed, 32 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 45c1d2315c..19ff9a40ce 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -2663,6 +2663,32 @@ sub version_check {
return 1; # Ok
} ## end sub version_check
+=head2 get_all_species
+
+ Arg [1] : String group type, such as core, or otherfeatures
+ Description: Method for getting all valid species names found in available
+ databases. This excludes the ancestral sequence databases, and
+ any species from a non-core database. Specifying a group allows
+ the list to apply to non-core database types.
+ Example : my @species_names = @{ $reg->get_all_species() };
+ Returntype : Listref of species names
+
+=cut
+
+sub get_all_species {
+ my ($self,$group) = @_;
+ $group ||= 'core';
+ my @species;
+ foreach my $name (keys %{$registry_register{_SPECIES}}) {
+ push @species, $name if (
+ # limit species names to given db group and no ancestral dbs
+ $registry_register{_SPECIES}->{$name}->{$group}
+ && $name !~ /^ancestral/i
+ );
+ }
+ return \@species;
+}
+
=head2 get_species_and_object_type
diff --git a/modules/t/registry.t b/modules/t/registry.t
index 3f13480287..86fd82ebef 100644
--- a/modules/t/registry.t
+++ b/modules/t/registry.t
@@ -97,4 +97,10 @@ TMPL
$tester->('verison');
}
+# Test get_all_species
+
+my @species = $reg->get_all_species();
+ok(scalar(@species) == 1, "get_all_species");
+ok(scalar(@{ $reg->get_all_species('cahoona') }) == 0, "get_all_species with bogus data.");
+
done_testing();
\ No newline at end of file
--
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