1# -*-Perl-*- Test Harness script for Bioperl
2# $Id$
3
4use strict;
5
6BEGIN {
7    use Bio::Root::Test;
8
9    test_begin(-tests => 14);
10
11	use_ok('Bio::Align::Utilities', qw(:all));
12	use_ok('Bio::SimpleAlign');
13	use_ok('Bio::PrimarySeq');
14	use_ok('Bio::LocatableSeq');
15	use_ok('Bio::AlignIO');
16}
17
18my $DEBUG = test_debug();
19
20my $aa_align = Bio::SimpleAlign->new();
21$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n1", -seq => "MLIDVG-MLVLR"));
22$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n2", -seq => "MLIDVRTPLALR"));
23$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n3", -seq => "MLI-VR-SLALR"));
24
25my %dnaseqs = ();
26$dnaseqs{'n1'} = Bio::PrimarySeq->new(-id => "n1dna", -seq => 'atgctgatagacgtaggcatgctagtactgaga');
27$dnaseqs{'n2'} = Bio::PrimarySeq->new(-id => "n2dna", -seq => 'atgctgatcgacgtacgcaccccgctagcactcaga');
28$dnaseqs{'n3'} = Bio::PrimarySeq->new(-id => "n3dna", -seq => 'atgttgattgtacgctcgcttgcacttaga');
29my $dna_aln;
30
31ok( $dna_aln = &aa_to_dna_aln($aa_align, \%dnaseqs));
32if( $DEBUG ) {
33	Bio::AlignIO->new(-format=>'clustalw')->write_aln($dna_aln);
34}
35
36is $dna_aln->length, 36;
37is $dna_aln->num_residues, 99;
38is $dna_aln->num_sequences, 3;
39is $dna_aln->consensus_string(50), "atgctgat?gacgtacgc????cgctagcact?aga";
40
41my @dnaseqs = $dna_aln->each_seq;
42is $dnaseqs[0]->display_id, 'n1dna';
43$dna_aln->verbose(-1);
44my $replicates;
45ok $replicates = &bootstrap_replicates($dna_aln,3);
46
47is scalar @$replicates, 3;
48my $repl_aln = pop @$replicates;
49is $repl_aln->num_sequences, 3;
50
51##use IO::String;
52##use Bio::AlignIO;
53##my $string;
54##my $out = IO::String->new($string);
55##
56##my $strout = Bio::AlignIO->new(-fh   => $out,'-format' => 'pfam');
57##$strout->write_aln($repl_aln);
58##is $string, "";
59