# -*-Perl-*- Test Harness script for Bioperl
# $Id: nexus.t 14971 2008-10-28 16:08:52Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 43);
use_ok('Bio::AlignIO::nexus');
}
my $DEBUG = test_debug();
my ($str,$aln,$strout,$status);
# NEXUS
$str = Bio::AlignIO->new(
'-file' => test_input_file('testaln.nexus'),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'Homo_sapiens/1-45';
$strout = Bio::AlignIO->new('-file' => ">".test_output_file(),
'-format' => 'nexus', );
$status = $strout->write_aln($aln);
is $status, 1, "nexus output test";
$str = Bio::AlignIO->new(
'-file' => test_input_file('Bird_Ovomucoids.nex'),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file('basic-ladder.nex'),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file('Kingdoms_DNA.nex'),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file('char-interleave.nex'),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file('Primate_mtDNA.nex'),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("char-matrix-spaces.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("SPAN_Family4nl.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("intrablock-comment.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("SPAN_Family7n.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("long-names.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("SPAN_Family8a.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("multiline-intrablock-comment.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("Treebase-chlamy-dna.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("quoted-strings1.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("UnaSmithHIV-both.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("quoted-strings2.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("barns-combined.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("radical-whitespace.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("basic-bush.nex"),
'-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
'-file' => test_input_file("radical-whitespace_02.nex"),
'-format' => 'nexus');