# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: scf.t,v 1.10.6.1 2006/11/08 17:25:55 sendu Exp $
#
use strict;
BEGIN {
    use vars qw($DEBUG $verbose);
    $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
    $verbose = $DEBUG ? 0 : -1;
    # 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 => 17;
}
END {
        unlink qw(
                                 write_scf.scf
                                 write_scf_synthetic_traces.scf 
                                 write_scf_subtrace.scf
                                 write_scf_version2.scf
                                );
}
use Dumpvalue();
my $dumper = new Dumpvalue();
$dumper->veryCompact(1) if $DEBUG;
use Bio::SeqIO::scf;
use Bio::Seq::SequenceTrace;
my $in_scf = Bio::SeqIO->new(-file => Bio::Root::IO->catfile
                                                                          ("t","data","chad100.scf"),
                                                                          -format => 'scf',
                                                                          -verbose => $verbose);
ok($in_scf);
my $swq = $in_scf->next_seq();
ok (ref($swq) eq "Bio::Seq::SequenceTrace");
ok (length($swq->seq())>10);
my $qualities = join(' ',@{$swq->qual()});
ok (length($qualities)>10);
my $id = $swq->id();
ok ($swq->id() eq "ML4942R");
my $a_channel = $swq->trace("a");
ok (scalar(@$a_channel) > 10);
my $c_channel = $swq->trace("c");
ok (length($c_channel) > 10);
my $g_channel = $swq->trace("g");
ok (length($g_channel) > 10);
my $t_channel = $swq->trace("t");
ok (length($t_channel) > 10);
my $ref = $swq->peak_indices();
my @indices = @$ref;
ok (scalar(@indices), 761);
warn("Now checking version3...\n") if $DEBUG;
my $in_scf_v3 = Bio::SeqIO->new(-file => Bio::Root::IO->catfile
                                                                                  ("t","data","version3.scf"),
                                                                                  -format => 'scf',
                                                                                  -verbose => $verbose);
my $v3 = $in_scf_v3->next_seq();
my $ind = $v3->peak_indices();
my @ff = @$ind;
@indices = @{$v3->peak_indices()};
ok (scalar(@indices) == 1106);
my %header = %{$in_scf_v3->get_header()};
ok $header{bases}, 1106;
ok $header{samples},  14107;
my $ac = $in_scf_v3->get_comments();
ok (ref($ac) eq "Bio::Annotation::Collection");
my @name_comments = grep {$_->tagname() eq 'NAME'} 
  $ac->get_Annotations('comment');
ok $name_comments[0]->as_text(), 'Comment: IIABP1D4373';
my @conv_comments = grep {$_->tagname() eq 'CONV'} 
  $ac->get_Annotations('comment');
ok $conv_comments[0]->as_text(), 'Comment: phred version=0.990722.h';
# is the SequenceTrace object annotated?
my $st_ac = $swq->annotation();
ok (ref($st_ac) eq "Bio::Annotation::Collection");
warn("Now testing the _writing_ of scfs\n") if $DEBUG;
my $out_scf = Bio::SeqIO->new(-file => ">write_scf.scf",
                                                                                -format => 'scf',
                                                                                -verbose => $verbose);
exit;   # the new way
$out_scf->write_seq(-target  =>   $v3,
                                                  -MACH         =>   'CSM sequence-o-matic 5000',
                                                  -TPSW         =>   'trace processing software',
                                                  -BCSW         =>   'basecalling software',
                                                  -DATF         =>   'AM_Version=2.00',
                                                  -DATN         =>   'a22c.alf',
                                                  -CONV         =>   'Bioperl-scf.pm');
ok( -e "write_scf.scf" && ! -z "write_scf.scf" );
$out_scf = Bio::SeqIO->new(-verbose => 1,
                                                                        -file => ">write_scf_synthetic_traces.scf",
                                                                        -format => 'scf');
$swq = Bio::Seq::Quality->new(-seq =>'ATCGATCGAA',
                                                                                -qual =>"10 20 30 40 50 20 10 30 40 50",
                                                                                -alphabet =>'dna');
my $trace = Bio::Seq::SequenceTrace->new(-swq => $swq);
$out_scf->write_seq( -target =>   $trace,
                                                        -MACH           =>   'CSM sequence-o-matic 5000',
                                                        -TPSW           =>   'trace processing software',
                                                        -BCSW           =>   'basecalling software',
                                                        -DATF           =>   'AM_Version=2.00',
                                                        -DATN           =>   'a22c.alf',
                                                        -CONV           =>   'Bioperl-scf.pm' );
warn("Trying to write an scf with a subset of a real scf...\n") if $DEBUG;
$out_scf = Bio::SeqIO->new(-verbose => 1,
                                                                        -file => ">write_scf_subtrace.scf",
                                                                        -format => 'scf');
$in_scf_v3 = Bio::SeqIO->new(-file => Bio::Root::IO->catfile
                                                                          ("t","data","version3.scf"),
                                                                          -format => 'scf',
                                                                          -verbose => $verbose);
$v3 = $in_scf_v3->next_seq();
my $sub_v3 = $v3->sub_trace_object(5,50);
warn("The subtrace object is this:\n") if $DEBUG;
$dumper->dumpValue($sub_v3) if $DEBUG;
$out_scf->write_seq(-target => $sub_v3 );
my $in_scf_v2 = Bio::SeqIO->new(-file => Bio::Root::IO->catfile
                                                                                  ("t","data","version2.scf"),
                                                                                  -format => 'scf',
                                                                                  -verbose => $verbose);
$v3 = $in_scf_v2->next_seq();
ok($v3);
$out_scf = Bio::SeqIO->new(-file   => ">write_scf_version2.scf",
                           -format => "scf");
$out_scf->write_seq( -target  => $v3,
                     -version => 2 );
# now some version 2 things.