# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Muscle.t,v 1.6 2006/10/26 14:32:21 sendu Exp $
use strict;
use vars qw($NUMTESTS);
BEGIN { 
    eval { require Test; };
    if( $@ ) {
        use lib 't';
    }
    use Test;
    $NUMTESTS = 12; 
    plan tests => $NUMTESTS; 
}
END { unlink qw(cysprot.dnd cysprot1a.dnd) }
use Bio::Tools::Run::Alignment::Muscle;
use Bio::AlignIO;
use Bio::SeqIO;
use Cwd qw(cwd);
use Bio::Root::IO;
use POSIX;
END {     
    for ( $Test::ntest..$NUMTESTS ) {
        skip("Muscle program not found. Skipping.",1);
    }
        unlink('muscle.log', 'muscle.out');
}
ok(1);
my @params = ('quiet' => 1);
my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);
ok($factory->quiet, 1);
my $inputfilename = Bio::Root::IO->catfile("t","data","cysprot.fa");
my $aln;
my $present = $factory->executable();
unless ($present && -e $present ) {
    warn "muscle program not found. Skipping tests $Test::ntest to $NUMTESTS.\n";
    exit(0);
}
my $version = $factory->version;
unless ($version >= 3.6) {
    warn "Only muscle version 3.6 or higher is supported by these tests. Skipping tests $Test::ntest to $NUMTESTS.\n";
    exit(0);
}
ok ($version >= 3.6, 1, "Code tested only on muscle versions > 3.6" );
$aln = $factory->align($inputfilename);
ok($aln);
ok( $aln->no_sequences, 7);
my $str = Bio::SeqIO->new('-file' => 
                          Bio::Root::IO->catfile("t","data","cysprot.fa"), 
                          '-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);
ok $aln->no_sequences, 7;
my $s1_perid = POSIX::ceil($aln->average_percentage_identity);
ok($s1_perid == 43 || $s1_perid == 44, 1,
   'diff versions of MUSCLE have different vals');
my $cwd = cwd;
my $logfile = Bio::Root::IO->catfile($cwd,'muscle.log');
my $outfile = Bio::Root::IO->catfile($cwd,'muscle.out');
# add some more params
@params = ('quiet'    => 1,
           '-outfile_name'      => $outfile,
           'diags'    => 1,
           'stable'   => 1,
           'maxmb'    => 50,
           'maxhours' => 1,
           'maxiters' => 20,
           'log'      => $logfile,
           );
$factory = Bio::Tools::Run::Alignment::Muscle->new(@params);
ok($factory->log, $logfile,'log file');
$aln = $factory->align($seq_array_ref);
ok $aln->no_sequences, 7;
$s1_perid = POSIX::ceil($aln->average_percentage_identity);
ok($s1_perid == 43 || $s1_perid == 44, 1,
   'diff versions of MUSCLE have different vals');
$inputfilename = Bio::Root::IO->catfile("t","data","cysprot1a.fa");
$aln = $factory->align($inputfilename);
ok $aln->no_sequences, 3;
$s1_perid = POSIX::ceil($aln->average_percentage_identity);
ok($s1_perid == 41 || $s1_perid == 42, 1,
   'diff versions of MUSCLE have different vals');