diff --git a/modules/t/overlap.dump b/modules/t/overlap.dump
new file mode 100755
index 0000000000000000000000000000000000000000..90b62c8b47daeebaf92249394fb8f98b35b27ea2
--- /dev/null
+++ b/modules/t/overlap.dump
@@ -0,0 +1,19 @@
+INSERT INTO clone VALUES ('pog','pog',1,1,-1,'0000-00-00 00:00:00','0000-00-00 00:00:00','0000-00-00 00:00:00');
+
+INSERT INTO contig VALUES ('contig1',1,'pog',5,NULL,NULL,1,0);
+INSERT INTO contig VALUES ('contig2',2,'pog',6,NULL,NULL,2,0);
+INSERT INTO contig VALUES ('contig3',3,'pog',5,NULL,NULL,3,0);
+INSERT INTO contig VALUES ('contig4',4,'pog',6,NULL,NULL,4,0);
+INSERT INTO contig VALUES ('contig5',5,'pog',5,NULL,NULL,5,0);
+
+INSERT INTO contigoverlap VALUES (1,2,4,5,'TEST',1,'right2right');
+INSERT INTO contigoverlap VALUES (2,3,1,4,'TEST',1,'left2right');
+INSERT INTO contigoverlap VALUES (3,4,2,2,'TEST',1,'left2left');
+INSERT INTO contigoverlap VALUES (4,5,5,2,'TEST',1,'right2left');
+
+INSERT INTO dna VALUES ('AAAAA','2000-04-27 08:31:59',1);
+INSERT INTO dna VALUES ('GGGGGG','2000-04-27 08:31:59',2);
+INSERT INTO dna VALUES ('AAAAA','2000-04-27 08:31:59',3);
+INSERT INTO dna VALUES ('GGGGGG','2000-04-27 08:31:59',4);
+INSERT INTO dna VALUES ('AAAAA','2000-04-27 08:31:59',5);
+
diff --git a/modules/t/overlap.exampleconf b/modules/t/overlap.exampleconf
new file mode 100755
index 0000000000000000000000000000000000000000..9c35b49638767f3c7b948b3680c85ff05f2ac6d2
--- /dev/null
+++ b/modules/t/overlap.exampleconf
@@ -0,0 +1,4 @@
+overlap testoverlap
+mysqladmin /nfs/disk89/michele/mysql/bin/mysqladmin
+mysql mysql
+user root
diff --git a/modules/t/overlap.t b/modules/t/overlap.t
new file mode 100755
index 0000000000000000000000000000000000000000..16ec98c5a677a68dc3b84380aed51449bed17ddd
--- /dev/null
+++ b/modules/t/overlap.t
@@ -0,0 +1,118 @@
+## Bioperl Test Harness Script for Modules
+##
+# CVS Version
+# $Id$
+
+
+# Before `make install' is performed this script should be runnable with
+# `make test'. After `make install' it should work as `perl test.t'
+
+#-----------------------------------------------------------------------
+## perl test harness expects the following output syntax only!
+## 1..3
+## ok 1 [not ok 1 (if test fails)]
+## 2..3
+## ok 2 [not ok 2 (if test fails)]
+## 3..3
+## ok 3 [not ok 3 (if test fails)]
+##
+## etc. etc. etc. (continue on for each tested function in the .t file)
+#-----------------------------------------------------------------------
+
+
+## We start with some black magic to print on failure.
+BEGIN { $| = 1; print "1..6\n";
+ use vars qw($loaded); }
+END {print "not ok 1\n" unless $loaded;}
+
+use Bio::EnsEMBL::DBSQL::Obj;
+use Bio::EnsEMBL::DBLoader;
+$loaded=1;
+print "ok \n"; # 1st test passed, loaded needed modules
+
+#Creating test overlap database
+
+$conf{'overlap'} = 'testoverlap';
+$conf{'mysqladmin'} = '/mysql/current/bin/mysqladmin';
+$conf{'mysql'} = '/mysql/current/bin/mysql';
+$conf{'user'} = 'ensembl';
+$conf{'perl'} = 'perl';
+
+if ( -e 't/overlap.conf' ) {
+ print STDERR "Reading configuration from overlap.conf\n";
+ open(C,"t/overlap.conf");
+ while(<C>) {
+ my ($key,$value) = split;
+ $conf{$key} = $value;
+ }
+} else {
+ print STDERR "Using default values\n";
+ foreach $key ( keys %conf ) {
+ print STDERR " $key $conf{$key}\n";
+ }
+ print STDERR "\nPlease use a file t/overlap.conf to alter these values if the test fails\nFile is written <key> <value> syntax\n\n";
+}
+
+$nuser = $conf{user};
+
+my $create_overlap = "$conf{mysqladmin} -u ".$nuser." create $conf{overlap}";
+
+system($create_overlap) == 0 or die "$0\nError running '$create_overlap' : $!";
+
+print "ok 2\n"; #Databases created successfuly
+
+#Initialising databases
+my $init_overlap = "$conf{mysql} -u ".$nuser." $conf{overlap} < ../sql/table.sql";
+
+system($init_overlap) == 0 or die "$0\nError running '$init_overlap' : $!";
+
+print "ok 3\n";
+
+#Suck test data into db
+print STDERR "Inserting test data in test overlap db...\n";
+my $suck_data = "$conf{mysql} -u ".$nuser." $conf{overlap} < t/overlap.dump";
+system($suck_data) == 0 or die "$0\nError running '$suck_data' : $!";
+
+print "ok 4\n";
+
+# Connect to test db
+
+my $db = new Bio::EnsEMBL::DBSQL::Obj(-host => 'localhost',
+ -user => $conf{user},
+ -dbname => $conf{overlap}
+ );
+
+die "$0\nError connecting to database : $!" unless defined($db);
+
+print "ok 5\n";
+
+my $contig = $db->get_Contig('contig1');
+
+die "$0\nError fetching contig1 : $!" unless defined ($contig);
+
+print "ok 6\n";
+
+my $vc = new Bio::EnsEMBL::DB::VirtualContig(-focuscontig => $contig,
+ -focusposition => 1,
+ -ori => 1,
+ -left => 20,
+ -right => 20);
+
+die ("$0\nCan't create virtual contig :$!") unless defined ($vc);
+
+print "ok 7\n";
+
+my $seq = $vc->primary_seq;
+
+die "$0\nVirtual contig sequence " . $seq->seq . "does not equal AAAACCCCTTGGGAAA : $!" if ($seq->seq ne "AAAACCCCTTGGGAAA");
+
+print "ok 8\n";
+
+END {
+ my $drop_overlap = "echo \"y\" | $conf{mysqladmin} -u ".$nuser." drop $conf{overlap}";
+ system($drop_overlap) == 0 or die "$0\nError running '$drop_overlap' : $!";
+}
+
+
+
+
diff --git a/modules/t/transfer.t b/modules/t/transfer.t
index 4623b4965c9ce2542cca4305219fd998c710588e..022a1a9e3e89c5e91c30d75c3af192660c89699e 100755
--- a/modules/t/transfer.t
+++ b/modules/t/transfer.t
@@ -32,49 +32,51 @@ print "ok \n"; # 1st test passed, loaded needed modules
#Creating test donor and recipient databases
-$conf{'donor'} = 'testdonor';
-$conf{'recipient'} = 'testrecipient';
+$conf{'donor'} = 'testdonor';
+$conf{'recipient'} = 'testrecipient';
$conf{'mysqladmin'} = '/mysql/current/bin/mysqladmin';
-$conf{'mysql'} = '/mysql/current/bin/mysql';
-$conf{'user'} = 'ensembl';
-$conf{'update'} = '../scripts/update_list_chunk.pl';
-$conf{'perl'} = 'perl';
+$conf{'mysql'} = '/mysql/current/bin/mysql';
+$conf{'user'} = 'ensembl';
+$conf{'update'} = '../scripts/update_list_chunk.pl';
+$conf{'perl'} = 'perl';
if ( -e 't/transfer.conf' ) {
- print STDERR "Reading configuration from transfer.conf\n";
- open(C,"t/transfer.conf");
- while(<C>) {
- my ($key,$value) = split;
- $conf{$key} = $value;
- }
+ print STDERR "Reading configuration from transfer.conf\n";
+ open(C,"t/transfer.conf");
+ while(<C>) {
+ my ($key,$value) = split;
+ $conf{$key} = $value;
+ }
} else {
- print STDERR "Using default values\n";
- foreach $key ( keys %conf ) {
- print STDERR " $key $conf{$key}\n";
- }
- print STDERR "\nPlease use a file t/transfer.conf to alter these values if the test fails\nFile is written <key> <value> syntax\n\n";
+ print STDERR "Using default values\n";
+ foreach $key ( keys %conf ) {
+ print STDERR " $key $conf{$key}\n";
+ }
+ print STDERR "\nPlease use a file t/transfer.conf to alter these values if the test fails\nFile is written <key> <value> syntax\n\n";
}
$nuser = $conf{user};
-my $create_donor = "$conf{mysqladmin} -u ".$nuser." create $conf{donor}";
-my $create_recipient = "$conf{mysqladmin} -u ".$nuser." create $conf{recipient}";
-system($create_donor) == 0 or die "$0\nError running '$create_donor' : $!";
+my $create_donor = "$conf{mysqladmin} -u ".$nuser." create $conf{donor}";
+my $create_recipient = "$conf{mysqladmin} -u ".$nuser." create $conf{recipient}";
+
+system($create_donor) == 0 or die "$0\nError running '$create_donor' : $!";
system($create_recipient) == 0 or die "$0\nError running '$create_recipient' : $!";
print "ok 2\n"; #Databases created successfuly
#Initialising databases
-my $init_donor = "$conf{mysql} -u ".$nuser." $conf{donor} < ../sql/table.sql";
-my $init_recipient = "$conf{mysql} -u ".$nuser." $conf{recipient} < ../sql/table.sql";
-system($init_donor) == 0 or die "$0\nError running '$init_donor' : $!";
+my $init_donor = "$conf{mysql} -u ".$nuser." $conf{donor} < ../sql/table.sql";
+my $init_recipient = "$conf{mysql} -u ".$nuser." $conf{recipient} < ../sql/table.sql";
+
+system($init_donor) == 0 or die "$0\nError running '$init_donor' : $!";
system($init_recipient) == 0 or die "$0\nError running '$init_recipient' : $!";
print "ok 3\n";
#Suck test data into donor
print STDERR "Inserting test data in test donor db... this will take a while...\n";
-my $suck_data = "$conf{mysql} -u ".$nuser." $conf{donor} < t/donor.dump";
+my $suck_data = "$conf{mysql} -u ".$nuser." $conf{donor} < t/donor.dump";
system($suck_data) == 0 or die "$0\nError running '$suck_data' : $!";
print "ok 4\n";
@@ -94,9 +96,9 @@ print "ok 6\n";
END {
- my $drop_donor = "echo \"y\" | $conf{mysqladmin} -u ".$nuser." drop $conf{donor}";
- my $drop_recipient = "echo \"y\" | $conf{mysqladmin} -u ".$nuser." drop $conf{recipient}";
- system($drop_donor) == 0 or die "$0\nError running '$drop_donor' : $!";
+ my $drop_donor = "echo \"y\" | $conf{mysqladmin} -u ".$nuser." drop $conf{donor}";
+ my $drop_recipient = "echo \"y\" | $conf{mysqladmin} -u ".$nuser." drop $conf{recipient}";
+ system($drop_donor) == 0 or die "$0\nError running '$drop_donor' : $!";
system($drop_recipient) == 0 or die "$0\nError running '$drop_recipient' : $!";
}