# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 101);
	
	use_ok('Bio::SeqIO');
}

my $verbosity = test_debug();

my ($seqio, $seq); # predeclare variables for strict

# default mode
ok $seqio = Bio::SeqIO->new('-file'=> test_input_file('test.genbank'), 
			 '-format' => 'GenBank');
$seqio->verbose($verbosity);

my $numseqs = 0;
my @loci = qw(U63596 U63595 M37762 NT_010368 L26462);
my @numfeas = (3,1,6,3,26);

while($seq = $seqio->next_seq()) {
    is ($seq->accession_number, $loci[$numseqs++]);
    ok ($seq->annotation->get_Annotations());
    is (scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1]);
    ok ($seq->species->binomial);
    ok ($seq->seq);
}
is ($numseqs, 5);

# minimalistic mode
$seqio = Bio::SeqIO->new('-file'=> test_input_file('test.genbank'), 
			 '-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
ok my $seqbuilder = $seqio->sequence_builder();
isa_ok $seqbuilder, "Bio::Factory::ObjectBuilderI";
$seqbuilder->want_none();
$seqbuilder->add_wanted_slot('display_id','accession_number','desc');

$numseqs = 0;

while($seq = $seqio->next_seq()) {
    is ($seq->accession_number, $loci[$numseqs++]);
    is (scalar(grep { ! ($_->tagname eq "keyword" ||
			 $_->tagname eq "date_changed" ||
			 $_->tagname eq "secondary_accession"); }
	       $seq->annotation->get_Annotations()), 0);
    if($numseqs <= 3) {
		is (scalar($seq->top_SeqFeatures), 0);
    }
	else {
		is (scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1]);
    }
    is ($seq->species, undef);
    is ($seq->seq, undef);
    # switch on features for the last 2 seqs
    $seqbuilder->add_wanted_slot('features') if $numseqs == 3;
}
is ($numseqs, 5);

# everything but no sequence, and no features
$seqio = Bio::SeqIO->new('-file'=> test_input_file('test.genbank'), 
			 '-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
$seqbuilder = $seqio->sequence_builder();
# want-all is default
$seqbuilder->add_unwanted_slot('seq','features');

$numseqs = 0;

while($seq = $seqio->next_seq()) {
    is ($seq->accession_number, $loci[$numseqs++]);
    ok scalar($seq->annotation->get_Annotations());
    if($numseqs <= 3) {
		is (scalar($seq->top_SeqFeatures), 0);
    }
	else {
		is (scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1]);
    }
    ok $seq->species->binomial;
    is ($seq->seq, undef);
    # switch on features for the last 2 seqs
    if($numseqs == 3) {
	$seqbuilder->add_unwanted_slot(
	     grep { $_ ne 'features'; } $seqbuilder->remove_unwanted_slots());
    }
}
is ($numseqs, 5);

# skip sequences less than 100bp or accession like 'NT_*'
$seqio = Bio::SeqIO->new('-file'=> test_input_file('test.genbank'), 
			 '-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
$seqbuilder = $seqio->sequence_builder();
# we could have as well combined the two conditions into one, but we want to
# test the implicit AND here
$seqbuilder->add_object_condition(sub {
    my $h = shift;
    return 0 if($h->{'-length'} < 100);
    return 1;
});
$seqbuilder->add_object_condition(sub {
    my $h = shift;
    return 0 if($h->{'-display_id'} =~ /^NT_/);
    return 1;
});

$numseqs = 0;
my $i = 0;

while($seq = $seqio->next_seq()) {
    $numseqs++;
    is ($seq->accession_number, $loci[$i]);
    ok scalar($seq->annotation->get_Annotations());
    is (scalar($seq->top_SeqFeatures), $numfeas[$i]);
    ok $seq->species->binomial;
    ok $seq->seq;
    $i += 2;
}
is ($numseqs, 3);