diff --git a/modules/t/mapper.t b/modules/t/mapper.t
new file mode 100644
index 0000000000000000000000000000000000000000..2c08fd3165710dfd98e2e2588996e7f34ff14797
--- /dev/null
+++ b/modules/t/mapper.t
@@ -0,0 +1,241 @@
+## 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)
+#-----------------------------------------------------------------------
+
+
+# This test script heavily edited by ihh@fruitfly.org
+
+## We start with some black magic to print on failure.
+BEGIN { $| = 1; print "1..6\n"; # 6 tests total
+ use vars qw($loaded); }
+END { print "not ok 1\n" unless $loaded; }
+
+use lib 't';
+
+$loaded = 1;
+$n_test = 0; # global test counter
+ok();
+
+use Bio::EnsEMBL::Mapper;
+
+# testing the Bio::EnsEMBL::Mapper module
+
+$mapper = Bio::EnsEMBL::Mapper->new( "rawcontig", "virtualcontig" );
+load_sgp_dump( $mapper, undef );
+
+# loading done successfully
+ok();
+
+# transform a segment entirely within the first rawcontig
+test_transform ($mapper,
+ [627012, 2, 5, -1, "rawcontig"],
+ ["chr1", 2, 5, -1]);
+
+# now a split coord
+test_transform ($mapper,
+ ["chr1", 383700, 444000, +1, "virtualcontig"],
+ [314696, 31917, 31937, -1],
+ [341, 126, 59773, -1],
+ [315843, 5332, 5963, +1]);
+
+
+# the following subroutine tests that a given source co-ordinate range
+# transforms into a given set of destination co-ordinates
+#
+# args: $src = [$srcid, $srcstart, $srcend, $srcstrand, $srctype]
+# @dest = ([$id1, $start1, $end1, $strand1],
+# [$id2, $start2, $end2, $strand2] ... )
+#
+# for @dest array, $strand=0 indicates gap.
+# for @dest array, $id=$srcid for gaps.
+
+sub test_transform {
+ my ($mapper, $src, @dest) = @_;
+ if (@$src != 5) { warn "Bad source coords: (@$src)\n"; notok(); return }
+ my ($srcid, $srcstart, $srcend, $srcstrand, $srctype) = @$src;
+ my @coord = $mapper->map_coordinates ($srcid, $srcstart, $srcend, $srcstrand, $srctype);
+ @coord = map ([isgap($_) ? $srcid : $_->id, # Gap object should do this, but currently doesn't.
+ $_->start,
+ $_->end,
+ isgap($_) ? 0 : $_->strand], # strand zero indicates a gap, within this subroutine
+ @coord);
+ if (@coord != @dest) {
+ warn "Source:\n(", join(",",@$src), ")\n";
+ warn "Dest:\n", map ("(".join(",",@$_).")\n", @coord);
+ warn "Expected:\n", map ("(".join(",",@$_).")\n", @dest);
+ warn "Wrong number of segments\n";
+ notok();
+ return;
+ }
+ ok();
+ for (my $i = 0; $i < @coord; ++$i) {
+ for (my $n = 0; $n < 4; ++$n) {
+ if ($coord[$i]->[$n] != $dest[$i]->[$n]) {
+ warn "Source:\n(", join(",",@$src), ")\n";
+ warn "Dest:\n", map ("(".join(",",@$_).")\n", @coord);
+ warn "Expected:\n", map ("(".join(",",@$_).")\n", @dest);
+ warn "Error in segment ", $i+1, " field ", $n+1, "\n";
+ notok();
+ return;
+ }
+ }
+ }
+ ok();
+ return;
+}
+
+
+
+sub load_sgp_dump {
+ my ($map, $reverse) = @_;
+
+#chr_name raw_id chr_start chr_end raw_start raw_end raw_ori
+ my @sgp_dump = split ( /\n/, qq {
+chr1 627012 1 31276 1 31276 1
+chr1 627010 31377 42949 72250 83822 -1
+chr1 2768 42950 180950 251 138251 1
+chr1 10423 180951 266154 1 85204 -1
+chr1 627011 266255 273761 1 7507 1
+chr1 314698 273862 283122 1 9261 -1
+chr1 627009 283223 331394 251 48422 -1
+chr1 314695 331395 352162 1 20768 -1
+chr1 314697 352263 359444 1 7182 -1
+chr1 314696 359545 383720 31917 56092 -1
+chr1 341 383721 443368 126 59773 -1
+chr1 315843 443369 444727 5332 6690 1
+chr1 315844 444828 453463 1 8636 -1
+chr1 315834 453564 456692 1 3129 1
+chr1 315831 456793 458919 1 2127 1
+chr1 315827 459020 468965 251 10196 -1
+chr1 544782 468966 469955 1 990 -1
+chr1 315837 470056 473446 186 3576 -1
+chr1 544807 473447 474456 1 1010 -1
+chr1 315832 474557 477289 1 2733 1
+chr1 544806 477390 477601 1086 1297 -1
+chr1 315840 477602 482655 21 5074 1
+chr1 544802 482656 483460 1 805 -1
+chr1 544811 483561 484162 6599 7200 -1
+chr1 315829 484163 498439 15 14291 -1
+chr1 544813 498440 500980 1 2541 -1
+chr1 544773 501081 502190 1217 2326 -1
+chr1 315828 502191 513296 72 11177 1
+chr1 544815 513297 517276 2179 6158 1
+chr1 315836 517277 517662 2958 3343 1
+chr1 544805 517663 520643 299 3279 1
+chr1 315835 520744 521682 2462 3400 -1
+chr1 544784 521683 526369 54 4740 1
+chr1 544796 526470 527698 1 1229 1
+chr1 315833 527799 528303 2530 3034 -1
+chr1 544803 528304 531476 1 3173 -1
+chr1 544821 531577 532691 1 1115 1
+chr1 544810 532792 533843 1 1052 1
+chr1 544800 533944 535249 1 1306 1
+chr1 544786 535350 536652 1 1303 1
+chr1 544814 536753 538358 1 1606 1
+chr1 544812 538459 540004 1 1546 1
+chr1 544818 540105 541505 1 1401 1
+chr1 544816 541606 542693 1 1088 1
+chr1 544778 542794 544023 1 1230 1
+chr1 544779 544124 545709 1 1586 1
+chr1 544804 545810 547660 1 1851 1
+chr1 544774 547761 550105 1 2345 1
+chr1 544817 550206 552105 1 1900 1
+chr1 544781 552206 553640 1 1435 1
+chr1 315830 553741 555769 1 2029 -1
+chr1 544819 555870 558904 1 3035 -1
+chr1 544777 559005 560670 1 1666 1
+chr1 544795 560771 563092 1 2322 1
+chr1 544809 563193 565523 1 2331 1
+chr1 544808 565624 568113 1 2490 1
+chr1 544798 568214 570324 1 2111 1
+chr1 544783 570425 574640 1 4216 1
+chr1 544824 574741 578101 1 3361 1
+chr1 544775 578202 580180 1 1979 -1
+chr1 544825 580281 581858 1 1578 -1
+chr1 544772 581959 585312 1 3354 1
+chr1 544793 585413 588740 1 3328 1
+chr1 544785 588841 591656 1 2816 -1
+chr1 544791 591757 594687 1 2931 1
+chr1 544820 594788 597671 1 2884 1
+chr1 544790 597772 601587 1 3816 1
+chr1 544794 601688 603324 1 1637 -1
+chr1 544823 603425 607433 1 4009 1
+chr1 544789 607534 610856 1 3323 1
+chr1 544799 610957 614618 1 3662 1
+chr1 544776 614719 618674 1 3956 -1
+chr1 544797 618775 624522 1 5748 -1
+chr1 544787 624623 629720 1 5098 -1
+chr1 544792 629821 637065 1 7245 1
+chr1 622020 837066 851064 1 13999 -1
+chr1 622021 851165 854101 1 2937 -1
+chr1 622016 854202 856489 1 2288 -1
+chr1 625275 856590 888524 420 32354 -1
+chr1 622015 888525 891483 1 2959 -1
+chr1 622024 891584 896208 8871 13495 -1
+chr1 625537 896209 952170 1 55962 -1
+chr1 625538 952271 1051812 251 99792 -1
+chr1 625277 1051813 1055193 1 3381 -1
+chr1 625266 1055294 1062471 1 7178 -1
+chr1 598266 1062572 1086504 11 23943 -1
+chr1 625271 1086505 1096571 3943 14009 1
+chr1 625265 1096572 1100161 2436 6025 -1
+chr1 173125 1100162 1106067 3329 9234 -1
+chr1 598265 1106068 1112101 286 6319 1
+chr1 625360 1112102 1172572 251 60721 1
+chr1 173111 1172573 1172716 1 144 -1
+chr1 173103 1172817 1173945 1 1129 1
+chr1 170531 1174046 1174188 8791 8933 -1
+chr1 625363 1174189 1183590 67 9468 1
+chr1 173120 1183591 1183929 153 491 -1
+chr1 170509 1183930 1184112 864 1046 1
+chr1 173119 1184213 1189703 1 5491 -1
+chr1 625357 1189804 1213915 1 24112 1
+chr1 625359 1214016 1216330 1 2315 1
+} );
+ @sgp_dump = reverse (@sgp_dump) if defined $reverse; # test the auto-sorting feature
+
+ my $first = 1;
+ for $line ( @sgp_dump ) {
+ if( $first ) { $first = 0; next; }
+ my ( $chr_name, $contig_id, $chr_start,
+ $chr_end, $contig_start, $contig_end, $contig_ori ) = split ( /\t/, $line );
+
+# new argument order:
+ $map->add_map_coordinates( $contig_id, $contig_start, $contig_end, $contig_ori,
+ $chr_name, $chr_start, $chr_end );
+
+ }
+}
+
+
+
+
+# Define a subroutine to say whether an object is a Coordinate or a Gap.
+# This should be in the Gap/Coordinate object itself but isn't.
+# It might change in future so it's abstracted out here in this test.
+#
+# this is damn ugly
+#
+sub isgap { my ($obj) = @_; return !$obj->can ('strand') }
+
+# ok & notok subroutines
+sub ok() { print "ok ", ++$n_test, "\n" }
+sub notok() { print "not ok ", ++$n_test, "\n" }
+