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# -*-Perl-*-
## Bioperl Test Harness Script for Modules

use strict;
BEGIN {
    use Bio::Root::Test;
    test_begin(-tests => 11);
use_ok(' Bio::Tools::Run::Alignment::Probcons');
use_ok(' Bio::AlignIO');
use_ok(' Bio::SeqIO');
}

END { unlink qw(cysprot.dnd cysprot1a.dnd) }

my @params = ();
my $factory = Bio::Tools::Run::Alignment::Probcons->new(@params);
my $inputfilename = test_input_file('cysprot.fa');
my $aln;

SKIP: {
test_skip(-requires_executable => $factory,
-tests => 8);
my $version = $factory->version;
cmp_ok ($version, '>=', 1.09, "Code tested only on probcons versions > 1.09" );
$aln = $factory->align($inputfilename);
ok($aln);
is( $aln->no_sequences, 7);

my $str = Bio::SeqIO->new('-file' => $inputfilename,
'-format' => 'Fasta');
my @seq_array =();

while ( my $seq = $str->next_seq() ) {
push (@seq_array, $seq) ;
}

my $seq_array_ref = \@seq_array;

$aln = $factory->align($seq_array_ref);
is $aln->no_sequences, 7;
my $s1_avg_perid = $aln->average_percentage_identity;
is(int($s1_avg_perid), 43);
my $s1_ovl_perid = $aln->overall_percentage_identity;
is(int($s1_ovl_perid), 15);

my ($paramsfilename) = test_output_file();
my ($annotfilename) = test_output_file();
my ($dummyfilename) = test_output_file();
my $factory2 = Bio::Tools::Run::Alignment::Probcons->new
(
'iterative-refinement' => '1000',
'consistency' => '5',
'emissions' => '',
'verbose' => '',
'train' => $paramsfilename,
);
$factory2->outfile_name($dummyfilename);

my $aln2 = $factory2->align($seq_array_ref);
$aln2 = '';
$factory2 = '';

$factory2 = Bio::Tools::Run::Alignment::Probcons->new
(
'iterative-refinement' => '1000',
'consistency' => '5',
'annot' => $annotfilename,
'paramfile' => $paramsfilename,
);
$factory->outfile_name($dummyfilename);
$aln2 = $factory2->align($seq_array_ref);
my $s2_avg_perid = $aln2->average_percentage_identity;
my $s2_ovl_perid = $aln2->overall_percentage_identity;
cmp_ok(int($s2_avg_perid), '>=', 42);
cmp_ok(int($s2_ovl_perid), '>=', 15);
}

END {
if (-e 'iterative-refinement') {
unlink('iterative-refinement');
}
}
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