From 30c90c5fbc1d8ba48c4992c99eabffe9e44d6032 Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Fri, 15 Nov 2002 16:47:54 +0000
Subject: [PATCH] clean up, not enough test yet
---
modules/t/repeatFeature.t | 39 +++++++++++++++++++++------------------
1 file changed, 21 insertions(+), 18 deletions(-)
diff --git a/modules/t/repeatFeature.t b/modules/t/repeatFeature.t
index fc22bbb3dd..1fb01c027f 100644
--- a/modules/t/repeatFeature.t
+++ b/modules/t/repeatFeature.t
@@ -8,30 +8,25 @@ BEGIN { $| = 1;
my $loaded = 0;
END {print "not ok 1\n" unless $loaded;}
-use EnsTestDB;
-use Bio::EnsEMBL::DBLoader;
+my $verbose = 0;
+use MultiTestDB;
+my $multi = MultiTestDB->new();
$loaded = 1;
ok(1);
-# Database will be dropped when this
-# object goes out of scope
-my $ens_test = EnsTestDB->new;
+my $db = $multi->get_DBAdaptor( 'core' );
-$ens_test->do_sql_file("t/minidatabase.dump");
-
-ok($ens_test);
+$cadp = $db->get_RawContigAdaptor();
+$contig = $cadp->fetch_by_dbID(1);
+my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name("RepeatMask");
+debug( "ANALYSIS ".$analysis );
-my $db = $ens_test->get_DBSQL_Obj;
-$cadp = $db->get_RawContigAdaptor();
-$contig = $cadp->fetch_by_dbID(1);
-my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name("dummy-repeatmask");
-print STDERR "ANALYSIS ".$analysis."\n";
ok($analysis);
ok($contig);
@@ -39,7 +34,7 @@ $repeat_f_ad = $db->get_RepeatFeatureAdaptor();
$repeat_c_ad = $db->get_RepeatConsensusAdaptor();
-print STDERR "DBID ".$analysis->dbID."\n";
+debug( "Analysis dbID ".$analysis->dbID );
my $repeat_consensus = Bio::EnsEMBL::RepeatConsensus->new();
@@ -56,7 +51,6 @@ ok(1);
my $repeat_feature = Bio::EnsEMBL::RepeatFeature->new();
-$repeat_feature->contig_id($contig->dbID);
$repeat_feature->start(26);
$repeat_feature->end(65);
$repeat_feature->strand(1);
@@ -65,20 +59,29 @@ $repeat_feature->hend(45);
$repeat_feature->score(100);
$repeat_feature->analysis($analysis);
$repeat_feature->repeat_consensus($repeat_consensus);
+$repeat_feature->contig( $contig );
ok($repeat_feature);
+$multi->hide( "core", "repeat_feature" );
+
+$repeat_f_ad->store( $repeat_feature );
-$repeat_f_ad->store($contig->dbID, $repeat_feature);
ok(1);
-my @repeats = $repeat_f_ad->fetch_by_RawContig($contig);
+my $repeats = $repeat_f_ad->fetch_all_by_RawContig($contig);
-my $repeat = $repeats[0];
+my $repeat = $repeats->[0];
ok($repeat);
ok($repeat->start == 26);
ok($repeat->hend == 45);
+sub debug {
+ my $txt = shift;
+ if( $verbose ) {
+ print STDERR $txt,"\n";
+ }
+}
--
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