# -*-Perl-*-
## Bioperl Test Harness Script for Modules
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
my $error;
use strict;
use vars qw($DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'};
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( $@ ) {
        use lib 't';
    }
    use Test;
    use vars qw($TESTCOUNT);
    $TESTCOUNT = 15;
    plan tests => $TESTCOUNT;
     
    $error  = 0;
    eval { require XML::Parser::PerlSAX; };
    if( $@ ) {
        print STDERR "XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping\n";
        foreach ( $Test::ntest..$TESTCOUNT ) {
            skip('XML::Parser::PerlSAX installed',1);
        }
        $error = 1;
    } 
    # make sure we can load it, assuming that the prerequisites are really met
    if( $error == 0 ) {
        eval { require Bio::SeqIO::tinyseq; };
        if( $@ ) {
            print STDERR "tinyseq.pm not loaded. This means tinyseq test cannot be executed. Skipping\n";
            foreach ( $Test::ntest..$TESTCOUNT ) {
                skip('tinyseq.pm not loaded because XML::Writer not loaded',1);
            }
            $error = 1;
        } 
    }
}
if( $error == 1 ) {
    exit(0);
}
use Bio::SeqIO;
use Bio::Seq;
my $file = File::Spec->catfile(qw(t data NM_002253.tseq));
my $outfile = 'tinyseqout.xml';
my $instream = Bio::SeqIO->new( -file                => $file,
                                -format         => 'tinyseq' );
my $outstream = Bio::SeqIO->new( -file               => ">$outfile",
                                 -format        => 'tinyseq' );
my $seq = $instream->next_seq;
ok(defined $seq);
ok(defined $seq->seq);
ok($seq->length, 5830);
ok($seq->accession_number,'NM_002253');
ok($seq->species);
ok($seq->species->binomial, 'Homo sapiens');
ok($seq->species->ncbi_taxid, 9606);   
$outstream->write_seq($seq);
undef $outstream;
#$outstream->close_writer;
  
ok(-e $outfile);
my $reread = Bio::SeqIO->new( -file          => $outfile,
                              -format           => 'tinyseq' );
my $seq2 = $reread->next_seq;
ok($seq2);
ok($seq2->seq);
ok($seq2->length, 5830);
ok($seq2->accession_number, 'NM_002253');
ok($seq2->species);
ok($seq2->species->binomial, 'Homo sapiens');
ok($seq2->species->ncbi_taxid, 9606);   
unlink $outfile;