testing old methods

modules/t/dnaDnaAlignFeature.t

@@ -134,5 +134,29 @@ ok($f);
 $f = $f->transfer($chr_slice->invert);
 ok($f);
 
+#
+# Test alignment strings
+#
+
+my $alignment_strings = $f->alignment_strings('NO_HSEQ');
+is($alignment_strings->[0], 'TACCTG', 'Retrieved query sequence');
+is($alignment_strings->[1], '', 'No target sequence');
+$alignment_strings = $f->alignment_strings('FIX_SEQ', 'NO_HSEQ');
+is($alignment_strings->[0], 'TACCTG', 'Retrieved fixed query sequence');
+
+#
+# Test restrict_between_positions
+#
+
+my $new_daf = $f->restrict_between_positions(104067, 104070, 'SEQ');
+is($new_daf->start, $f->start, 'Start has not changed');
+is($new_daf->end, $f->end - 2, 'New end');
+$new_daf = $f->restrict_between_positions(1, 104070, 'SEQ');
+is($new_daf->start, 104067, 'No start change if beyond the start');
+is($new_daf->end, 104070, 'New daf end');
+$new_daf = $f->restrict_between_positions(1, 5, 'SEQ');
+is($new_daf, undef, "Restriction out of bounds");
+
+
 
 done_testing();