From 8abf94cb3c33ad000a7a6ee85eb77bc4818566cc Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 12 Nov 2010 09:49:28 +0000
Subject: [PATCH] tests for seq region synonym added
---
modules/t/slice.t | 72 ++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 71 insertions(+), 1 deletion(-)
diff --git a/modules/t/slice.t b/modules/t/slice.t
index b6e0eeddf3..13e454ce7c 100644
--- a/modules/t/slice.t
+++ b/modules/t/slice.t
@@ -4,7 +4,7 @@ use warnings;
BEGIN { $| = 1;
use Test;
- plan tests => 54;
+ plan tests => 60;
}
use Bio::EnsEMBL::Test::TestUtils;
@@ -367,3 +367,73 @@ ok($sr_slice->start() == 1 &&
$sr_slice->strand() == 1);
+
+
+
+
+
+
+# synonym tests
+debug("START syn test");
+my $multi = $multi_db;
+$multi->save("core", "seq_region_synonym");
+
+debug("get slice");
+$slice = $slice_adaptor->fetch_by_region('chromosome', 20, 1, 10);
+
+my @alt_names = @{$slice->get_all_synonyms()};
+foreach my $syn (@alt_names){
+ debug("syn\t".$syn->name."\n");
+}
+debug("altnames ".scalar(@alt_names)."\n");
+ok(@alt_names == 2);
+
+
+$slice->add_synonym("20ish");
+@alt_names = @{$slice->get_all_synonyms()};
+
+ok(@alt_names == 3);
+
+
+#slcie aleady stored so need to store syns
+my $syn_adap = $db->get_SeqRegionSynonymAdaptor;
+foreach my $syn (@alt_names){
+ $syn_adap->store($syn);
+}
+
+$slice = $slice_adaptor->fetch_by_region('chromosome', 20, 1, 10);
+
+@alt_names = @{$slice->get_all_synonyms()};
+
+ok(@alt_names == 3);
+
+$multi->restore();
+
+
+
+$multi->save("core", 'seq_region_synonym');
+
+$slice = $slice_adaptor->fetch_by_region('chromosome', 1, 1, 10);
+
+@alt_names = @{$slice->get_all_synonyms()};
+
+ok(@alt_names == 0);
+
+$slice->add_synonym("1ish");
+
+@alt_names = @{$slice->get_all_synonyms()};
+
+ok(@alt_names == 1);
+
+foreach my $syn (@alt_names){
+ $syn_adap->store($syn);
+}
+
+
+$slice = $slice_adaptor->fetch_by_region('chromosome', 1, 1, 10);
+
+@alt_names = @{$slice->get_all_synonyms()};
+
+ok(@alt_names == 1);
+
+$multi->restore();
--
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