# Do not use this object directly - it is used as part of the
   # Bio::SearchIO system.

    use Bio::SearchIO;
    my $searchio = Bio::SearchIO->new(-format => 'blast',
                                     -file   => 't/data/ecolitst.bls');
    while( my $result = $searchio->next_result ) {
        while( my $hit = $result->next_hit ) {
            while( my $hsp = $hit->next_hsp ) {
                # ...
            }
        }
    }

  my $parser = Bio::SearchIO->new(-format => 'blast',
                                 -file => 'bl2seq.tblastn.report',
                                 -report_type => 'tblastn');

    # mapping of NCBI Blast terms to Bioperl hash keys
    %MODEMAP = (
        'BlastOutput' => 'result',
        'Iteration'   => 'iteration',
        'Hit'         => 'hit',
        'Hsp'         => 'hsp'
    );

    # This should really be done more intelligently, like with
    # XSLT

    %MAPPING = (
        'Hsp_bit-score'   => 'HSP-bits',
        'Hsp_score'       => 'HSP-score',
        'Hsp_evalue'      => 'HSP-evalue',
        'Hsp_n',          => 'HSP-n',
        'Hsp_pvalue'      => 'HSP-pvalue',
        'Hsp_query-from'  => 'HSP-query_start',
        'Hsp_query-to'    => 'HSP-query_end',
        'Hsp_hit-from'    => 'HSP-hit_start',
        'Hsp_hit-to'      => 'HSP-hit_end',
        'Hsp_positive'    => 'HSP-conserved',
        'Hsp_identity'    => 'HSP-identical',
        'Hsp_gaps'        => 'HSP-hsp_gaps',
        'Hsp_hitgaps'     => 'HSP-hit_gaps',
        'Hsp_querygaps'   => 'HSP-query_gaps',
        'Hsp_qseq'        => 'HSP-query_seq',
        'Hsp_hseq'        => 'HSP-hit_seq',
        'Hsp_midline'     => 'HSP-homology_seq',
        'Hsp_align-len'   => 'HSP-hsp_length',
        'Hsp_query-frame' => 'HSP-query_frame',
        'Hsp_hit-frame'   => 'HSP-hit_frame',
        'Hsp_links'       => 'HSP-links',
        'Hsp_group'       => 'HSP-hsp_group',
        'Hsp_features'    => 'HSP-hit_features',

        'Hit_id'        => 'HIT-name',
        'Hit_len'       => 'HIT-length',
        'Hit_accession' => 'HIT-accession',
        'Hit_def'       => 'HIT-description',
        'Hit_signif'    => 'HIT-significance',
        # For NCBI blast, the description line contains bits.
        # For WU-blast, the  description line contains score.
        'Hit_score' => 'HIT-score',
        'Hit_bits'  => 'HIT-bits',

        'Iteration_iter-num'  => 'ITERATION-number',
        'Iteration_converged' => 'ITERATION-converged',

        'BlastOutput_program'             => 'RESULT-algorithm_name',
        'BlastOutput_version'             => 'RESULT-algorithm_version',
        'BlastOutput_algorithm-reference' => 'RESULT-algorithm_reference',
        'BlastOutput_rid'                 => 'RESULT-rid',
        'BlastOutput_query-def'           => 'RESULT-query_name',
        'BlastOutput_query-len'           => 'RESULT-query_length',
        'BlastOutput_query-acc'           => 'RESULT-query_accession',
        'BlastOutput_query-gi'            => 'RESULT-query_gi',
        'BlastOutput_querydesc'           => 'RESULT-query_description',
        'BlastOutput_db'                  => 'RESULT-database_name',
        'BlastOutput_db-len'              => 'RESULT-database_entries',
        'BlastOutput_db-let'              => 'RESULT-database_letters',
        'BlastOutput_inclusion-threshold' => 'RESULT-inclusion_threshold',

        'Parameters_matrix'      => { 'RESULT-parameters' => 'matrix' },
        'Parameters_expect'      => { 'RESULT-parameters' => 'expect' },
        'Parameters_include'     => { 'RESULT-parameters' => 'include' },
        'Parameters_sc-match'    => { 'RESULT-parameters' => 'match' },
        'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' },
        'Parameters_gap-open'    => { 'RESULT-parameters' => 'gapopen' },
        'Parameters_gap-extend'  => { 'RESULT-parameters' => 'gapext' },
        'Parameters_filter'      => { 'RESULT-parameters' => 'filter' },
        'Parameters_allowgaps'   => { 'RESULT-parameters' => 'allowgaps' },
        'Parameters_full_dbpath' => { 'RESULT-parameters' => 'full_dbpath' },
        'Statistics_db-len'      => { 'RESULT-statistics' => 'dbentries' },
        'Statistics_db-let'      => { 'RESULT-statistics' => 'dbletters' },
        'Statistics_hsp-len'     =>
          { 'RESULT-statistics' => 'effective_hsplength' },
        'Statistics_query-len' => { 'RESULT-statistics' => 'querylength' },
        'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace' },
        'Statistics_eff-spaceused' =>
          { 'RESULT-statistics' => 'effectivespaceused' },
        'Statistics_eff-dblen' =>
          { 'RESULT-statistics' => 'effectivedblength' },
        'Statistics_kappa'         => { 'RESULT-statistics' => 'kappa' },
        'Statistics_lambda'        => { 'RESULT-statistics' => 'lambda' },
        'Statistics_entropy'       => { 'RESULT-statistics' => 'entropy' },
        'Statistics_gapped_kappa'  => { 'RESULT-statistics' => 'kappa_gapped' },
        'Statistics_gapped_lambda' =>
          { 'RESULT-statistics' => 'lambda_gapped' },
        'Statistics_gapped_entropy' =>
          { 'RESULT-statistics' => 'entropy_gapped' },

        'Statistics_framewindow' =>
          { 'RESULT-statistics' => 'frameshiftwindow' },
        'Statistics_decay' => { 'RESULT-statistics' => 'decayconst' },

        'Statistics_hit_to_db' => { 'RESULT-statistics' => 'Hits_to_DB' },
        'Statistics_num_suc_extensions' =>
          { 'RESULT-statistics' => 'num_successful_extensions' },
        'Statistics_length_adjustment' => { 'RESULT-statistics' => 'length_adjustment' },
        'Statistics_number_of_hsps_better_than_expect_value_cutoff_without_gapping' =>
		  { 'RESULT-statistics' => 'number_of_hsps_better_than_expect_value_cutoff_without_gapping' },
        'Statistics_number_of_hsps_gapped' => { 'RESULT-statistics' => 'number_of_hsps_gapped' },
        'Statistics_number_of_hsps_successfully_gapped' => { 'RESULT-statistics' => 'number_of_hsps_successfully_gapped' },

        # WU-BLAST stats
        'Statistics_DFA_states' => { 'RESULT-statistics' => 'num_dfa_states' },
        'Statistics_DFA_size'   => { 'RESULT-statistics' => 'dfa_size' },
        'Statistics_noprocessors' =>
          { 'RESULT-statistics' => 'no_of_processors' },
        'Statistics_neighbortime' =>
          { 'RESULT-statistics' => 'neighborhood_generate_time' },
        'Statistics_starttime' => { 'RESULT-statistics' => 'start_time' },
        'Statistics_endtime'   => { 'RESULT-statistics' => 'end_time' },
    );

    # add WU-BLAST Frame-Based Statistics
    for my $frame ( 0 .. 3 ) {
        for my $strand ( '+', '-' ) {
            for my $ind (
                qw(length efflength E S W T X X_gapped E2
                E2_gapped S2)
              )
            {
                $MAPPING{"Statistics_frame$strand$frame\_$ind"} =
                  { 'RESULT-statistics' => "Frame$strand$frame\_$ind" };
            }
            for my $val (qw(lambda kappa entropy )) {
                for my $type (qw(used computed gapped)) {
                    my $key = "Statistics_frame$strand$frame\_$val\_$type";
                    my $val =
                      { 'RESULT-statistics' =>
                          "Frame$strand$frame\_$val\_$type" };
                    $MAPPING{$key} = $val;
                }
            }
        }
    }

    # add Statistics
    for my $stats (
        qw(T A X1 X2 X3 S1 S2 X1_bits X2_bits X3_bits
        S1_bits S2_bits  num_extensions
        num_successful_extensions
        seqs_better_than_cutoff
        posted_date
        search_cputime total_cputime
        search_actualtime total_actualtime
        no_of_processors ctxfactor)
      )
    {
        my $key = "Statistics_$stats";
        my $val = { 'RESULT-statistics' => $stats };
        $MAPPING{$key} = $val;
    }

    # add WU-BLAST Parameters
    for my $param (
        qw(span span1 span2 links warnings notes hspsepsmax
        hspsepqmax topcomboN topcomboE postsw cpus wordmask
        filter sort_by_pvalue sort_by_count sort_by_highscore
        sort_by_totalscore sort_by_subjectlength noseqs gi qtype
        qres V B Z Y M N)
      )
    {
        my $key = "Parameters_$param";
        my $val = { 'RESULT-parameters' => $param };
        $MAPPING{$key} = $val;
    }

    $DEFAULT_BLAST_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
    $MAX_HSP_OVERLAP   = 2;           # Used when tiling multiple HSPs.
    $DEFAULTREPORTTYPE = 'BLASTP';    # for bl2seq

    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);

    # Blast reports require a specialized version of the SREB due to the
    # possibility of iterations (PSI-BLAST). Forwarding all arguments to it. An
    # issue here is that we want to set new default object factories if none are
    # supplied.

    my $handler = Bio::SearchIO::IteratedSearchResultEventBuilder->new(@args);
    $self->attach_EventHandler($handler);

    # 2006-04-26 move this to the attach_handler function in this module so we
    # can really reset the handler
    # Optimization: caching
    # the EventHandler since it is used a lot during the parse.

    # $self->{'_handler_cache'} = $handler;

    my ($rpttype ) = $self->_rearrange(
        [
            qw(
              REPORT_TYPE)
        ],
        @args
    );
    defined $rpttype   && ( $self->{'_reporttype'} = $rpttype );

    my ($self,$handler) = @_;

    $self->SUPER::attach_EventHandler($handler);

    # Optimization: caching the EventHandler since it is used a lot
    # during the parse.

    $self->{'_handler_cache'} = $handler;
    return;

    my ($self) = @_;
    my $v      = $self->verbose;
    my $data   = '';
    my $flavor = '';
    $self->{'_seentop'} = 0;     # start next report at top
    $self->{'_seentop'} = 0;
    my ( $reporttype, $seenquery, $reportline, $reportversion );
    my ( $seeniteration, $found_again );
    my $incl_threshold = $self->inclusion_threshold;
    my $bl2seq_fix;
    $self->start_document();  # let the fun begin...
    my (@hit_signifs);
    my $gapped_stats = 0;    # for switching between gapped/ungapped
                             # lambda, K, H
    local $_ = "\n";   #consistency
    PARSER:
    while ( defined( $_ = $self->_readline ) ) {
        next if (/^\s+$/);       # skip empty lines
        next if (/CPU time:/);
        next if (/^>\s*$/);
        next if (/\Q[*]+\s+No hits found\s+[*]+\E/);
        if (
               /^((?:\S+?)?BLAST[NPX]?)\s+(.+)$/i  # NCBI BLAST, PSIBLAST
                                                   # RPSBLAST, MEGABLAST
            || /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i    #Paracel BTK
          )
        {
            ($reporttype, $reportversion) = ($1, $2);
            # need to keep track of whether this is WU-BLAST
            if ($reportversion && $reportversion =~ m{WashU$}) {
                $self->{'_wublast'}++;
            }
            $self->debug("blast.pm: Start of new report: $reporttype, $reportversion\n");
            if ( $self->{'_seentop'} ) {
                # This handles multi-result input streams
                $self->_pushback($_);
                last PARSER;
            }
            $self->_start_blastoutput;
            if ($reporttype =~ /RPS-BLAST/) {
                $reporttype .= '(BLASTP)'; # default RPS-BLAST type
            }
            $reportline = $_;   # to fix the fact that RPS-BLAST output is wrong
            $self->element(
                {
                    'Name' => 'BlastOutput_program',
                    'Data' => $reporttype
                }
            );

            $self->element(
                {
                    'Name' => 'BlastOutput_version',
                    'Data' => $reportversion
                }
            );
            $self->element(
                {
                    'Name' => 'BlastOutput_inclusion-threshold',
                    'Data' => $incl_threshold
                }
            );
        }
        # parse the BLAST algorithm reference
        elsif(/^Reference:\s+(.*)$/) {
            # want to preserve newlines for the BLAST algorithm reference
            my $algorithm_reference = "$1\n";
            $_ = $self->_readline;
            # while the current line, does not match an empty line, a RID:, a
            # Database:, or a query definition line (Query=) we are still
            # looking at the algorithm_reference, append it to what we parsed so
            # far
            while($_ !~ /^$/ && $_ !~ /^RID:/ && $_ !~ /^Database:/ && $_ !~ /^Query=/) {
                $algorithm_reference .= "$_";
                $_ = $self->_readline;
            }
            # if we exited the while loop, we saw an empty line, a RID:, or a
            # Database:, so push it back
            $self->_pushback($_);
            $self->element(
                {
                    'Name' => 'BlastOutput_algorithm-reference',
                    'Data' => $algorithm_reference
                }
            );
        }
        # parse BLAST RID (Request ID)
        elsif(/^RID:\s+(.*)$/) {
            my $rid = $1;
            $self->element(
                {
                    'Name' => 'BlastOutput_rid',
                    'Data' => $rid
                }
            );
        }
        # added Windows workaround for bug 1985
        elsif (/^(Searching|Results from round)/) {
            next unless $1 =~ /Results from round/;
            $self->debug("blast.pm: Possible psi blast iterations found...\n");

            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            $self->in_element('hit')
              && $self->end_element( { 'Name' => 'Hit' } );
            if ( defined $seeniteration ) {
                $self->within_element('iteration')
                  && $self->end_element( { 'Name' => 'Iteration' } );
                $self->start_element( { 'Name' => 'Iteration' } );
            }
            else {
                $self->start_element( { 'Name' => 'Iteration' } );
            }
            $seeniteration = 1;
        }
        elsif (/^Query=\s*(.*)$/) {
            my $q    = $1;
            $self->debug("blast.pm: Query= found...$_\n");
            my $size = 0;
            if ( defined $seenquery ) {
                $self->_pushback($_);
                $self->_pushback($reportline) if $reportline;
                last PARSER;
            }
            if ( !defined $reporttype ) {
                $self->_start_blastoutput;
                if ( defined $seeniteration ) {
                    $self->in_element('iteration')
                      && $self->end_element( { 'Name' => 'Iteration' } );
                    $self->start_element( { 'Name' => 'Iteration' } );
                }
                else {
                    $self->start_element( { 'Name' => 'Iteration' } );
                }
                $seeniteration = 1;
            }
            $seenquery = $q;
            $_ = $self->_readline;
            while ( defined($_) ) {
                if (/^Database:/) {
                    $self->_pushback($_);
                    last;
                }
                # below line fixes length issue with BLAST v2.2.13; still works
                # with BLAST v2.2.12
                if ( /\((\-?[\d,]+)\s+letters.*\)/ || /^Length=(\-?[\d,]+)/ ) {
                    $size = $1;
                    $size =~ s/,//g;
                    last;
                }
                else {
                    # bug 2391
                    $q .= ($q =~ /\w$/ && $_ =~ /^\w/) ? " $_" : $_;
                    $q =~ s/\s+/ /g; # this catches the newline as well
                    $q =~ s/^ | $//g;
                }

                $_ = $self->_readline;
            }
            chomp($q);
            my ( $nm, $desc ) = split( /\s+/, $q, 2 );
            $self->element(
                {
                    'Name' => 'BlastOutput_query-def',
                    'Data' => $nm
                }
            ) if $nm;
            $self->element(
                {
                    'Name' => 'BlastOutput_query-len',
                    'Data' => $size
                }
            );
            defined $desc && $desc =~ s/\s+$//;
            $self->element(
                {
                    'Name' => 'BlastOutput_querydesc',
                    'Data' => $desc
                }
            );
            my ( $gi, $acc, $version ) = $self->_get_seq_identifiers($nm);
            $version = defined($version) && length($version) ? ".$version" : "";
            $self->element(
                {
                    'Name' => 'BlastOutput_query-acc',
                    'Data' => "$acc$version"
                }
            ) if $acc;
        }
		# added check for WU-BLAST -echofilter option (bug 2388)
		elsif (/^>Unfiltered[+-]1$/) {
        	# skip all of the lines of unfiltered sequence
			while($_ !~ /^Database:/) {
				$self->debug("Bypassing features line: $_");
        		$_ = $self->_readline;
        	}
			$self->_pushback($_);
		}
        elsif (/Sequences producing significant alignments:/) {
            $self->debug("blast.pm: Processing NCBI-BLAST descriptions\n");
            $flavor = 'ncbi';

            # PSI-BLAST parsing needs to be fixed to specifically look
            # for old vs new per iteration, as sorting based on duplication
            # leads to bugs, see bug 1986

            # The next line is not necessarily whitespace in psiblast reports.
            # Also note that we must look for the end of this section by testing
            # for a line with a leading >. Blank lines occur with this section
            # for psiblast.
            if ( !$self->in_element('iteration') ) {
                $self->start_element( { 'Name' => 'Iteration' } );
            }
            # these elements are dropped with some multiquery reports; add
            # back here
            $self->element(
                {
                    'Name' => 'BlastOutput_db-len',
                    'Data' => $self->{'_blsdb_length'}
                }
            ) if $self->{'_blsdb_length'};
            $self->element(
                {
                    'Name' => 'BlastOutput_db-let',
                    'Data' => $self->{'_blsdb_letters'}
                }
            ) if $self->{'_blsdb_letters'};
            $self->element(
                {
                    'Name' => 'BlastOutput_db',
                    'Data' => $self->{'_blsdb'}
                }
            ) if $self->{'_blsdb_letters'};

            # changed 8/28/2008 to exit hit table if blank line is found after an
            # appropriate line
            my $h_regex;
            my $seen_block;
          DESCLINE:
            while ( defined( my $descline = $self->_readline() ) ) {
                if ($descline =~ m{^\s*$}) {
                    last DESCLINE if $seen_block;
                    next DESCLINE;
                }
                # any text match is part of block...
                $seen_block++;
                # GCG multiline oddness...
                if ($descline =~ /^(\S+)\s+Begin:\s\d+\s+End:\s+\d+/xms) {
                    my ($id, $nextline) = ($1, $self->_readline);
                    $nextline =~ s{^!}{};
                    $descline = "$id $nextline";
                }
                # NCBI style hit table (no N)
                if ($descline =~ /(?<!cor)          # negative lookahead
                    (\d*\.?(?:[\+\-eE]+)?\d+)       # number (float or scientific notation)
                    \s+                             # space
                    (\d*\.?(?:[\+\-eE]+)?\d+)       # number (float or scientific notation)
                    \s*$/xms) {

                    my ( $score, $evalue ) = ($1, $2);

                    # Some data clean-up so e-value will appear numeric to perl
                    $evalue =~ s/^e/1e/i;

                    # This to handle no-HSP case
                    my @line = split ' ',$descline;

                    # we want to throw away the score, evalue
                    pop @line, pop @line;

                    # and N if it is present (of course they are not
                    # really in that order, but it doesn't matter
                    if ($3) { pop @line }

                    # add the last 2 entries s.t. we can reconstruct
                    # a minimal Hit object at the end of the day
                    push @hit_signifs, [ $evalue, $score, shift @line, join( ' ', @line ) ];
                } elsif ($descline =~ /^CONVERGED/i) {
                    $self->element(
                        {
                            'Name' => 'Iteration_converged',
                            'Data' => 1
                        }
                    );
                } else {
                    $self->_pushback($descline); # Catch leading > (end of section)
                    last DESCLINE;
                }
            }
        }
        elsif (/Sequences producing High-scoring Segment Pairs:/) {

     # This block is for WU-BLAST, so we don't have to check for psi-blast stuff
     # skip the next line
            $self->debug("blast.pm: Processing WU-BLAST descriptions\n");
            $_      = $self->_readline();
            $flavor = 'wu';

            if ( !$self->in_element('iteration') ) {
                $self->start_element( { 'Name' => 'Iteration' } );
            }

            while ( defined( $_ = $self->_readline() )
                && !/^\s+$/ )
            {
                my @line = split;
                pop @line;    # throw away first number which is for 'N'col

                # add the last 2 entries to array s.t. we can reconstruct
                # a minimal Hit object at the end of the day
                push @hit_signifs,
                  [ pop @line, pop @line, shift @line, join( ' ', @line ) ];
            }

        }
        elsif (/^Database:\s*(.+)$/) {

            $self->debug("blast.pm: Database: $1\n");
            my $db = $1;
            while ( defined( $_ = $self->_readline ) ) {
                if (
                    /^\s+(\-?[\d\,]+|\S+)\s+sequences\;
\s                   +(\-?[\d,]+|\S+)\s+ # Deal with NCBI 2.2.8 OSX problems
                   total\s+letters/ox
                  )
                {
                    my ( $s, $l ) = ( $1, $2 );
                    $s =~ s/,//g;
                    $l =~ s/,//g;
                    $self->element(
                        {
                            'Name' => 'BlastOutput_db-len',
                            'Data' => $s
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'BlastOutput_db-let',
                            'Data' => $l
                        }
                    );
                    # cache for next round in cases with multiple queries
                    $self->{'_blsdb'} = $db;
                    $self->{'_blsdb_length'} = $s;
                    $self->{'_blsdb_letters'} = $l;
                    last;
                }
                else {
                    chomp;
                    $db .= $_;
                }
            }
            $self->element(
                {
                    'Name' => 'BlastOutput_db',
                    'Data' => $db
                }
            );
        }

        # move inside of a hit
        elsif (/^>\s*(\S+)\s*(.*)?/) {
            chomp;

            $self->debug("blast.pm: Hit: $1\n");
            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            $self->in_element('hit')
              && $self->end_element( { 'Name' => 'Hit' } );

            # special case when bl2seq reports don't have a leading
            # Query=
            if ( !$self->within_element('result') ) {
                $self->_start_blastoutput;
                $self->start_element( { 'Name' => 'Iteration' } );
            }
            elsif ( !$self->within_element('iteration') ) {
                $self->start_element( { 'Name' => 'Iteration' } );
            }
            $self->start_element( { 'Name' => 'Hit' } );
            my $id         = $1;
            my $restofline = $2;

            $self->debug("Starting a hit: $1 $2\n");
            $self->element(
                {
                    'Name' => 'Hit_id',
                    'Data' => $id
                }
            );
            my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id);
            $self->element(
                {
                    'Name' => 'Hit_accession',
                    'Data' => $acc
                }
            );
            # add hit significance (from the hit table)
            # this is where Bug 1986 went awry

            # Changed for Bug2409; hit->significance and hit->score/bits derived
            # from HSPs, not hit table unless necessary

            HITTABLE:
            while (my $v = shift @hit_signifs) {
                my $tableid = $v->[2];
                if ($tableid !~ m{\Q$id\E}) {
                    $self->debug("Hit table ID $tableid doesn't match current hit id $id, checking next hit table entry...\n");
                    next HITTABLE;
                } else {
                    last HITTABLE;
                }
            }
            while ( defined( $_ = $self->_readline() ) ) {
                next if (/^\s+$/);
                chomp;
                if (/Length\s*=\s*([\d,]+)/) {
                    my $l = $1;
                    $l =~ s/\,//g;
                    $self->element(
                        {
                            'Name' => 'Hit_len',
                            'Data' => $l
                        }
                    );
                    last;
                }
                else {
                    if ($restofline !~ /\s$/) { # bug #3235
                        s/^\s(?!\s)/\x01/; #new line to concatenate desc lines with <soh>
                    }
                    $restofline .= $_;
                }
            }
            $restofline =~ s/\s+/ /g;
            $self->element(
                {
                    'Name' => 'Hit_def',
                    'Data' => $restofline
                }
            );
        }
        elsif (/\s+(Plus|Minus) Strand HSPs:/i) {
            next;
        }
        elsif (
            ( $self->in_element('hit') || $self->in_element('hsp') )
            &&    # paracel genewise BTK
            m/Score\s*=\s*(\S+)\s*bits\s* # Bit score
                (?:\((\d+)\))?,                 # Raw score
		\s+Log\-Length\sScore\s*=\s*(\d+) # Log-Length score
                /ox
          )
        {
            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            $self->start_element( { 'Name' => 'Hsp' } );

            $self->debug( "Got paracel genewise HSP score=$1\n");

            # Some data clean-up so e-value will appear numeric to perl
            my ( $bits, $score, $evalue ) = ( $1, $2, $3 );
            $evalue =~ s/^e/1e/i;
            $self->element(
                {
                    'Name' => 'Hsp_score',
                    'Data' => $score
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_bit-score',
                    'Data' => $bits
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_evalue',
                    'Data' => $evalue
                }
            );
        }
        elsif (
            ( $self->in_element('hit') || $self->in_element('hsp') )
            &&    # paracel hframe BTK
            m/Score\s*=\s*([^,\s]+),     # Raw score
		\s*Expect\s*=\s*([^,\s]+),  # E-value
                \s*P(?:\(\S+\))?\s*=\s*([^,\s]+) # P-value
                /ox
          )
        {
            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            $self->start_element( { 'Name' => 'Hsp' } );

            $self->debug( "Got paracel hframe HSP score=$1\n");

            # Some data clean-up so e-value will appear numeric to perl
            my ( $score, $evalue, $pvalue ) = ( $1, $2, $3 );
            $evalue = "1$evalue" if $evalue =~ /^e/;
            $pvalue = "1$pvalue" if $pvalue =~ /^e/;

            $self->element(
                {
                    'Name' => 'Hsp_score',
                    'Data' => $score
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_evalue',
                    'Data' => $evalue
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_pvalue',
                    'Data' => $pvalue
                }
            );
        }
        elsif (
            ( $self->in_element('hit') || $self->in_element('hsp') )
            &&    # wublast
            m/Score\s*=\s*(\S+)\s*         # Bit score
                \(([\d\.]+)\s*bits\),         # Raw score
                \s*Expect\s*=\s*([^,\s]+),    # E-value
                \s*(?:Sum)?\s*                # SUM
                P(?:\(\d+\))?\s*=\s*([^,\s]+) # P-value
                (?:\s*,\s+Group\s*\=\s*(\d+))?    # HSP Group
                /ox
          )
        {         # wu-blast HSP parse
            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            $self->start_element( { 'Name' => 'Hsp' } );

            # Some data clean-up so e-value will appear numeric to perl
            my ( $score, $bits, $evalue, $pvalue, $group ) =
              ( $1, $2, $3, $4, $5 );
            $evalue =~ s/^e/1e/i;
            $pvalue =~ s/^e/1e/i;

            $self->element(
                {
                    'Name' => 'Hsp_score',
                    'Data' => $score
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_bit-score',
                    'Data' => $bits
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_evalue',
                    'Data' => $evalue
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_pvalue',
                    'Data' => $pvalue
                }
            );

            if ( defined $group ) {
                $self->element(
                    {
                        'Name' => 'Hsp_group',
                        'Data' => $group
                    }
                );
            }

        }
        elsif (
            ( $self->in_element('hit') || $self->in_element('hsp') )
            &&    # ncbi blast, works with 2.2.17
            m/^\sFeatures\s\w+\sthis\spart/xmso
            # If the line begins with "Features in/flanking this part of subject sequence:"
            )
        {
            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            my $featline;
            $_ = $self->_readline;
            while($_ !~ /^\s*$/) {
                chomp;
                $featline .= $_;
                $_ = $self->_readline;
            }
            $self->_pushback($_);
            $featline =~ s{(?:^\s+|\s+^)}{}g;
            $featline =~ s{\n}{;}g;
            $self->start_element( { 'Name' => 'Hsp' } );
            $self->element(
                {
                    'Name' => 'Hsp_features',
                    'Data' => $featline
                }
            );
            $self->{'_seen_hsp_features'} = 1;
        }
        elsif (
            ( $self->in_element('hit') || $self->in_element('hsp') )
            &&    # ncbi blast, works with 2.2.17
            m/Score\s*=\s*(\S+)\s*bits\s* # Bit score
                (?:\((\d+)\))?,            # Missing for BLAT pseudo-BLAST fmt
                \s*Expect(?:\((\d+\+?)\))?\s*=\s*([^,\s]+) # E-value
                /ox
          )
        {         # parse NCBI blast HSP
            if( !$self->{'_seen_hsp_features'} ) {
                $self->in_element('hsp')
                  && $self->end_element( { 'Name' => 'Hsp' } );
                $self->start_element( { 'Name' => 'Hsp' } );
            }

            # Some data clean-up so e-value will appear numeric to perl
            my ( $bits, $score, $n, $evalue ) = ( $1, $2, $3, $4 );
            $evalue =~ s/^e/1e/i;
            $self->element(
                {
                    'Name' => 'Hsp_score',
                    'Data' => $score
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_bit-score',
                    'Data' => $bits
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_evalue',
                    'Data' => $evalue
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_n',
                    'Data' => $n
                }
            ) if defined $n;
            $score = '' unless defined $score;    # deal with BLAT which
                                                  # has no score only bits
            $self->debug("Got NCBI HSP score=$score, evalue $evalue\n");
        }
        elsif (
            $self->in_element('hsp')
            && m/Identities\s*=\s*(\d+)\s*\/\s*(\d+)\s*[\d\%\(\)]+\s*
                (?:,\s*Positives\s*=\s*(\d+)\/(\d+)\s*[\d\%\(\)]+\s*)? # pos only valid for Protein alignments
                (?:\,\s*Gaps\s*=\s*(\d+)\/(\d+))? # Gaps
                /oxi
          )
        {
            $self->element(
                {
                    'Name' => 'Hsp_identity',
                    'Data' => $1
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_align-len',
                    'Data' => $2
                }
            );
            if ( defined $3 ) {
                $self->element(
                    {
                        'Name' => 'Hsp_positive',
                        'Data' => $3
                    }
                );
            }
            else {
                $self->element(
                    {
                        'Name' => 'Hsp_positive',
                        'Data' => $1
                    }
                );
            }
            if ( defined $6 ) {
                $self->element(
                    {
                        'Name' => 'Hsp_gaps',
                        'Data' => $5
                    }
                );
            }

            $self->{'_Query'} = { 'begin' => 0, 'end' => 0 };
            $self->{'_Sbjct'} = { 'begin' => 0, 'end' => 0 };

            if (/(Frame\s*=\s*.+)$/) {

                # handle wu-blast Frame listing on same line
                $self->_pushback($1);
            }
        }
        elsif ( $self->in_element('hsp')
            && /Strand\s*=\s*(Plus|Minus)\s*\/\s*(Plus|Minus)/i )
        {

            # consume this event ( we infer strand from start/end)
            if (!defined($reporttype)) {
                $self->{'_reporttype'} = $reporttype = 'BLASTN';
                $bl2seq_fix = 1;    # special case to resubmit the algorithm
                                    # reporttype
            }
            next;
        }
        elsif ( $self->in_element('hsp')
            && /Links\s*=\s*(\S+)/ox )
        {
            $self->element(
                {
                    'Name' => 'Hsp_links',
                    'Data' => $1
                }
            );
        }
        elsif ( $self->in_element('hsp')
            && /Frame\s*=\s*([\+\-][1-3])\s*(\/\s*([\+\-][1-3]))?/ )
        {

            # this is for bl2seq only
            unless ( defined $reporttype ) {
                $bl2seq_fix = 1;
                if ( $1 && $2 ) { $reporttype = 'TBLASTX' }
                else {
                    $reporttype = 'BLASTX';

    # we can't distinguish between BLASTX and TBLASTN straight from the report }
                }
                $self->{'_reporttype'} = $reporttype;
            }

            my ( $queryframe, $hitframe );
            if ( $reporttype eq 'TBLASTX' ) {
                ( $queryframe, $hitframe ) = ( $1, $2 );
                $hitframe =~ s/\/\s*//g;
            }
            elsif ( $reporttype eq 'TBLASTN' || $reporttype eq 'PSITBLASTN') {
                ( $hitframe, $queryframe ) = ( $1, 0 );
            }
            elsif ( $reporttype eq 'BLASTX' || $reporttype eq 'RPS-BLAST(BLASTP)') {
                ( $queryframe, $hitframe ) = ( $1, 0 );
                # though NCBI doesn't report it, this is a special BLASTX-like
                # RPS-BLAST; should be handled differently
                if ($reporttype eq 'RPS-BLAST(BLASTP)') {
                    $self->element(
                        {
                            'Name' => 'BlastOutput_program',
                            'Data' => 'RPS-BLAST(BLASTX)'
                        }
                    );
                }
            }
            $self->element(
                {
                    'Name' => 'Hsp_query-frame',
                    'Data' => $queryframe
                }
            );

            $self->element(
                {
                    'Name' => 'Hsp_hit-frame',
                    'Data' => $hitframe
                }
            );
        }
        elsif (/^Parameters:/
            || /^\s+Database:\s+?/
            || /^\s+Subset/
            || /^\s*Lambda/
            || /^\s*Histogram/
            || ( $self->in_element('hsp') && /WARNING|NOTE/ ) )
        {

            # Note: Lambda check was necessary to parse
            # t/data/ecoli_domains.rpsblast AND to parse bl2seq
            $self->debug("blast.pm: found parameters section\n ");

            $self->in_element('hsp')
              && $self->end_element( { 'Name' => 'Hsp' } );
            $self->in_element('hit')
              && $self->end_element( { 'Name' => 'Hit' } );

            # This is for the case when we specify -b 0 (or B=0 for WU-BLAST)
            # and still want to construct minimal Hit objects
            $self->_cleanup_hits(\@hit_signifs) if scalar(@hit_signifs);
            $self->within_element('iteration')
              && $self->end_element( { 'Name' => 'Iteration' } );

            next if /^\s+Subset/;
            my $blast = (/^(\s+Database\:)|(\s*Lambda)/) ? 'ncbi' : 'wublast';
            if (/^\s*Histogram/) {
                $blast = 'btk';
            }

            my $last = '';

            # default is that gaps are allowed
            $self->element(
                {
                    'Name' => 'Parameters_allowgaps',
                    'Data' => 'yes'
                }
            );
            while ( defined( $_ = $self->_readline ) ) {
                if (
                    /^((?:\S+)?BLAST[NPX]?)\s+(.+)$/i  # NCBI BLAST, PSIBLAST
                                                      # RPSBLAST, MEGABLAST
                    || /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i    #Paracel BTK
                  )
                {
                    $self->_pushback($_);

                    # let's handle this in the loop
                    last;
                }
                elsif (/^Query=/) {
                    $self->_pushback($_);
                    $self->_pushback($reportline) if $reportline;
                    last PARSER;
                }

                # here is where difference between wublast and ncbiblast
                # is better handled by different logic
                if (   /Number of Sequences:\s+([\d\,]+)/i
                    || /of sequences in database:\s+(\-?[\d,]+)/i )
                {
                    my $c = $1;
                    $c =~ s/\,//g;
                    $self->element(
                        {
                            'Name' => 'Statistics_db-len',
                            'Data' => $c
                        }
                    );
                }
                elsif (/letters in database:\s+(\-?[\d,]+)/i) {
                    my $s = $1;
                    $s =~ s/,//g;
                    $self->element(
                        {
                            'Name' => 'Statistics_db-let',
                            'Data' => $s
                        }
                    );
                }
                elsif ( $blast eq 'btk' ) {
                    next;
                }
                elsif ( $blast eq 'wublast' ) {

                    #		   warn($_);
                    if (/E=(\S+)/) {
                        $self->element(
                            {
                                'Name' => 'Parameters_expect',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/nogaps/) {
                        $self->element(
                            {
                                'Name' => 'Parameters_allowgaps',
                                'Data' => 'no'
                            }
                        );
                    }
                    elsif (/ctxfactor=(\S+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_ctxfactor',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (
/(postsw|links|span[12]?|warnings|notes|gi|noseqs|qres|qype)/
                      )
                    {
                        $self->element(
                            {
                                'Name' => "Parameters_$1",
                                'Data' => 'yes'
                            }
                        );
                    }
                    elsif (/(\S+)=(\S+)/) {
                        $self->element(
                            {
                                'Name' => "Parameters_$1",
                                'Data' => $2
                            }
                        );
                    }
                    elsif ( $last =~ /(Frame|Strand)\s+MatID\s+Matrix name/i ) {
                        my $firstgapinfo = 1;
                        my $frame        = undef;
                        while ( defined($_) && !/^\s+$/ ) {
                            s/^\s+//;
                            s/\s+$//;
                            if ( $firstgapinfo
                                && s/Q=(\d+),R=(\d+)\s+//x )
                            {
                                $firstgapinfo = 0;

                                $self->element(
                                    {
                                        'Name' => 'Parameters_gap-open',
                                        'Data' => $1
                                    }
                                );
                                $self->element(
                                    {
                                        'Name' => 'Parameters_gap-extend',
                                        'Data' => $2
                                    }
                                );
                                my @fields = split;

                                for my $type (
                                    qw(lambda_gapped
                                    kappa_gapped
                                    entropy_gapped)
                                  )
                                {
                                    next if $type eq 'n/a';
                                    if ( !@fields ) {
                                        warn "fields is empty for $type\n";
                                        next;
                                    }
                                    $self->element(
                                        {
                                            'Name' =>
                                              "Statistics_frame$frame\_$type",
                                            'Data' => shift @fields
                                        }
                                    );
                                }
                            }
                            else {
                                my ( $frameo, $matid, $matrix, @fields ) =
                                  split;
                                if ( !defined $frame ) {

                                    # keep some sort of default feature I guess
                                    # even though this is sort of wrong
                                    $self->element(
                                        {
                                            'Name' => 'Parameters_matrix',
                                            'Data' => $matrix
                                        }
                                    );
                                    $self->element(
                                        {
                                            'Name' => 'Statistics_lambda',
                                            'Data' => $fields[0]
                                        }
                                    );
                                    $self->element(
                                        {
                                            'Name' => 'Statistics_kappa',
                                            'Data' => $fields[1]
                                        }
                                    );
                                    $self->element(
                                        {
                                            'Name' => 'Statistics_entropy',
                                            'Data' => $fields[2]
                                        }
                                    );
                                }
                                $frame = $frameo;
                                my $ii = 0;
                                for my $type (
                                    qw(lambda_used
                                    kappa_used
                                    entropy_used
                                    lambda_computed
                                    kappa_computed
                                    entropy_computed)
                                  )
                                {
                                    my $f = $fields[$ii];
                                    next unless defined $f;    # deal with n/a
                                    if ( $f eq 'same' ) {
                                        $f = $fields[ $ii - 3 ];
                                    }
                                    $ii++;
                                    $self->element(
                                        {
                                            'Name' =>
                                              "Statistics_frame$frame\_$type",
                                            'Data' => $f
                                        }
                                    );

                                }
                            }

                            # get the next line
                            $_ = $self->_readline;
                        }
                        $last = $_;
                    }
                    elsif ( $last =~ /(Frame|Strand)\s+MatID\s+Length/i ) {
                        my $frame = undef;
                        while ( defined($_) && !/^\s+/ ) {
                            s/^\s+//;
                            s/\s+$//;
                            my @fields = split;
                            if ( @fields <= 3 ) {
                                for my $type (qw(X_gapped E2_gapped S2)) {
                                    last unless @fields;
                                    $self->element(
                                        {
                                            'Name' =>
                                              "Statistics_frame$frame\_$type",
                                            'Data' => shift @fields
                                        }
                                    );
                                }
                            }
                            else {

                                for my $type (
                                    qw(length
                                    efflength
                                    E S W T X E2 S2)
                                  )
                                {
                                    $self->element(
                                        {
                                            'Name' =>
                                              "Statistics_frame$frame\_$type",
                                            'Data' => shift @fields
                                        }
                                    );
                                }
                            }
                            $_ = $self->_readline;
                        }
                        $last = $_;
                    }
                    elsif (/(\S+\s+\S+)\s+DFA:\s+(\S+)\s+\((.+)\)/) {
                        if ( $1 eq 'states in' ) {
                            $self->element(
                                {
                                    'Name' => 'Statistics_DFA_states',
                                    'Data' => "$2 $3"
                                }
                            );
                        }
                        elsif ( $1 eq 'size of' ) {
                            $self->element(
                                {
                                    'Name' => 'Statistics_DFA_size',
                                    'Data' => "$2 $3"
                                }
                            );
                        }
                    }
                    elsif (
                        m/^\s+Time to generate neighborhood:\s+
			    (\S+\s+\S+\s+\S+)/x
                      )
                    {
                        $self->element(
                            {
                                'Name' => 'Statistics_neighbortime',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/processors\s+used:\s+(\d+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_noprocessors',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (
                        m/^\s+(\S+)\s+cpu\s+time:\s+# cputype
			    (\S+\s+\S+\s+\S+)           # cputime
			    \s+Elapsed:\s+(\S+)/x
                      )
                    {
                        my $cputype = lc($1);
                        $self->element(
                            {
                                'Name' => "Statistics_$cputype\_cputime",
                                'Data' => $2
                            }
                        );
                        $self->element(
                            {
                                'Name' => "Statistics_$cputype\_actualtime",
                                'Data' => $3
                            }
                        );
                    }
                    elsif (/^\s+Start:/) {
                        my ( $junk, $start, $stime, $end, $etime ) =
                          split( /\s+(Start|End)\:\s+/, $_ );
                        chomp($stime);
                        $self->element(
                            {
                                'Name' => 'Statistics_starttime',
                                'Data' => $stime
                            }
                        );
                        chomp($etime);
                        $self->element(
                            {
                                'Name' => 'Statistics_endtime',
                                'Data' => $etime
                            }
                        );
                    }
                    elsif (/^\s+Database:\s+(.+)$/) {
                        $self->element(
                            {
                                'Name' => 'Parameters_full_dbpath',
                                'Data' => $1
                            }
                        );

                    }
                    elsif (/^\s+Posted:\s+(.+)/) {
                        my $d = $1;
                        chomp($d);
                        $self->element(
                            {
                                'Name' => 'Statistics_posted_date',
                                'Data' => $d
                            }
                        );
                    }
                }
                elsif ( $blast eq 'ncbi' ) {

                    if (m/^Matrix:\s+(.+)\s*$/oxi) {
                        $self->element(
                            {
                                'Name' => 'Parameters_matrix',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/^Gapped/) {
                        $gapped_stats = 1;
                    }
                    elsif (/^Lambda/) {
                        $_ = $self->_readline;
                        s/^\s+//;
                        my ( $lambda, $kappa, $entropy ) = split;
                        if ($gapped_stats) {
                            $self->element(
                                {
                                    'Name' => "Statistics_gapped_lambda",
                                    'Data' => $lambda
                                }
                            );
                            $self->element(
                                {
                                    'Name' => "Statistics_gapped_kappa",
                                    'Data' => $kappa
                                }
                            );
                            $self->element(
                                {
                                    'Name' => "Statistics_gapped_entropy",
                                    'Data' => $entropy
                                }
                            );
                        }
                        else {
                            $self->element(
                                {
                                    'Name' => "Statistics_lambda",
                                    'Data' => $lambda
                                }
                            );
                            $self->element(
                                {
                                    'Name' => "Statistics_kappa",
                                    'Data' => $kappa
                                }
                            );
                            $self->element(
                                {
                                    'Name' => "Statistics_entropy",
                                    'Data' => $entropy
                                }
                            );
                        }
                    }
                    elsif (m/effective\s+search\s+space\s+used:\s+(\d+)/oxi) {
                        $self->element(
                            {
                                'Name' => 'Statistics_eff-spaceused',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (m/effective\s+search\s+space:\s+(\d+)/oxi) {
                        $self->element(
                            {
                                'Name' => 'Statistics_eff-space',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (
                        m/Gap\s+Penalties:\s+Existence:\s+(\d+)\,
			    \s+Extension:\s+(\d+)/ox
                      )
                    {
                        $self->element(
                            {
                                'Name' => 'Parameters_gap-open',
                                'Data' => $1
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Parameters_gap-extend',
                                'Data' => $2
                            }
                        );
                    }
                    elsif (/effective\s+HSP\s+length:\s+(\d+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_hsp-len',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/Number\s+of\s+HSP's\s+better\s+than\s+(\S+)\s+without\s+gapping:\s+(\d+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_number_of_hsps_better_than_expect_value_cutoff_without_gapping',
                                'Data' => $2
                            }
                        );
                    }
                    elsif (/Number\s+of\s+HSP's\s+gapped:\s+(\d+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_number_of_hsps_gapped',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/Number\s+of\s+HSP's\s+successfully\s+gapped:\s+(\d+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_number_of_hsps_successfully_gapped',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/Length\s+adjustment:\s+(\d+)/) {
                        $self->element(
                            {
                                'Name' => 'Statistics_length_adjustment',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (/effective\s+length\s+of\s+query:\s+([\d\,]+)/i) {
                        my $c = $1;
                        $c =~ s/\,//g;
                        $self->element(
                            {
                                'Name' => 'Statistics_query-len',
                                'Data' => $c
                            }
                        );
                    }
                    elsif (/effective\s+length\s+of\s+database:\s+([\d\,]+)/i) {
                        my $c = $1;
                        $c =~ s/\,//g;
                        $self->element(
                            {
                                'Name' => 'Statistics_eff-dblen',
                                'Data' => $c
                            }
                        );
                    }
                    elsif (
/^(T|A|X1|X2|X3|S1|S2):\s+(\d+(\.\d+)?)\s+(?:\(\s*(\d+\.\d+) bits\))?/
                      )
                    {
                        my $v = $2;
                        chomp($v);
                        $self->element(
                            {
                                'Name' => "Statistics_$1",
                                'Data' => $v
                            }
                        );
                        if ( defined $4 ) {
                            $self->element(
                                {
                                    'Name' => "Statistics_$1_bits",
                                    'Data' => $4
                                }
                            );
                        }
                    }
                    elsif (
                        m/frameshift\s+window\,
			    \s+decay\s+const:\s+(\d+)\,\s+([\.\d]+)/x
                      )
                    {
                        $self->element(
                            {
                                'Name' => 'Statistics_framewindow',
                                'Data' => $1
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Statistics_decay',
                                'Data' => $2
                            }
                        );
                    }
                    elsif (m/^Number\s+of\s+Hits\s+to\s+DB:\s+(\S+)/ox) {
                        $self->element(
                            {
                                'Name' => 'Statistics_hit_to_db',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (m/^Number\s+of\s+extensions:\s+(\S+)/ox) {
                        $self->element(
                            {
                                'Name' => 'Statistics_num_extensions',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (
                        m/^Number\s+of\s+successful\s+extensions:\s+
			    (\S+)/ox
                      )
                    {
                        $self->element(
                            {
                                'Name' => 'Statistics_num_suc_extensions',
                                'Data' => $1
                            }
                        );
                    }
                    elsif (
                        m/^Number\s+of\s+sequences\s+better\s+than\s+
			    (\S+):\s+(\d+)/ox
                      )
                    {
                        $self->element(
                            {
                                'Name' => 'Parameters_expect',
                                'Data' => $1
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Statistics_seqs_better_than_cutoff',
                                'Data' => $2
                            }
                        );
                    }
                    elsif (/^\s+Posted\s+date:\s+(.+)/) {
                        my $d = $1;
                        chomp($d);
                        $self->element(
                            {
                                'Name' => 'Statistics_posted_date',
                                'Data' => $d
                            }
                        );
                    }
                    elsif ( !/^\s+$/ ) {
                        #$self->debug( "unmatched stat $_");
                    }
                }
                $last = $_;
            }
        } elsif ( $self->in_element('hsp') ) {
            $self->debug("blast.pm: Processing HSP\n");
            # let's read 3 lines at a time;
            # bl2seq hackiness... Not sure I like
            $self->{'_reporttype'} ||= $DEFAULTREPORTTYPE;
            my %data = (
                'Query' => '',
                'Mid'   => '',
                'Hit'   => ''
            );
            my $len;
            for ( my $i = 0 ; defined($_) && $i < 3 ; $i++ ) {
                # $self->debug("$i: $_") if $v;
                if ( ( $i == 0 && /^\s+$/) ||
		     /^\s*(?:Lambda|Minus|Plus|Score)/i )
                {
                    $self->_pushback($_) if defined $_;
                    $self->end_element( { 'Name' => 'Hsp' } );
                    last;
                }
                chomp;
                if (/^((Query|Sbjct):?\s+(\-?\d+)?\s*)(\S+)\s+(\-?\d+)?/) {
                    my ( $full, $type, $start, $str, $end ) =
                      ( $1, $2, $3, $4, $5 );

                    if ( $str eq '-' ) {
                        $i = 3 if $type eq 'Sbjct';
                    }
                    else {
                        $data{$type} = $str;
                    }
                    $len = length($full);
                    $self->{"\_$type"}->{'begin'} = $start
                      unless $self->{"_$type"}->{'begin'};
                    $self->{"\_$type"}->{'end'} = $end;
                } elsif (/^((Query|Sbjct):?\s+(\-?0+)\s*)/) {
                   # Bug from NCBI's BLAST: unaligned output
                   $_ = $self->_readline() for 0..1;
                   last;
                } else {
                    $self->throw("no data for midline $_")
                      unless ( defined $_ && defined $len );
                    $data{'Mid'} = substr( $_, $len );
                }
                $_ = $self->_readline();
            }
            $self->characters(
                {
                    'Name' => 'Hsp_qseq',
                    'Data' => $data{'Query'}
                }
            );
            $self->characters(
                {
                    'Name' => 'Hsp_hseq',
                    'Data' => $data{'Sbjct'}
                }
            );
            $self->characters(
                {
                    'Name' => 'Hsp_midline',
                    'Data' => $data{'Mid'}
                }
            );
        }
        else {
            #$self->debug("blast.pm: unrecognized line $_");
        }
    }

    $self->debug("blast.pm: End of BlastOutput\n");
    if ( $self->{'_seentop'} ) {
        $self->within_element('hsp')
          && $self->end_element( { 'Name' => 'Hsp' } );
        $self->within_element('hit')
          && $self->end_element( { 'Name' => 'Hit' } );
        # cleanup extra hits
        $self->_cleanup_hits(\@hit_signifs) if scalar(@hit_signifs);
        $self->within_element('iteration')
          && $self->end_element( { 'Name' => 'Iteration' } );
        if ($bl2seq_fix) {
            $self->element(
                {
                    'Name' => 'BlastOutput_program',
                    'Data' => $reporttype
                }
            );
        }
        $self->end_element( { 'Name' => 'BlastOutput' } );
    }
    return $self->end_document();
}

# Private method for internal use only.

    my $self = shift;
    $self->start_element( { 'Name' => 'BlastOutput' } );
    $self->{'_seentop'} = 1;
    $self->{'_result_count'}++;
    $self->{'_handler_rc'} = undef;

    my ( $self, $type ) = @_;
    my $handler     = $self->{'_handler_cache'};
    my $will_handle =
      defined( $self->{'_will_handle_cache'}->{$type} )
      ? $self->{'_will_handle_cache'}->{$type}
      : ( $self->{'_will_handle_cache'}->{$type} =
          $handler->will_handle($type) );

    return $will_handle ? $handler : undef;

    my ( $self, $data ) = @_;

    # we currently don't care about attributes
    my $nm   = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    if ($type) {
        my $handler = $self->_will_handle($type);
        if ($handler) {
            my $func = sprintf( "start_%s", lc $type );
            $self->{'_handler_rc'} = $handler->$func( $data->{'Attributes'} );
        }
        #else {
            #$self->debug( # changed 4/29/2006 to play nice with other event handlers
            #    "Bio::SearchIO::InternalParserError ".
            #    "\nCan't handle elements of type \'$type.\'"
            #);
        #}
        unshift @{ $self->{'_elements'} }, $type;
        if ( $type eq 'result' ) {
            $self->{'_values'} = {};
            $self->{'_result'} = undef;
        } else {
            # cleanup some things
            if ( defined $self->{'_values'} ) {
                foreach my $k (
                    grep { /^\U$type\-/ }
                    keys %{ $self->{'_values'} }
                  )
                {
                    delete $self->{'_values'}->{$k};
                }
            }
        }
    }

    my ( $self, $data ) = @_;

    my $nm   = $data->{'Name'};
    my $type;
    my $rc;
    # cache these (TODO: we should probably cache all cross-report data)
    if ( $nm eq 'BlastOutput_program' ) {
        if ( $self->{'_last_data'} =~ /(t?blast[npx])/i ) {
            $self->{'_reporttype'} = uc $1;
        }
        $self->{'_reporttype'} ||= $DEFAULTREPORTTYPE;
    }

    if ( $nm eq 'BlastOutput_version' ) {
        $self->{'_reportversion'} = $self->{'_last_data'};
    }

    # Hsps are sort of weird, in that they end when another
    # object begins so have to detect this in end_element for now
    if ( $nm eq 'Hsp' ) {
        foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq Hsp_features)) {
            $self->element(
                {
                    'Name' => $_,
                    'Data' => $self->{'_last_hspdata'}->{$_}
                }
            ) if defined $self->{'_last_hspdata'}->{$_};
        }
        $self->{'_last_hspdata'} = {};
        $self->element(
            {
                'Name' => 'Hsp_query-from',
                'Data' => $self->{'_Query'}->{'begin'}
            }
        );
        $self->element(
            {
                'Name' => 'Hsp_query-to',
                'Data' => $self->{'_Query'}->{'end'}
            }
        );

        $self->element(
            {
                'Name' => 'Hsp_hit-from',
                'Data' => $self->{'_Sbjct'}->{'begin'}
            }
        );
        $self->element(
            {
                'Name' => 'Hsp_hit-to',
                'Data' => $self->{'_Sbjct'}->{'end'}
            }
        );

        #    } elsif( $nm eq 'Iteration' ) {
        # Nothing special needs to be done here.
    }
    if ( $type = $MODEMAP{$nm} ) {
        my $handler = $self->_will_handle($type);
        if ($handler) {
            my $func = sprintf( "end_%s", lc $type );
            $rc = $handler->$func( $self->{'_reporttype'}, $self->{'_values'} );
        }
        shift @{ $self->{'_elements'} };

    }
    elsif ( $MAPPING{$nm} ) {
        if ( ref( $MAPPING{$nm} ) =~ /hash/i ) {

            # this is where we shove in the data from the
            # hashref info about params or statistics
            my $key = ( keys %{ $MAPPING{$nm} } )[0];
            $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } =
              $self->{'_last_data'};
        }
        else {
            $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'};
        }
    }
    else {
        #$self->debug("blast.pm: unknown nm $nm, ignoring\n");
    }
    $self->{'_last_data'} = '';    # remove read data if we are at
                                   # end of an element
    $self->{'_result'} = $rc if ( defined $type && $type eq 'result' );
	$self->{'_seen_hsp_features'} = 0;
    return $rc;

    my ( $self, $data ) = @_;
    # Note that start element isn't needed for character data
    # Not too SAX-y, though
    #$self->start_element($data);
    $self->characters($data);
    $self->end_element($data);

    my ( $self, $data ) = @_;
    if (   $self->in_element('hsp')
        && $data->{'Name'} =~ /^Hsp\_(qseq|hseq|midline)$/ )
    {
        $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'}
          if defined $data->{'Data'};
    }
    return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
    $self->{'_last_data'} = $data->{'Data'};

    my ( $self, $name ) = @_;
    return 0
      if ( !defined $name && !defined $self->{'_elements'}
        || scalar @{ $self->{'_elements'} } == 0 );
    foreach ( @{ $self->{'_elements'} } ) {
        if ( $_ eq $name ) {
            return 1;
        }
    }
    return 0;

    my ( $self, $name ) = @_;
    return 0 if !defined $self->{'_elements'}->[0];
    return ( $self->{'_elements'}->[0] eq $name );

    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'}   = {};
    $self->{'_result'}   = undef;
    $self->{'_elements'} = [];

    my ( $self, @args ) = @_;

    #$self->debug("blast.pm: end_document\n");
    return $self->{'_result'};

    my ( $self, $blast, @args ) = @_;

    if ( not defined( $self->writer ) ) {
        $self->warn("Writer not defined. Using a $DEFAULT_BLAST_WRITER_CLASS");
        $self->writer( $DEFAULT_BLAST_WRITER_CLASS->new() );
    }
    $self->SUPER::write_result( $blast, @args );

    my $self = shift;
    return $self->{'_result_count'};

    my ($self, $hits) = @_;
    while ( my $v = shift @{ $hits }) {
        next unless defined $v;
        $self->start_element( { 'Name' => 'Hit' } );
        my $id   = $v->[2];
        my $desc = $v->[3];
        $self->element(
            {
                'Name' => 'Hit_id',
                'Data' => $id
            }
        );
        my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id);
        $self->element(
            {
                'Name' => 'Hit_accession',
                'Data' => $acc
            }
        );
        if ( defined $v ) {
            $self->element(
                {
                    'Name' => 'Hit_signif',
                    'Data' => $v->[0]
                }
            );
            if (exists $self->{'_wublast'}) {
                $self->element(
                    {
                        'Name' => 'Hit_score',
                        'Data' => $v->[1]
                    }
                );
            } else {
                $self->element(
                    {
                        'Name' => 'Hit_bits',
                        'Data' => $v->[1]
                    }
                );
            }

        }
        $self->element(
            {
                'Name' => 'Hit_def',
                'Data' => $desc
            }
        );
        $self->end_element( { 'Name' => 'Hit' } );
    }
}


1;

__END__

Developer Notes
---------------

The following information is added in hopes of increasing the
maintainability of this code. It runs the risk of becoming obsolete as
the code gets updated. As always, double check against the actual
source. If you find any discrepencies, please correct them.
[ This documentation added on 3 Jun 2003. ]

The logic is the brainchild of Jason Stajich, documented by Steve
Chervitz. Jason: please check it over and modify as you see fit.

Question:
Elmo wants to know: How does this module unmarshall data from the input stream?
(i.e., how does information from a raw input file get added to
the correct Bioperl object?)

Answer:

This answer is specific to SearchIO::blast, but may apply to other
SearchIO.pm subclasses as well. The following description gives the
basic idea. The actual processing is a little more complex for
certain types of data (HSP, Report Parameters).

You can think of blast::next_result() as faking a SAX XML parser,
making a non-XML document behave like its XML. The overhead to do this
is quite substantial (~650 lines of code instead of ~80 in
blastxml.pm).

0. First, add a key => value pair for the datum of interest to %MAPPING
    Example:
           'Foo_bar'   => 'Foo-bar',

1. next_result() collects the datum of interest from the input stream,
   and calls element().
    Example:
            $self->element({ 'Name' => 'Foo_bar',
                             'Data' => $foobar});

2. The element() method is a convenience method that calls start_element(),
   characters(), and end_element().

3. start_element() checks to see if the event handler can handle a start_xxx(),
   where xxx = the 'Name' parameter passed into element(), and calls start_xxx()
   if so. Otherwise, start_element() does not do anything.

   Data that will have such an event handler are defined in %MODEMAP.
   Typically, there are only handler methods for the main parts of
   the search result (e.g., Result, Iteration, Hit, HSP),
   which have corresponding Bioperl modules. So in this example,
   there was an earlier call such as $self->element({'Name'=>'Foo'})
   and the Foo_bar datum is meant to ultimately go into a Foo object.

   The start_foo() method in the handler will typically do any
   data initialization necessary to prepare for creating a new Foo object.
   Example: SearchResultEventBuilder::start_result()

4. characters() takes the value of the 'Data' key from the hashref argument in
   the elements() call and saves it in a local data member:
   Example:
   $self->{'_last_data'} = $data->{'Data'};

5. end_element() is like start_element() in that it does the check for whether
   the event handler can handle end_xxx() and if so, calls it, passing in
   the data collected from all of the characters() calls that occurred
   since the start_xxx() call.

   If there isn't any special handler for the data type specified by 'Name',
   end_element() will place the data saved by characters() into another
   local data member that saves it in a hash with a key defined by %MAPPING.
   Example:
           $nm = $data->{'Name'};
           $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};

   In this case, $MAPPING{$nm} is 'Foo-bar'.

   end_element() finishes by resetting the local data member used by
   characters(). (i.e., $self->{'_last_data'} = '';)

6. When the next_result() method encounters the end of the Foo element in the
   input stream. It will invoke $self->end_element({'Name'=>'Foo'}).
   end_element() then sends all of the data in the $self->{'_values'} hash.
   Note that $self->{'_values'} is cleaned out during start_element(),
   keeping it at a resonable size.

   In the event handler, the end_foo() method takes the hash from end_element()
   and creates a new hash containing the same data, but having keys lacking
   the 'Foo' prefix (e.g., 'Foo-bar' becomes '-bar'). The handler's end_foo()
   method then creates the Foo object, passing in this new hash as an argument.
   Example: SearchResultEventBuilder::end_result()

7. Objects created from the data in the search result are managed by
   the event handler which adds them to a ResultI object (using API methods
   for that object). The ResultI object gets passed back to
   SearchIO::end_element() when it calls end_result().

   The ResultI object is then saved in an internal data member of the
   SearchIO object, which returns it at the end of next_result()
   by calling end_document().

   (Technical Note: All objects created by end_xxx() methods in the event
    handler are returned to SearchIO::end_element(), but the SearchIO object
    only cares about the ResultI objects.)

(Sesame Street aficionados note: This answer was NOT given by Mr. Noodle ;-P)

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://redmine.open-bio.org/projects/bioperl/

 Title   : new
 Usage   : my $obj = Bio::SearchIO::blast->new(%args);
 Function: Builds a new Bio::SearchIO::blast object
 Returns : Bio::SearchIO::blast
 Args    : Key-value pairs:
           -fh/-file => filehandle/filename to BLAST file
           -format   => 'blast'
           -report_type => 'blastx', 'tblastn', etc -- only for bl2seq
                           reports when you want to distinguish between
                           tblastn and blastx reports (this only controls
                           where the frame information is put - on the query
                           or subject object.
           -inclusion_threshold => e-value threshold for inclusion in the
                                   PSI-BLAST score matrix model (blastpgp)
           -signif      => float or scientific notation number to be used
                           as a P- or Expect value cutoff
           -score       => integer or scientific notation number to be used
                           as a blast score value cutoff
           -bits        => integer or scientific notation number to be used
                           as a bit score value cutoff
           -hit_filter  => reference to a function to be used for
                           filtering hits based on arbitrary criteria.
                           All hits of each BLAST report must satisfy
                           this criteria to be retained.
                           If a hit fails this test, it is ignored.
                           This function should take a
                           Bio::Search::Hit::BlastHit.pm object as its first
                           argument and return true
                           if the hit should be retained.
                           Sample filter function:
                              -hit_filter => sub { $hit = shift;
                                                   $hit->gaps == 0; },
                           (Note: -filt_func is synonymous with -hit_filter)
           -overlap     => integer. The amount of overlap to permit between
                           adjacent HSPs when tiling HSPs. A reasonable value is 2.
                           Default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP.

            The following criteria are not yet supported:
            (these are probably best applied within this module rather than in the
             event handler since they would permit the parser to take some shortcuts.)

           -check_all_hits => boolean. Check all hits for significance against
                              significance criteria.  Default = false.
                              If false, stops processing hits after the first
                              non-significant hit or the first hit that fails
                              the hit_filter call. This speeds parsing,
                              taking advantage of the fact that the hits
                              are processed in the order they appear in the report.
           -min_query_len => integer to be used as a minimum for query sequence length.
                             Reports with query sequences below this length will
                             not be processed. Default = no minimum length.
           -best        => boolean. Only process the best hit of each report;
                           default = false.

 Title   : inclusion_threshold
 Usage   : my $incl_thresh = $isreb->inclusion_threshold;
         : $isreb->inclusion_threshold(1e-5);
 Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
           score matrix model (blastpgp) that was used for generating the reports
           being parsed.
 Returns : number (real)
           Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD
 Args    : number (real)  (e.g., 0.0001 or 1e-4 )

 Usage     : $obj->max_significance();
 Purpose   : Set/Get the P or Expect value used as significance screening cutoff.
             This is the value of the -signif parameter supplied to new().
             Hits with P or E-value above this are skipped.
 Returns   : Scientific notation number with this format: 1.0e-05.
 Argument  : Scientific notation number or float (when setting)
 Comments  : Screening of significant hits uses the data provided on the
           : description line. For NCBI BLAST1 and WU-BLAST, this data
           : is P-value. for NCBI BLAST2 it is an Expect value.

 Usage     : $obj->min_score();
 Purpose   : Set/Get the Blast score used as screening cutoff.
             This is the value of the -score parameter supplied to new().
             Hits with scores below this are skipped.
 Returns   : Integer or scientific notation number.
 Argument  : Integer or scientific notation number (when setting)
 Comments  : Screening of significant hits uses the data provided on the
           : description line.

 Usage     : $obj->min_query_length();
 Purpose   : Gets the query sequence length used as screening criteria.
             This is the value of the -min_query_len parameter supplied to new().
             Hits with sequence length below this are skipped.
 Returns   : Integer
 Argument  : n/a

 Title     : best_hit_only
 Usage     : print "only getting best hit.\n" if $obj->best_hit_only;
 Purpose   : Set/Get the indicator for whether or not to process only
           : the best BlastHit.
 Returns   : Boolean (1 | 0)
 Argument  : Boolean (1 | 0) (when setting)

 Title     : check_all_hits
 Usage     : print "checking all hits.\n" if $obj->check_all_hits;
 Purpose   : Set/Get the indicator for whether or not to process all hits.
           : If false, the parser will stop processing hits after the
           : the first non-significance hit or the first hit that fails
           : any hit filter.
 Returns   : Boolean (1 | 0)
 Argument  : Boolean (1 | 0) (when setting)