From f06e08b9ad0b9a97d8bb2ddf22ace021b56c001a Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Mon, 21 Mar 2005 14:24:11 +0000
Subject: [PATCH] adapted to new assembly test case
---
modules/t/assemblyMapper.t | 38 ++++++++++++++++++++++++++++++++--
modules/t/coordSystemAdaptor.t | 2 +-
2 files changed, 37 insertions(+), 3 deletions(-)
diff --git a/modules/t/assemblyMapper.t b/modules/t/assemblyMapper.t
index 2e3354a42b..ba9868ad2e 100644
--- a/modules/t/assemblyMapper.t
+++ b/modules/t/assemblyMapper.t
@@ -2,7 +2,7 @@ use strict;
BEGIN { $| = 1;
use Test ;
- plan tests => 9;
+ plan tests => 27;
}
use Bio::EnsEMBL::Test::MultiTestDB;
@@ -30,8 +30,42 @@ my $csa = $db->get_CoordSystemAdaptor();
my $ctg_cs = $csa->fetch_by_name('contig');
my $chr_cs = $csa->fetch_by_name('chromosome');
my $cln_cs = $csa->fetch_by_name('clone');
+my $chnk_cs = $csa->fetch_by_name('chunk');
-my $asm_mapper = $asma->fetch_by_CoordSystems($ctg_cs, $chr_cs);
+my $asm_mapper = $asma->fetch_by_CoordSystems($chnk_cs, $chr_cs);
+ok( $asm_mapper && $asm_mapper->isa( "Bio::EnsEMBL::ChainedAssemblyMapper" ));
+
+#
+# Test if the multi mapping works (meta_key=assembly.mapping entry with #)
+#
+
+my @coords = $asm_mapper->map( '1', 1, 50, 1, $chr_cs );
+ok( $coords[0]->id() eq "multimap_testregion" );
+ok( $coords[0]->start() == 10 );
+ok( $coords[0]->end() == 59 );
+ok( $coords[0]->strand() == 1 );
+
+@coords = $asm_mapper->map( "multimap_testregion", 100, 800, 1, $chnk_cs );
+
+ok( $coords[0]->id() eq "1" );
+ok( $coords[0]->start() == 91 );
+ok( $coords[0]->end() == 200 );
+ok( $coords[0]->strand() == 1 );
+
+ok( $coords[1]->isa( "Bio::EnsEMBL::Mapper::Gap" ) );
+
+ok( $coords[2]->id() eq "1" );
+ok( $coords[2]->start() == 201 );
+ok( $coords[2]->end() == 400 );
+ok( $coords[2]->strand() == -1 );
+
+ok( $coords[4]->id() eq "2" );
+ok( $coords[4]->start() == 1 );
+ok( $coords[4]->end() == 100 );
+ok( $coords[4]->strand() == -1 );
+
+
+$asm_mapper = $asma->fetch_by_CoordSystems($ctg_cs, $chr_cs);
ok($asm_mapper && $asm_mapper->isa('Bio::EnsEMBL::AssemblyMapper'));
diff --git a/modules/t/coordSystemAdaptor.t b/modules/t/coordSystemAdaptor.t
index fe29d57f03..b22c4b8fd2 100644
--- a/modules/t/coordSystemAdaptor.t
+++ b/modules/t/coordSystemAdaptor.t
@@ -2,7 +2,7 @@ use strict;
BEGIN { $| = 1;
use Test ;
- plan tests => 32;
+ plan tests => 33;
}
use Bio::EnsEMBL::Test::MultiTestDB;
--
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