added tests for new SeqEdit class

modules/t/seqEdit.t

+use lib 't';
+
+BEGIN { $| = 1;
+	use Test;
+	plan tests => 27;
+}
+
+use Bio::EnsEMBL::SeqEdit;
+use Bio::EnsEMBL::Attribute;
+use TestUtils qw(debug test_getter_setter);
+
+my $code  = 'rna edit';
+my $desc  = 'Post transcriptional RNA edit';
+my $value = '2 3 ACTG';
+my $name  = 'RNA Edit';
+
+my $a = Bio::EnsEMBL::Attribute->new
+  (-CODE  => $code,
+   -DESCRIPTION  => $desc,
+   -VALUE => $value,
+   -NAME  => $name);
+
+my $se = Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $a);
+
+ok(ref($se) && $se->isa('Bio::EnsEMBL::SeqEdit'));
+
+ok($se->name() eq $name);
+ok($se->description() eq $desc);
+ok($se->code() eq $code);
+
+ok($se->alt_seq() eq 'ACTG');
+ok($se->start()   == 2);
+ok($se->end()     == 3);
+
+ok(test_getter_setter($se, 'start', 10));
+ok(test_getter_setter($se, 'end', 12));
+ok(test_getter_setter($se, 'alt_seq', 'GGAAA'));
+ok(test_getter_setter($se, 'name', 'test name'));
+ok(test_getter_setter($se, 'description', 'test desc'));
+ok(test_getter_setter($se, 'code', 'test cpde'));
+
+ok($se->length_diff == 2);
+
+my $seq = 'CCCC';
+$se->apply_edit(\$seq);
+ok($seq eq 'CACTGC');
+
+# test insert before first base
+$seq = 'ACTG';
+$se->alt_seq('CC');
+$se->start(1);
+$se->end(0);
+ok($se->apply_edit(\$seq));
+ok($seq eq 'CCACTG');
+
+ok($se->length_diff() == 2);
+
+# test insert after last base
+$seq = 'ACTG';
+$se->alt_seq('CC');
+$se->start(5);
+$se->end(4);
+$se->apply_edit(\$seq);
+ok($seq eq 'ACTGCC');
+
+ok($se->length_diff() == 2);
+
+# test deletion of entire sequence
+$seq = 'ACTG';
+$se->alt_seq('');
+$se->start(1);
+$se->end(4);
+$se->apply_edit(\$seq);
+ok($seq eq '');
+
+ok($se->length_diff() == -4);
+
+# test replacement of some sequence
+$seq = 'ACTG';
+$se->alt_seq('TC');
+$se->start(2);
+$se->end(3);
+$se->apply_edit(\$seq);
+ok($seq eq 'ATCG');
+
+# test conversion to attribute
+$a = $se->get_Attribute();
+ok($a->name() eq $se->name());
+ok($a->description() eq $se->description());
+ok($a->code() eq $se->code());
+ok($a->value eq '2 3 TC');