# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: MetaSeq.t,v 1.5 2005/08/16 11:51:04 heikki Exp $
use strict;
BEGIN {
        # to handle systems with no installed Test module
        # we include the t dir (where a copy of Test.pm is located)
        # as a fallback
    eval { require Test; };
    if( $@ ) {
        use lib 't';
    }
    use Test;
    plan tests => 124;
}
my $DEBUG = $ENV{'BIOPERLDEBUG'};
use Bio::Seq::Meta;
use Bio::Seq::Meta::Array;
use Bio::SeqIO;
use Bio::AlignIO;
use Bio::Root::IO;
use Bio::Seq::Quality;
use Data::Dumper;
ok(1);
ok my $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA");
ok $seq->meta, "";
ok $seq->force_flush(1);
ok $seq->meta, "          ";
$seq->seq("AT-CGATCGATT");
ok $seq->meta, "            ";
ok not $seq->force_flush(0);
#print Dumper $seq;
ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA");
ok $seq->meta_text, "";
ok $seq->force_flush(1);
$seq->seq("AT-CGATCGATT");
ok $seq->meta_text, "0 0 0 0 0 0 0 0 0 0 0 0";
ok not $seq->force_flush(0);
#print Dumper $seq;
ok $seq = Bio::Seq::Quality->new( -seq => "AT-CGATCGA");
ok $seq->meta_text, "";
ok $seq->force_flush(1);
ok $seq->meta_text, "0 0 0 0 0 0 0 0 0 0";
$seq->seq("AT-CGATCGATT");
ok $seq->meta_text, "0 0 0 0 0 0 0 0 0 0 0 0";
ok not $seq->force_flush(0);
#print Dumper $seq;
#exit;
ok $seq = Bio::Seq::Meta->new
    ( -seq => "",
      -meta => "",
      -alphabet => 'dna',
      -id => 'myid'
    );
# create a sequence object
ok $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA",
                               -id => 'test',
                               -verbose => 2,
                               -force_flush => 1
                             );
ok $seq->meta, "          ";
ok $seq->meta_length, 10;
# Create some random meta values, but gap in the wrong place
my $metastring = "a-abb  bb ";
eval {
    $seq->meta($metastring);
};
ok 1 if $@ =~ 'column [2]';
$seq->verbose(1);
# create some random meta values, but not for the last residue
$metastring = "aa-bb  bb";
ok $seq->meta($metastring), $metastring. " ";
#print Dumper $seq;
#exit;
# truncate the sequence by assignment
$seq->force_flush(1);
$seq->seq('AT-CGA');
$seq->alphabet('dna');
ok $seq->meta, 'aa-bb ';
ok $seq->start, 1;
ok $seq->end, 5;
$seq->force_flush(0);
# truncate the sequence with trunc()
ok $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
ok $seq->start, 2;
ok $seq->end, 5;
ok $seq->seq, 'AT-CG';
ok $seq->meta, 'aa-bb';
ok $seq->strand, -1;
# revcom
ok $seq = $seq->revcom;
ok $seq->seq, 'CG-AT';
ok $seq->meta, 'bb-aa';
ok $seq->strand, 1;
# submeta
ok $seq->subseq(2,4), 'G-A';
ok $seq->submeta(2,4), 'b-a';
ok $seq->submeta(2,undef, 'c-c'), 'c-ca';
ok $seq->submeta(2,4), 'c-c';
ok $seq->meta, 'bc-ca';
ok $seq->meta(''), '     ';
ok $seq->submeta(2,undef, 'c-c'), 'c-c ';
ok $seq->meta, ' c-c ';
# add named meta annotations
my $first = '11-22';
ok $seq->named_meta('first', $first), $first;
ok $seq->named_meta('first'), $first;
my $second = '[[-]]';
ok $seq->named_meta('second', $second);
# undefined range arguments
ok $seq->named_submeta('second', 3, 4), '-]';
ok $seq->named_submeta('second', 3), '-]]';
ok $seq->named_submeta('second'), '[[-]]';
my @names =  $seq->meta_names;
ok @names, 3;
ok $names[0], 'DEFAULT';
#
# IO tests
#
sub diff {
    my ($infile, $outfile) = @_;
    my ($in, $out);
    open FH, $infile;
    $in .= $_ while (<FH>);
    close FH;
    open FH, $outfile;
    $out .= $_ while (<FH>);
    close FH;
    print "|$in||$out|\n" if $DEBUG;
    ok $in, $out;
}
# SeqIO
my $str = Bio::SeqIO->new
    ( '-file'=> Bio::Root::IO->catfile("t","data","test.metafasta"),
      '-format' => 'metafasta');
ok  $seq = $str->next_seq;
my $strout = Bio::SeqIO->new
    ('-file'=> ">". Bio::Root::IO->catfile("t","data","test.metafasta.out"),
     '-format' => 'metafasta');
ok $strout->write_seq($seq);
diff (Bio::Root::IO->catfile("t","data","test.metafasta"),
      Bio::Root::IO->catfile("t","data","test.metafasta.out")
     );
#exit;
# AlignIO
$str = Bio::AlignIO->new
    ( '-file'=> Bio::Root::IO->catfile("t","data","testaln.metafasta"),
      '-format' => 'metafasta');
ok my $aln = $str->next_aln;
$strout = Bio::AlignIO->new
    ('-file'=> ">". Bio::Root::IO->catfile("t","data","testaln.metafasta.out"),
     '-format' => 'metafasta');
ok $strout->write_aln($aln);
diff (Bio::Root::IO->catfile("t","data","testaln.metafasta"),
      Bio::Root::IO->catfile("t","data","testaln.metafasta.out")
     );
END {
    unlink(Bio::Root::IO->catfile("t","data","test.metafasta.out"));
    unlink(Bio::Root::IO->catfile("t","data","testaln.metafasta.out"));
}
#
##
### tests for Meta::Array
##
#
ok $seq = Bio::Seq::Meta::Array->new
    ( -seq => "",
      -meta => "",
      -alphabet => 'dna',
      -id => 'myid'
    );
# create a sequence object
ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA",
                                      -id => 'test',
                                      -force_flush => 1,
                                      -verbose => 2
                             );
ok $seq->is_flush, 1;
#ok $seq->meta_text, "          ";
ok $seq->meta_text, '0 0 0 0 0 0 0 0 0 0';
#print Dumper $seq; exit;
# create some random meta values, but not for the last residue
$metastring = "a a - b b 0 b b 0";
ok join (' ',  @{$seq->meta($metastring)}), $metastring. ' 0';
ok $seq->meta_text, $metastring. ' 0';
# truncate the sequence by assignment
$seq->seq('AT-CGA');
$seq->alphabet('dna');
ok $seq->meta_text, 'a a - b b 0';
# truncate the sequence with trunc()
ok $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
ok $seq->seq, 'AT-CG';
ok $seq->meta_text, 'a a - b b';
ok $seq->strand, -1;
#ok $seq->length, 5;
#ok $seq->meta_length, 6;
#ok $seq->force_flush(1);
#ok $seq->meta_length, 5;
#print Dumper $seq; exit;
#exit;
# revcom
ok $seq = $seq->revcom;
ok $seq->seq, 'CG-AT';
ok $seq->meta_text, 'b b - a a';
ok $seq->strand, 1;
# submeta
ok $seq->subseq(2,4), 'G-A';
ok $seq->submeta_text(2,4), 'b - a';
ok $seq->submeta_text(2,undef, 'c - c'), 'c - c';
ok $seq->submeta_text(2,4), 'c - c';
ok $seq->meta_text, 'b c - c a';
ok $seq->meta_text(''), '0 0 0 0 0';
ok $seq->submeta_text(2,undef, 'c - c'), 'c - c';
ok $seq->meta_text, '0 c - c 0';
# add named meta annotations
$first = '1 10 - 222 23';
ok $seq->named_meta_text('first', $first), $first;
ok $seq->named_meta_text('first'), $first;
$second = '[ [ - ] ]';
ok $seq->named_meta_text('second', $second);
# undefined range arguments
ok $seq->named_submeta_text('second', 3, 4), '- ]';
ok $seq->named_submeta_text('second', 3), '- ] ]';
ok $seq->named_submeta_text('second'), '[ [ - ] ]';
@names =  $seq->meta_names;
ok @names, 3;
ok $names[0], 'DEFAULT';
#
# testing the forcing of flushed meta values
#
ok $seq = Bio::Seq::Meta->new( -seq =>  "AT-CGATCGA",
                                  -id => 'test',
                                  -verbose => 2
                             );
ok $seq->submeta(4, 6, '456'), '456';
ok $seq->meta_length, 6;
ok $seq->length, 10;
ok $seq->meta, "   456";
ok $seq->force_flush(1);
ok $seq->meta, "   456    ";
ok $seq->seq('aaatttc');
ok $seq->meta, "   456 ";
ok $seq = Bio::Seq::Meta::Array->new( -seq =>  "AT-CGATCGA",
                                  -id => 'test',
                                  -verbose => 2
                             );
ok join (' ', @{$seq->submeta(4, 6, '4 5 6')}), '4 5 6';
ok $seq->meta_length, 6;
ok $seq->length, 10;
ok $seq->meta_text, "0 0 0 4 5 6";
ok $seq->force_flush(1);
ok $seq->meta_text, "0 0 0 4 5 6 0 0 0 0";
ok $seq->seq('aaatttc');
ok $seq->meta_text, "0 0 0 4 5 6 0";
ok $seq->meta_length, 7;
ok  $seq = Bio::Seq::Quality->new( -seq =>  "AT-CGATCGA",
                                  -id => 'test',
                                  -verbose => 2
                             );
ok join (' ', @{$seq->submeta(4, 6, '4 5 6')}), '4 5 6';
ok $seq->meta_length, 6;
ok $seq->length, 10;
ok $seq->meta_text, "0 0 0 4 5 6";
#print Dumper $seq;
ok $seq->force_flush(1);
ok $seq->meta_text, "0 0 0 4 5 6 0 0 0 0";
ok $seq->seq('aaatttc');
ok $seq->meta_text, "0 0 0 4 5 6 0";
ok $seq->meta_length, 7;
ok $seq->trace_length, 7;
#ok $seq->quality_length, 7;
ok $seq->is_flush, 1;
ok $seq->trace_is_flush, 1;
ok $seq->quality_is_flush, 1;
#print Dumper $seq;
# quality: trace_lengths, trace_is_flush, quality_is_flush