# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 166);
	
	use_ok('Bio::SearchIO');
    use_ok('Bio::Search::SearchUtils');
}

my ($searchio, $result,$iter,$hit,$hsp);

# test blasttable output
my @eqset = qw( c200-vs-yeast.BLASTN.m9);
$searchio = Bio::SearchIO->new(-file => test_input_file('c200-vs-yeast.BLASTN'),
			      -format => 'blast');
$result = $searchio->next_result;
isa_ok($result,'Bio::Search::Result::ResultI');
my %ref = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %ref, 67);
$searchio = Bio::SearchIO->new(-file => test_input_file('c200-vs-yeast.BLASTN.m8'),
			      -program_name => 'BLASTN',
			      -format => 'blasttable');
$result = $searchio->next_result;
my %tester = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %tester, 67);
foreach my $key ( sort keys %ref ) {
    is($tester{$key}, $ref{$key},$key);
}

# test WU-BLAST blasttable output
$searchio = Bio::SearchIO->new(-file => test_input_file('test1.wublastp'),
			      			   -format => 'blast');
$result = $searchio->next_result;
isa_ok($result,'Bio::Search::Result::ResultI');
my %wuref = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %wuref, 31);
$searchio = Bio::SearchIO->new(-file => test_input_file('test1.blasttab3'),
			      -program_name => 'BLASTP',
			      -format => 'blasttable');
$result = $searchio->next_result;
my %wutester = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %wutester, 31);
foreach my $key ( sort keys %ref ) {
    is($wutester{$key}, $wuref{$key},$key);
}

# BLAST 2.2.18+ tabular output (has 13 columns instead of 12)
$searchio = Bio::SearchIO->new(-format => 'blasttable',
							  -file   => test_input_file('2008.blasttable'));

while(my $res = $searchio->next_result) {
    is($res->query_name, 'gi|1786183|gb|AAC73113.1|');
    is($res->algorithm, 'BLASTP');
    is($res->algorithm_version, '2.2.18+');
    my $hit = $res->next_hit;
    is($hit->name, 'gi|34395933|sp|P00561.2|AK1H_ECOLI');
    $hit = $res->next_hit;
    is($hit->score, 331, 'hit score');
    is($hit->raw_score, 331, 'hit raw_score');
    my $hsp = $hit->next_hsp;
	isa_ok($hsp, 'Bio::SeqFeatureI');
    is($hsp->bits, 331);
    float_is($hsp->evalue, 2e-91);
    is($hsp->start('hit'), 16);
    is($hsp->end('hit'), 805);
    is($hsp->start('query'), 5);
    is($hsp->end('query'), 812);
    is($hsp->length, 821);
    float_is($hsp->percent_identity, 30.0852618757613, 'fixed bug 3343 (percent identity)');
    is($hsp->gaps, 44, 'side effect of fixing bug 3343 (number of gaps)');
	my $hit_sf = $hsp->hit;
	my $query_sf = $hsp->query;
	isa_ok($hit_sf, 'Bio::SeqFeatureI');
    is($hit_sf->start(), 16);
    is($hit_sf->end(), 805);
    is($hit_sf->strand(), 0);	
	isa_ok($query_sf, 'Bio::SeqFeatureI');
    is($query_sf->start(), 5);
    is($query_sf->end(), 812);
    is($query_sf->strand(), 0);
}