# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: phd.t,v 1.8.4.2 2006/11/08 17:25:55 sendu Exp $
#
use strict;
use vars qw($DEBUG);
use Bio::Root::IO;
$DEBUG = $ENV{'BIOPERLDEBUG'};
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::More; };
    if( $@ ) {
        use lib 't/lib';
    }
    use Test::More;
    plan tests => 9;
}
END  {
    unlink qw(write_phd.phd);
}
print("Checking if the Bio::SeqIO::phd module could be used, even though it shouldn't be directly used...\n") if ( $DEBUG);
        # test 1
use_ok('Bio::SeqIO::phd');
print("Checking to see if SeqWithQuality objects can be created from a file...\n") if ($DEBUG);
my $in_phd  = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
                                                                "phredfile.phd"),
                              '-format'  => 'phd',
                              '-verbose' => $DEBUG || 0);
isa_ok($in_phd,'Bio::SeqIO::phd');
my @phreds;
print("I saw these in qualfile.qual:\n") if($DEBUG);
my $phd = $in_phd->next_seq();
print("Did you get the 'QUALITY_LEVELS' comment?\n") if ($DEBUG);
is($phd->{comments}->{'QUALITY_LEVELS'}, 99);
print("Checking to see if this is the right reference...\n") if( $DEBUG);
isa_ok($phd,"Bio::Seq::Quality");
my $position = 6;
if( $DEBUG ) {
    print("What is the base at position $position (using subseq)?\n");
    print($phd->subseq($position,$position)."\n");
    print("What is the base at position $position (using baseat)?\n");
    print($phd->baseat($position)."\n");
    print("What is the quality at $position? (using subqual)\n");
}
my @qualsretr = @{$phd->subqual($position,$position)};
if( $DEBUG ) {
    print($qualsretr[0]."\n");
    print("What is the quality at $position? (using qualat)\n");
    print($phd->qualat($position)."\n");
}
print("OK. Now testing write_phd...\n") if($DEBUG);
my $out_phd = Bio::SeqIO->new(-file => ">write_phd.phd",
                              '-format' => 'phd');
print("Did it return the right reference?\n") if($DEBUG);
isa_ok($out_phd,"Bio::SeqIO::phd");
$out_phd->write_seq( -SeqWithQuality         =>   $phd,
                        -CHROMAT_FILE           =>   $phd->id(),
                        -ABI_THUMBPRINT         =>   "",
                        -PHRED_VERSION          =>   "",
                        -CALL_METHOD            =>   "",
                        -QUALITY_LEVELS         =>   "",
                        -TIME                   =>   "",
                        -TRACE_ARRAY_MIN_INDEX  =>   "",
                        -TRACE_ARRAY_MAX_INDEX  =>   "",
                        -CHEM   =>   "",
                        -DYE    =>   ""      
                        );
ok( -e "write_phd.phd");
# Bug 2120
my @qual = q(9 9 12 12 8 8 9 8 8 8 9);
my @trace = q(113 121 130 145 153 169 177 203 210 218 234);
$in_phd  = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
                                                                "bug2120.phd"),
                              '-format'  => 'phd',
                              '-verbose' => $DEBUG || 0);
my $seq = $in_phd->next_seq;
is($seq->subseq(10,20),'gggggccttat','$seq->subseq()');
my @seq_qual =$seq->subqual_text(10,20);
is_deeply(\@seq_qual,\@qual,'$seq->subqual_tex()');
my @seq_trace = $seq->subtrace_text(10,20);
is_deeply(\@seq_trace,\@trace,'$seq->subqual_tex()');