1# -*-Perl-*-
2## Bioperl Test Harness Script for Modules
3
4use strict;
5BEGIN {
6    use Bio::Root::Test;
7    test_begin(-tests => 8);
8	use_ok('Bio::Tools::Run::Alignment::Kalign');
9	use_ok('Bio::AlignIO');
10	use_ok('Bio::SeqIO');
11}
12
13END { unlink qw(cysprot.dnd cysprot1a.dnd) }
14
15my @params = ();
16my $factory = Bio::Tools::Run::Alignment::Kalign->new(@params);
17my $inputfilename = test_input_file("cysprot.fa");
18my $aln;
19
20SKIP: {
21	test_skip(-requires_executable => $factory, -tests => 5);
22	my $version = $factory->version;
23	is($version >= 2, 1, "Code tested only on kalign versions >= 2" );
24	$aln = $factory->align($inputfilename);
25	ok($aln);
26	is( $aln->num_sequences, 7);
27
28	my $str = Bio::SeqIO->new('-file' => test_input_file("cysprot.fa"),
29				  '-format' => 'Fasta');
30	my @seq_array =();
31
32	while ( my $seq = $str->next_seq() ) {
33		push (@seq_array, $seq) ;
34	}
35
36	my $seq_array_ref = \@seq_array;
37
38	$aln = $factory->align($seq_array_ref);
39	is $aln->num_sequences, 7;
40	my $s1_perid = $aln->average_percentage_identity;
41	is(int($s1_perid), 42);
42}
43
44