use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 391,
               -requires_module => 'XML::SAX');

    use_ok('Bio::SearchIO');
}

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

eval {
    # test with RPSBLAST data first
    # this needs to be eval'd b/c the XML::SAX parser object is
    # instantiated in the constructor
    $searchio = Bio::SearchIO->new('-tempfile' => 1,
           '-format' => 'blastxml',
           '-file'   => test_input_file('ecoli_domains.rps.xml'),
           '-blasttype' => 'blast',
           '-verbose' => -1);
    # PurePerl works with these BLAST reports, so removed verbose promotion
    $result = $searchio->next_result;
    die if !defined $result;
};

SKIP: {
    # this should be fixed with newer installations of XML::SAX::Expat, but as we
    # don't require a certain version (multiple backends can be used) we catch
    # and skip if needed
    if ($@ && $@ =~ m{Handler could not resolve external entity}) {
        skip("Older versions of XML::SAX::Expat may not work with XML tests; skipping",297);
    } elsif ($@) {
        skip("Problem with XML::SAX setup: $@. Check ParserDetails.ini; skipping XML tests",297);
    }
    is($searchio->result_count, 1);

    # basic ResultI data
    isa_ok($result, 'Bio::Search::Result::ResultI');
    is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
    is($result->query_name,'gi|1786182|gb|AAC73112.1|','query_name()');
    is($result->query_description, '(AE000111) thr operon leader peptide [Escherichia coli]');
    is($result->query_accession, 'AAC73112.1');
    is($result->query_gi, 1786182);
    is($result->query_length, 21);
    is($result->algorithm, 'BLASTP');
    is($result->algorithm_version, 'blastp 2.1.3 [Apr-1-2001]');

    # check parameters
    is($result->available_parameters, 8);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), '1e-05');
    is($result->get_parameter('include'), 0);
    is($result->get_parameter('match'), 0);
    is($result->get_parameter('mismatch'), 0);
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), 'F');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 0);
    is($result->database_letters, 0);
    is($result->get_statistic('hsplength'), 0);
    float_is($result->get_statistic('effectivespace'), 4.16497e+11);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.041);
    is($result->get_statistic('entropy'), 0.14);

    # this result actually has a hit
    $result = $searchio->next_result;

    # does the parser catch everything in the next result?
    is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
    is($result->query_name,'gi|1786183|gb|AAC73113.1|');
    is($result->query_description, '(AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli]');
    is($result->query_accession, 'AAC73113.1');
    is($result->query_gi, 1786183);
    is($result->query_length, 820);
    is($result->algorithm, 'BLASTP');
    is($result->algorithm_version, 'blastp 2.1.3 [Apr-1-2001]');

    is($searchio->result_count, 2);

    # check parameters
    is($result->available_parameters, 8);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), '1e-05');
    is($result->get_parameter('include'), 0);
    is($result->get_parameter('match'), 0);
    is($result->get_parameter('mismatch'), 0);
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), 'F');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 0);
    is($result->database_letters, 0);
    is($result->get_statistic('hsplength'), 0);
    float_is($result->get_statistic('effectivespace'), 3.82682e+07);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.041);
    is($result->get_statistic('entropy'), 0.14);

    $hit = $result->next_hit;
    is($hit->name, 'gnl|Pfam|pfam00742');
    is($hit->description(), 'HomoS_dh, HomoS dehydrogenase');
    is($hit->accession, 'pfam00742');
    is($hit->ncbi_gi, ''); # not found
    is($hit->length, 310);

    $hsp = $hit->next_hsp;
    is($hsp->query->seq_id, $result->query_name,'query name on HSP');
    is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
    is($hsp->hit->seq_id, $hit->name,'hitname');
    is($hsp->hit->seqdesc, $hit->description,'hitdesc');
    is($hsp->pvalue, undef);
    float_is($hsp->evalue, 1.46134e-90);
    is($hsp->score, 838);
    is($hsp->bits,327.405);
    is($hsp->query->start, 498);
    is($hsp->query->end,815);
    is($hsp->hit->start, 3);
    is($hsp->hit->end, 310);
    is($hsp->query->frame,0);
    is($hsp->hit->frame,0);
    is(sprintf("%.2f", $hsp->percent_identity), 37.73);
    is(sprintf("%.4f", $hsp->frac_identical('hit')), 0.3994);
    is(sprintf("%.4f", $hsp->frac_identical('query')), 0.3868);
    is(sprintf("%.4f",$hsp->query->frac_identical), 0.3868);

    is(sprintf("%.4f",$hsp->frac_conserved('total')),0.5245);
    is(sprintf("%.4f",$hsp->frac_conserved('hit')),0.5552);
    is(sprintf("%.4f",$hsp->frac_conserved('query')),0.5377);
    # gaps should match calculated sequence indices for gaps and vice versa
    is($hsp->gaps('total'), $hsp->seq_inds('hit', 'gaps') + $hsp->seq_inds('query', 'gaps'));
    is($hsp->gaps('hit'), $hsp->seq_inds('hit', 'gaps'));
    is($hsp->gaps('query'), $hsp->seq_inds('query', 'gaps'));
    is($hsp->length('total'), 326);
    is($hsp->query_string, 'LRVCGVANSKALLTNVHGLNLENWQEELAQAKEPF-NLGRLIRLVKEYHLLN----PVIVDCTSSQAVAD-QYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDE-GMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARET-GRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLS');
    is($hsp->hit_string, 'GVVTGITDSREMLLSRIGLPLEIWKVALRDLEKPRKDLGKLDLTDDAFAVVDDPDIDVVVELTGGIEVARELYLDALEEGKHVVTANKALNASHGDEYLAL---AEKSGVDVLYEAAVAGGIPIIKTLRELLATGDRILKIEGIFNGTTNFILSEMDEKGLPFSDVLAEAQELGYTEADPRDDVEGIDAARKLAILARIAFGIELELDDVYVEGISPITAEDISSADEFGYTLKLLDEAMRQRVEDAESGGEVLRYPTLIPE-------------DHPLASVKGSDNAVAVEGEAYG--PLMFYGPGAGAEPTASAVVADIVRIAR');
    is($hsp->homology_string, '  V G+ +S+ +L +  GL LE W+  L   ++P  +LG+L      + +++     V+V+ T    VA   Y D L EG HVVT NK  N S  D Y  L   AEKS    LY+  V  G+P+I+ L+ LL  GD ++K  GI +G+ ++I  ++DE G+ FS+    A+E+GYTE DPRDD+ G+D ARKL ILAR   G ELEL D+ +E + P           F   L  LD+    RV  A   G+VLRY   I E             + PL  VK  +NA+A     Y   PL+  G GAG + TA+ V AD++R   ');
    is(join(' ', $hsp->seq_inds('query', 'gap',1)), '532 548 562 649 690');
    is($hsp->ambiguous_seq_inds, '');

    # one more
    $hit = $result->next_hit;
    isa_ok($hit,'Bio::Search::Hit::HitI');

    my $results_left = 8;
    while( $result = $searchio->next_result ) { ok($result); $results_left--; }
    is($results_left, 0);

    $searchio = Bio::SearchIO->new(-format => 'blastxml',
                                  -verbose => -1,
                  -file => test_input_file('plague_yeast.bls.xml'));

    $result = $searchio->next_result;
    is($searchio->result_count, 1);
    is($result->database_name, 'yeast.aa');
    is($result->query_name, 'gi|5763811|emb|CAB53164.1|');
    is($result->query_description,  'putative transposase [Yersinia pestis]');
    is($result->query_accession, 'CAB53164.1');
    is($result->query_gi, 5763811);
    is($result->query_length, 340);

    $hit = $result->next_hit;
    ok(! $hit);

    $searchio = Bio::SearchIO->new(-format => 'blastxml',
                                  -verbose => -1,
                  -file => test_input_file('mus.bls.xml'));

    $result = $searchio->next_result;
    is($searchio->result_count, 1);
    is($result->database_name,'Hs15_up1000');
    is($result->query_name,'NM_011441_up_1000_chr1_4505586_r');
    is($result->query_description,'chr1:4505586-4506585');
    is($result->query_accession,'NM_011441_up_1000_chr1_4505586_r');
    is($result->query_gi, '');
    is($result->query_length,'1000');

    # check parameters
    is($result->available_parameters, 6);
    is($result->get_parameter('matrix'), undef); # not set
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), undef); # not set
    is($result->get_parameter('match'), 1);
    is($result->get_parameter('mismatch'), -3);
    is($result->get_parameter('gapopen'), 5);
    is($result->get_parameter('gapext'), 2);
    is($result->get_parameter('filter'), 'D');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 17516);
    is($result->database_letters, 17516000);
    is($result->get_statistic('hsplength'), 0);
    float_is($result->get_statistic('effectivespace'), 1.69255e+10);
    is($result->get_statistic('lambda'), 1.37407);
    is($result->get_statistic('kappa'), 0.710605);
    is($result->get_statistic('entropy'), 1.30725);

    $hit = $result->next_hit;
    is($hit->name,'NM_001938_up_1000_chr1_93161154_f');
    is($hit->description,'chr1:93161154-93162153');
    is($hit->ncbi_gi, ''); # none reported
    is($hit->accession,'3153');
    is($hit->length,'1000');

    # deal with new BLAST XML changes
    $searchio = Bio::SearchIO->new(-format => 'blastxml',
                                  -verbose => -1,
                  -file => test_input_file('newblast.xml'));

    $result = $searchio->next_result;
    is($searchio->result_count, 1);
    is($result->database_name,'nr');
    is($result->algorithm,'BLASTP');
    is($result->algorithm_version,'BLASTP 2.2.15 [Oct-15-2006]');
    # some XML::SAX parsers (PurePerl, XML::SAX::LibXML) don't decode entities
    # properly, not fixable using decode_entities()
    like($result->algorithm_reference, qr{Nucleic Acids Res} );
    is($result->query_name,'gi|15600734|ref|NP_254228.1|');
    is($result->query_description,'dihydroorotase [Pseudomonas aeruginosa PAO1]');
    is($result->query_accession,'NP_254228.1');
    is($result->query_gi, 15600734);
    is($result->query_length,'445');

    # check parameters
    is($result->available_parameters, 4);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), undef); # not set
    is($result->get_parameter('match'), undef);   # not set
    is($result->get_parameter('mismatch'), undef);# not set
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), undef);  # not set

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 4299737);
    is($result->database_letters, 1479795817);
    is($result->get_statistic('hsplength'), 0);
    float_is($result->get_statistic('effectivespace'), 0);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.041);
    is($result->get_statistic('entropy'), 0.14);

    $hit = $result->next_hit;
    is($hit->name,'gi|15600734|ref|NP_254228.1|');
    is($hit->description,'dihydroorotase [Pseudomonas aeruginosa PAO1] '.
       '>gi|107104643|ref|ZP_01368561.1| hypothetical protein PaerPA_01005722 '.
       '[Pseudomonas aeruginosa PACS2] >gi|9951880|gb|AAG08926.1|AE004966_8 '.
       'dihydroorotase [Pseudomonas aeruginosa PAO1]');
    is($hit->accession,'NP_254228');
    is($hit->length,'445');
    $hsp = $hit->next_hsp;
    is($hsp->query->seq_id, $result->query_name,'query name on HSP');
    is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
    is($hsp->hit->seq_id, $hit->name,'hitname');
    is($hsp->hit->seqdesc, $hit->description,'hitdesc');
    is($hsp->pvalue, undef);
    float_is($hsp->evalue, 0);
    is($hsp->score, 2251);
    is($hsp->bits,871.692);
    is($hsp->query->start, 1);
    is($hsp->query->end,445);
    is($hsp->hit->start, 1);
    is($hsp->hit->end, 445);
    is($hsp->query->frame,0);
    is($hsp->hit->frame,0);

    $result = $searchio->next_result;
    is($searchio->result_count, 2);
    is($result->database_name,'nr');
    is($result->algorithm,'BLASTP');
    is($result->algorithm_version,'BLASTP 2.2.15 [Oct-15-2006]');
    like($result->algorithm_reference, qr{Nucleic Acids Res} );
    is($result->query_name,'gi|15598723|ref|NP_252217.1|');
    is($result->query_description,'dihydroorotase [Pseudomonas aeruginosa PAO1]');
    is($result->query_accession,'NP_252217.1');
    is($result->query_gi, 15598723);
    is($result->query_length,'348');

    # check parameters
    is($result->available_parameters, 4);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), undef); # not set
    is($result->get_parameter('match'), undef);   # not set
    is($result->get_parameter('mismatch'), undef);# not set
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), undef);  # not set

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 4299737);
    is($result->database_letters, 1479795817);
    is($result->get_statistic('hsplength'), 0);
    float_is($result->get_statistic('effectivespace'), 0);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.041);
    is($result->get_statistic('entropy'), 0.14);

    $hit = $result->next_hit;
    is($hit->name,'gi|15598723|ref|NP_252217.1|');
    is($hit->description,'dihydroorotase [Pseudomonas aeruginosa PAO1] '.
       '>gi|6226683|sp|P72170|PYRC_PSEAE Dihydroorotase (DHOase) '.
       '>gi|9949676|gb|AAG06915.1|AE004773_4 dihydroorotase [Pseudomonas aeruginosa PAO1] '.
       '>gi|3868712|gb|AAC73109.1| dihydroorotase [Pseudomonas aeruginosa]');
    is($hit->ncbi_gi, 15598723);
    is($hit->accession,'NP_252217');
    is($hit->length,'348');
    $hsp = $hit->next_hsp;
    is($hsp->query->seq_id, $result->query_name,'query name on HSP');
    is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
    is($hsp->hit->seq_id, $hit->name,'hitname');
    is($hsp->hit->seqdesc, $hit->description,'hitdesc');
    is($hsp->pvalue, undef);
    float_is($hsp->evalue, 0);
    is($hsp->score, 1780);
    is($hsp->bits,690.263);
    is($hsp->query->start, 1);
    is($hsp->query->end,348);
    is($hsp->hit->start, 1);
    is($hsp->hit->end, 348);
    is($hsp->query->frame,0);
    is($hsp->hit->frame,0);

    # PSIBLAST XML parsing

    $searchio = Bio::SearchIO->new('-tempfile' => 1,
           '-format' => 'blastxml',
           '-file'   => test_input_file('psiblast.xml'),
           '-blasttype' => 'psiblast');

    $result = $searchio->next_result;
    is($searchio->result_count, 1);
    is($result->database_name, 'AL591824.faa');
    is($result->algorithm, 'BLASTP');
    like($result->algorithm_version, qr/2\.2\.16/);
    is($result->query_name, 'gi|1373160|gb|AAB57770.1|');
    is($result->query_accession, 'AAB57770.1');
    is($result->query_gi, '1373160');
    is($result->query_length, 173);

    # check parameters
    is($result->available_parameters, 6);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), 0.002);
    is($result->get_parameter('match'), undef);   # not set
    is($result->get_parameter('mismatch'), undef);# not set
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), 'F');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 2846);
    is($result->database_letters, 870878);
    is($result->get_statistic('hsplength'), 75);
    float_is($result->get_statistic('effectivespace'), 6.44279e+07);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.0475563);
    is($result->get_statistic('entropy'), 0.14);

    my $iter_count = 0;
    my @valid_hit_data = ( [ 'gi|16411294|emb|CAC99918.1|', 183, 'CAC99918', 16411294, '4.5377e-56', 209.92],
                   [ 'gi|16409584|emb|CAD00746.1|', 648, 'CAD00746', 16409584, '0.000286309', 37.7354],
                   [ 'gi|16411285|emb|CAC99909.1|', 209, 'CAC99909', 16411285, '0.107059', 29.261]);
    my @valid_iter_data = ( [ 16, 16, 0, 2, 14, 0, 0, 0, 0],
                [ 16, 8, 8, 0, 8, 0, 2, 0, 6]);

    while (my $iter = $result->next_iteration) {
        $iter_count++;
        my $di = shift @valid_iter_data;
        is($iter->number, $iter_count);
        is($iter->num_hits, shift @$di);
        is($iter->num_hits_new, shift @$di);
        is($iter->num_hits_old, shift @$di);
        is(scalar($iter->newhits_below_threshold), shift @$di);
        is(scalar($iter->newhits_not_below_threshold), shift @$di);
        is(scalar($iter->newhits_unclassified), shift @$di);
        is(scalar($iter->oldhits_below_threshold), shift @$di);
        is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
        is(scalar($iter->oldhits_not_below_threshold), shift @$di);
        my $hit_count = 0;
        if ($iter_count == 1) {
            while( my $hit = $result->next_hit ) {
                my $d = shift @valid_hit_data;
                is($hit->name, shift @$d);
                is($hit->length, shift @$d);
                is($hit->accession, shift @$d);
                is($hit->ncbi_gi, shift @$d);
                float_is($hit->significance, shift @$d);
                is($hit->bits, shift @$d );
                if( $hit_count == 1 ) {
                    my $hsps_left = 1;
                    while( my $hsp = $hit->next_hsp ){
                        is($hsp->query->start, 4);
                        is($hsp->query->end, 155);
                        is($hsp->hit->start, 475);
                        is($hsp->hit->end, 617);
                        is($hsp->length('total'), 153);
                        is($hsp->start('hit'), $hsp->hit->start);
                        is($hsp->end('query'), $hsp->query->end);
                        is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
                        float_is($hsp->evalue, 0.000286309);
                        is($hsp->score, 86);
                        is($hsp->bits, 37.7354);
                        is(sprintf("%.1f",$hsp->percent_identity), 20.9);
                        is(sprintf("%.4f",$hsp->frac_identical('query')), 0.2105);
                        is(sprintf("%.3f",$hsp->frac_identical('hit')), 0.224);
                        is($hsp->gaps('total'), 11);
                        $hsps_left--;
                    }
                    is($hsps_left, 0);
                }
                last if( $hit_count++ > @valid_hit_data );
            }
        }
    }
    is(@valid_hit_data, 0);
    is(@valid_iter_data, 0);
    is($iter_count, 2);

    $result = $searchio->next_result;
    is($searchio->result_count, 2);
    is($result->database_name, 'AL591824.faa');
    is($result->algorithm, 'BLASTP');
    like($result->algorithm_version, qr/2\.2\.16/);
    is($result->query_name, 'gi|154350371|gb|ABS72450.1|');
    is($result->query_accession, 'ABS72450.1');
    is($result->query_gi, '154350371');
    is($result->query_length, 378);

    # check parameters
    is($result->available_parameters, 6);
    is($result->get_parameter('matrix'), 'BLOSUM62');
    float_is($result->get_parameter('expect'), 10);
    is($result->get_parameter('include'), 0.002);
    is($result->get_parameter('match'), undef);   # not set
    is($result->get_parameter('mismatch'), undef);# not set
    is($result->get_parameter('gapopen'), 11);
    is($result->get_parameter('gapext'), 1);
    is($result->get_parameter('filter'), 'F');

    # check statistics
    is($result->available_statistics, 5);
    is($result->database_entries, 2846);
    is($result->database_letters, 870878);
    is($result->get_statistic('hsplength'), 82);
    float_is($result->get_statistic('effectivespace'), 1.88702e+08);
    is($result->get_statistic('lambda'), 0.267);
    is($result->get_statistic('kappa'), 0.0450367);
    is($result->get_statistic('entropy'), 0.14);

    $iter_count = 0;

    @valid_hit_data = ( [ 'gi|16409361|emb|CAC98217.1|', 381, 'CAC98217', 16409361, '5.57178e-119', 420.239],
                   [ 'gi|16409959|emb|CAC98662.1|', 776, 'CAC98662', 16409959, '0.0242028', 32.7278],
                   [ 'gi|16410942|emb|CAC99591.1|', 382, 'CAC99591', 16410942, '0.340848', 28.8758]);
    @valid_iter_data = ( [ 11, 11, 0, 1, 10, 0, 0, 0, 0],
                [ 19, 11, 8, 0, 11, 0, 1, 0, 7]);

    while (my $iter = $result->next_iteration) {
        $iter_count++;
        my $di = shift @valid_iter_data;
        is($iter->number, $iter_count);
        is($iter->num_hits, shift @$di);
        is($iter->num_hits_new, shift @$di);
        is($iter->num_hits_old, shift @$di);
        is(scalar($iter->newhits_below_threshold), shift @$di);
        is(scalar($iter->newhits_not_below_threshold), shift @$di);
        is(scalar($iter->newhits_unclassified), shift @$di);
        is(scalar($iter->oldhits_below_threshold), shift @$di);
        is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
        is(scalar($iter->oldhits_not_below_threshold), shift @$di);
        my $hit_count = 0;
        if ($iter_count == 1) {
            while( my $hit = $result->next_hit ) {
                my $d = shift @valid_hit_data;
                is($hit->name, shift @$d);
                is($hit->length, shift @$d);
                is($hit->accession, shift @$d);
                is($hit->ncbi_gi, shift @$d);
                float_is($hit->significance, shift @$d);
                is($hit->bits, shift @$d );
                if( $hit_count == 1 ) {
                    my $hsps_left = 1;
                    while( my $hsp = $hit->next_hsp ){
                        is($hsp->query->start, 63);
                        is($hsp->query->end, 181);
                        is($hsp->hit->start, 304);
                        is($hsp->hit->end, 432);
                        is($hsp->length('total'), 129);
                        is($hsp->start('hit'), $hsp->hit->start);
                        is($hsp->end('query'), $hsp->query->end);
                        is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
                        float_is($hsp->evalue, 0.0242028);
                        is($hsp->score, 73);
                        is($hsp->bits, 32.7278);
                        is(sprintf("%.1f",$hsp->percent_identity), '24.0');
                        is(sprintf("%.4f",$hsp->frac_identical('query')), '0.2605');
                        is(sprintf("%.3f",$hsp->frac_identical('hit')), '0.240');
                        is($hsp->gaps, 10);
                        $hsps_left--;
                    }
                    is($hsps_left, 0);
                }
                last if( $hit_count++ > @valid_hit_data );
            }
        }
    }
    is(@valid_hit_data, 0);
    is(@valid_iter_data, 0);
    is($iter_count, 2);
}
