# Do not use this object directly, use it through the SearchIO system
   use Bio::SearchIO;
   my $searchio = Bio::SearchIO->new(-format => 'fasta',
                    -file   => 'report.FASTA');
   while( my $result = $searchio->next_result ) {
    # ... do what you would normally doi with Bio::SearchIO.
   }

    # Set IDLENGTH to a new value if you have
    # compile FASTA with a different ID length
    # (actually newest FASTA allows the setting of this
    #  via -C parameter, default is 6)
    $IDLENGTH = 6;

    # mapping of NCBI Blast terms to Bioperl hash keys
    %MODEMAP = (
        'FastaOutput' => 'result',
        '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_sw-score'    => 'HSP-swscore',
        'Hsp_evalue'      => 'HSP-evalue',
        'Hsp_evalue2'     => 'HSP-evalue2',
        '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',

        'Hit_id'        => 'HIT-name',
        'Hit_len'       => 'HIT-length',
        'Hit_accession' => 'HIT-accession',
        'Hit_def'       => 'HIT-description',
        'Hit_signif'    => 'HIT-significance',
        'Hit_score'     => 'HIT-score',

        'FastaOutput_program'   => 'RESULT-algorithm_name',
        'FastaOutput_version'   => 'RESULT-algorithm_version',
        'FastaOutput_query-def' => 'RESULT-query_name',
        'FastaOutput_querydesc' => 'RESULT-query_description',
        'FastaOutput_query-len' => 'RESULT-query_length',
        'FastaOutput_db'        => 'RESULT-database_name',
        'FastaOutput_db-len'    => 'RESULT-database_entries',
        'FastaOutput_db-let'    => 'RESULT-database_letters',

        '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-ext'     => { 'RESULT-parameters' => 'gapext' },
        'Parameters_word-size'   => { 'RESULT-parameters' => 'wordsize' },
        'Parameters_ktup'        => { 'RESULT-parameters' => 'ktup' },
        'Parameters_filter'      => { 'RESULT-parameters' => 'filter' },
        'Statistics_db-num'      => { 'RESULT-statistics' => 'dbentries' },
        'Statistics_db-len'      => { 'RESULT-statistics' => 'dbletters' },
        'Statistics_hsp-len'     => { 'RESULT-statistics' => 'hsplength' },
        'Statistics_eff-space'   => { 'RESULT-statistics' => 'effectivespace' },
        'Statistics_kappa'       => { 'RESULT-statistics' => 'kappa' },
        'Statistics_lambda'      => { 'RESULT-statistics' => 'lambda' },
        'Statistics_entropy'     => { 'RESULT-statistics' => 'entropy' },
    );

    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    return unless @args;
    my ($idlength) = $self->_rearrange( [qw(IDLENGTH)], @args );
    $self->idlength( $idlength || $IDLENGTH );
    $self->_eventHandler->register_factory(
        'hsp',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::HSP::FastaHSP',
            -interface => 'Bio::Search::HSP::HSPI'
        )
    );
    return 1;

    my ($self) = @_;
    local $/ = "\n";
    local $_;

    my $data    = '';
    my $seentop = 0;
    my $current_hsp;
    my $m9HSP = 0;
    $self->start_document();
    my @hit_signifs;
    while ( defined( $_ = $self->_readline ) ) {
        next if ( !$self->in_element('hsp')
            && /^\s+$/ );    # skip empty lines
        if (
               m/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/oxi
            || /(\S+)\s+compares\s+a/
	    || /(\S+)\s+performs\s+a/
	    || /(\S+)\s+produces\s/
	    || /(\S+)\s+finds\s+/	# for lalign, but does not work because no "The best scores are:"
            || (   m/^\#\s+/	# has a command log line
                && ( $_ = $self->_readline )
                && /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/oxi
		   || /(\S+)\s+compares\s+a/
		   || /(\S+)\s+performs\s+a/
		   || /(\S+)\s+produces\s/
		   || /(\S+)\s+finds\s+/	# for lalign, but does not work because no "The best scores are:"
	    )
          )
        {
            if ($seentop) {
                $self->_pushback($_);
                $self->end_element( { 'Name' => 'FastaOutput' } );
                return $self->end_document();
            }
            $self->{'_reporttype'} = $1;
            $self->start_element( { 'Name' => 'FastaOutput' } );
            $self->{'_result_count'}++;
            $seentop = 1;
            #$self->debug( "reporttype is " . $self->{'_reporttype'} . "\n" );
            $self->element(
                {
                    'Name' => 'FastaOutput_program',
                    'Data' => $self->{'_reporttype'}
                }
            );
            my $version;
            # version 35 version string on same line
            if (/version/) {
                ($version) = (/version\s+(\S+)/);
            }
            # earlier versions, it's on the next line
            else {
                $_ = $self->_readline();
                ($version) = (/version\s+(\S+)/);
            }
            $version = '' unless defined $version;
            $self->{'_version'} = $version;
            $self->element(
                {
                    'Name' => 'FastaOutput_version',
                    'Data' => $version
                }
            );

            my ( $last, $leadin, $type, $querylen, $querytype, $querydef );

            while ( defined( $_ = $self->_readline() ) ) {
                if (
                    /^ (
                       (?:\s+>) |             # fa33 lead-in
                       (?:\s*\d+\s*>>>)       # fa34 mlib lead-in
                      )
                      (.*)
                   /x
                  )
                {
                    ( $leadin, $querydef ) = ( $1, $2 );
                    if ( $leadin =~ m/>>>/ ) {
                        if ( $querydef =~
                            /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o )
                        {
                            ( $querydef, $querylen, $querytype ) =
                              ( $1, $2, $3 );
                            last;
                        }
                    }
                    else {
                        if ( $last =~ /(\S+)[:,]\s*(\d+)\s+(aa|nt)/ ) {
                            ( $querylen, $querytype ) = ( $2, $3 );
                            $querydef ||= $1;
                            last;
                        }
                    }
                }
                elsif (m/^\s*vs\s+\S+/o) {
                    if ( $last =~ /(\S+)[,:]\s+(\d+)\s+(aa|nt)/o ) {
                        ( $querydef, $querylen, $querytype ) = ( $1, $2, $3 );
                        last;
                    }
                }
                $last = $_;
            }
            if (   $self->{'_reporttype'}
                && $self->{'_reporttype'} eq 'FASTA' )
            {
                if ( $querytype eq 'nt' ) {
                    $self->{'_reporttype'} = 'FASTN';
                }
                elsif ( $querytype eq 'aa' ) {
                    $self->{'_reporttype'} = 'FASTP';
                }
            }
            my ( $name, $descr ) = $querydef =~ m/^(\S+)\s*(.*?)\s*$/o;
            $self->element(
                {
                    'Name' => 'FastaOutput_query-def',
                    'Data' => $name
                }
            );
            $self->element(
                {
                    'Name' => 'FastaOutput_querydesc',
                    'Data' => $descr
                }
            );
            if ($querylen) {
                $self->element(
                    {
                        'Name' => 'FastaOutput_query-len',
                        'Data' => $querylen
                    }
                );
            }
            else {
                $self->warn("unable to find and set query length");
            }
            if (
                   $last =~ /^\s*vs\s+(\S+)/
                || ( $last =~ /^searching\s+(\S+)\s+library/ )
                || ( $last =~ /^Library:\s+(\S+)\s+/ )
                || (
                    defined $_
                    && (   /^\s*vs\s+(\S+)/
                        || /^Library:\s+(\S+)\s+/ )
                )
                || ( defined( $_ = $self->_readline() )
                    && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ ) )
              )
            {
                $self->element(
                    {
                        'Name' => 'FastaOutput_db',
                        'Data' => $1
                    }
                );
            }
            elsif (m/^\s+opt(?:\s+E\(\))?$/o) {

           # histogram ... read over it more rapidly than the larger outer loop:
                while ( defined( $_ = $self->_readline ) ) {
                    last if m/^>\d+/;
                }
            }
        }
        elsif (/(\d+)\s+residues\s+in\s+(\d+)\s+(?:library\s+)?sequences/) {
            $self->element(
                {
                    'Name' => 'FastaOutput_db-let',
                    'Data' => $1
                }
            );
            $self->element(
                {
                    'Name' => 'FastaOutput_db-len',
                    'Data' => $2
                }
            );
            $self->element(
                {
                    'Name' => 'Statistics_db-len',
                    'Data' => $1
                }
            );
            $self->element(
                {
                    'Name' => 'Statistics_db-num',
                    'Data' => $2
                }
            );
        }
        elsif (/Lambda=\s*(\S+)/) {
            $self->element(
                {
                    'Name' => 'Statistics_lambda',
                    'Data' => $1
                }
            );
        }
        elsif (/K=\s*(\S+)/) {
            $self->element(
                {
                    'Name' => 'Statistics_kappa',
                    'Data' => $1
                }
            );
        }
        elsif (/^\s*(Smith-Waterman)/) {

            $self->{'_reporttype'} = $1;

	    m/\[\s*(\S+)\s+matrix \([^\)]+\)(xS)?\],/;

            $self->element(
                {
                    'Name' => 'Parameters_matrix',
                    'Data' => $1
                }
            );
            $self->element(
                {
                    'Name' => 'Parameters_filter',
                    'Data' => defined $2 ? 1 : 0,
                }
            );
	    if (/\s*gap\-penalty:\s*(\-?\d+)\/(\-?\d+)/) {
		$self->element(
		    {
			'Name' => 'Parameters_gap-open',
			'Data' => $1,
		    }
		    );

		$self->element(
		    {
			'Name' => 'Parameters_gap-ext',
			'Data' => $2,
		    }
		    );
	    }
	    elsif (/\s*open\/ext:\s*(\-?\d+)\/(\-?\d+)/) {
		$self->element(
		    {
			'Name' => 'Parameters_gap-open',
			'Data' => $1,
		    }
		    );

		$self->element(
		    {
			'Name' => 'Parameters_gap-ext',
			'Data' => $2,
		    }
		    );
	    }

            $self->element(
                {
                    'Name' => 'FastaOutput_program',
                    'Data' => $self->{'_reporttype'}
                }
            );
        }
        elsif (/The best( related| unrelated)? scores are:/) {
            my $rel    = $1;
            my @labels = split;
            @labels = map {
                if ( $_ =~ m/^E\((\d+)\)$/o )
                {
                    $self->element(
                        { 'Name' => 'Statistics_eff-space', 'Data' => $1 } );
                    "evalue";
                }
                else {
                    # canonicalize changed column headers
                    if ($_ eq "gapl") {
                        $_ = "lgaps";
                    } elsif ($_ eq "gapq") {
                        $_ = "qgaps";
                    } elsif ($_ eq "E2()") {
                        $_ = "evalue2";
                    }
                    
                    $_;
                }
            } @labels[ $rel ? 5 : 4 .. $#labels ];

            while ( defined( $_ = $self->_readline() )
                && !/^\s+$/ )
            {
                my @line = split;

                if ( $line[-1] =~ m/\=/o && $labels[-1] ne 'aln_code' ) {
                    # unlabelled alignment hit;
                    push @labels, "aln_code";
                }

                if ($line[0] eq "+-") {
		    $m9HSP = 1;
                    # parse HSP, add to last parsed Hit
                    my %hspData;
                    
                    my @line = split;

                    @hspData{@labels} = splice( @line, @line - @labels );
                    $hspData{lframe} = $hit_signifs[-1]->{lframe};
                    
                    push @{$hit_signifs[-1]->{HSPs}},\% hspData;

                    next;
                }
		elsif ($line[0] eq '>>><<<') {
		    last;
		}

                my (%data, %hspData);
                @data{@labels} = @hspData{@labels} = splice( @line, @line - @labels );
                if ( $line[-1] =~ m/\[([1-6rf])\]/o ) {
                    my $fr = $1;
                    $hspData{lframe} = $data{lframe} = (
                        $fr =~ /\d/o
                        ? ( $fr <= 3 ? "+$fr" : "-@{[$fr-3]}" )
                        : ( $fr eq 'f' ? '+1' : '-1' )
                    );
                    pop @line;
                }
                else {
                    $hspData{lframe} = $data{lframe} = '0';
                }

                if ( $line[-1] =~ m/^\(?(\d+)\)$/ ) {
                    $data{hit_len} = $1;
                    pop @line;
                    if ( $line[-1] =~ m/^\($/ ) {
                        pop @line;
                    }
                }
                else {
                    $data{hit_len} = 0;
                }

                # rebuild the first part of the line, preserving spaces:
                ($_) = m/^(\S+(?:\s+\S+){$#line})/;

                my ( $id, $desc ) = split( /\s+/, $_, 2 );
                my @pieces = split( /\|/, $id );
                my $acc = pop @pieces;
                $acc =~ s/\.\d+$//;

                @data{qw(id desc acc)} = ( $id, $desc, $acc );
                $data{HSPs} = [\% hspData ];
                
                push @hit_signifs,\% data;
            }
        }
        elsif (
/^\s*([T]?FAST[XYAF]).+,\s*(\S+)\s*matrix[^\]]+?(xS)?\]\s*ktup:\s*(\d+)/
          )
        {

            $self->element(
                {
                    'Name' => 'Parameters_matrix',
                    'Data' => $2
                }
            );
            $self->element(
                {
                    'Name' => 'Parameters_filter',
                    'Data' => defined $3 ? 1 : 0,
                }
            );
            $self->element(
                {
                    'Name' => 'Parameters_ktup',
                    'Data' => $4
                }
            );
            $self->{'_reporttype'} = $1
              if ( $self->{'_reporttype'} !~ /FAST[PN]/i );

#
# get gap-pen line for FASTA33, which is not on the matrix line
#
# FASTA (3.36 June 2000) function [optimized, BL50 matrix (15:-5)] ktup: 2
#  join: 36, opt: 24, gap-pen: -12/ -2, width:  16
#
	    $_ = $self->_readline();
	    if (/(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+)/) {
		$self->element(
		    {
			'Name' => 'Parameters_gap-open',
			'Data' => $1
		    }
		    );
		$self->element(
		    {
			'Name' => 'Parameters_gap-ext',
			'Data' => $2
		    }
		    );
	    }

            $self->element(
                {
                    'Name' => 'FastaOutput_program',
                    'Data' => $self->{'_reporttype'}
                }
            );

        }
        elsif (/^Algorithm:\s+(\S+)\s+.*\s*\(([^)]+)\)\s+(\S+)/) {
            $self->{'_reporttype'} = $1
              if ( $self->{'_reporttype'} !~ /FAST[PN]/i );
        }
        elsif ( /^Parameters:/ ) {    # FASTA 35.04/FASTA 36
	    m/Parameters:\s+(\S+)\s+matrix\s+\([^\)]+\)(xS)?,?\s/;
            $self->element(
                {
                    'Name' => 'Parameters_matrix',
                    'Data' => $1
                }
            );
            $self->element(
                {
                    'Name' => 'Parameters_filter',
                    'Data' => defined $2 ? $2 : 0,
                }
            );
	    if (/ktup:\s(\d+)/) {
		$self->element(
		    {
			'Name' => 'Parameters_ktup',
			'Data' => $1
		    }
		    );
		if (/ktup:\s\d+$/) {
		    $_ = $self->_readline();
		}

	    }
	    if (/(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+)/) {
		$self->element(
		    {
			'Name' => 'Parameters_gap-open',
			'Data' => $1
		    }
		    );
		$self->element(
		    {
			'Name' => 'Parameters_gap-ext',
			'Data' => $2
		    }
		    );
	    }
            $self->element(
                {
                    'Name' => 'FastaOutput_program',
                    'Data' => $self->{'_reporttype'}
                }
            );
        }
        elsif (
	    /^\s+ktup:\s*(\d+),/
          )
        {
            $self->element(
                {
                    'Name' => 'Parameters_ktup',
                    'Data' => $1
                }
            );
        }
        elsif (/^(>--)$/ || /^>>(?!>)(.+?)\s+(?:\((\d+)\s*(aa|nt)\))?$/) {
            if ( $self->in_element('hsp') ) {
                $self->end_element( { 'Name' => 'Hsp' } );
            }
            
            my $firstHSP = 0;
            if ($1 ne ">--") {
                $firstHSP = 1;

                my ($hit_id, $len, $alphabet) = ($1, $2, $3);
                if (!$len || !$alphabet) {
                    WRAPPED:
                    while (defined($_ = $self->_readline)) {
                        if (/(.*?)\s+\((\d+)\s*(aa|nt)\)/) {
                            ($len, $alphabet) = ($2, $3);
                            $hit_id .= $1 ? " ".$1 : '';
                            last WRAPPED;
                        }
                        if (/^>>(?!>)/) { # too far, throw
                            $self->throw("Couldn't find length, bailing");
                        }
                    }
                }
                if ( $self->in_element('hit') ) {
                    $self->end_element( { 'Name' => 'Hit' } );
                    shift @hit_signifs if @hit_signifs;
                }
    
                $self->start_element( { 'Name' => 'Hit' } );
                $self->element(
                    {
                        'Name' => 'Hit_len',
                        'Data' => $len
                    }
                );
                my ( $id, $desc ) = split( /\s+/, $hit_id, 2 );
                $self->element(
                    {
                        'Name' => 'Hit_id',
                        'Data' => $id
                    }
                );
    
                #$self->debug("Hit ID is $id\n");
                my @pieces = split( /\|/, $id );
                my $acc = pop @pieces;
                $acc =~ s/\.\d+$//;
                $self->element(
                    {
                        'Name' => 'Hit_accession',
                        'Data' => $acc
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hit_def',
                        'Data' => $desc
                    }
                );
            }
	    else {
#		push @{$hit_signifs[0]->{HSPs}}, $current_hsp;
	    }


            $_ = $self->_readline();
            my ( $score, $bits, $e, $e2 ) = /Z-score: \s* (\S+) \s*
                               (?: bits: \s* (\S+) \s+ )?
                               (?: E|expect ) \s* \((?:\d+)?\) :? \s*(\S+)
                               (?: \s* E2 \s* \(\) :? \s*(\S+) )?
                               /ox;
            $bits = $score unless defined $bits;

            my ($v);

	    if ($firstHSP && !$m9HSP) {
	      $v = shift @{$hit_signifs[0]->{HSPs}}
		if (@hit_signifs && @{$hit_signifs[0]->{HSPs}});
	      $current_hsp = $v;
	    }
	    else {
	      $v = $current_hsp;
	    }

            if ( defined $v ) {
                @{$v}{qw(evalue evalue2 bits z-sc)} = ( $e, $e2, $bits, $score );
            }

            if ($firstHSP) {
                $self->element(
                    {
                        'Name' => 'Hit_signif',
                        'Data' => $v ? $v->{evalue} : $e
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hit_score',
                        'Data' => $v ? $v->{bits} : $bits
                    }
                );
            }
            
            $self->start_element( { 'Name' => 'Hsp' } );

            $self->element(
                {
                    'Name' => 'Hsp_score',
                    'Data' => $v ? $v->{'z-sc'} : $score
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_evalue',
                    'Data' => $v ? $v->{evalue} : $e
                }
            );
            $self->element(
                {
                    'Name' => 'Hsp_evalue2',
                    'Data' => $v && exists($v->{evalue2}) ? $v->{evalue2} : $e2
                }
            ) if (($v && exists($v->{evalue2})) || defined $e2);

            $self->element(
                {
                    'Name' => 'Hsp_bit-score',
                    'Data' => $v ? $v->{bits} : $bits
                }
            );
            $_ = $self->_readline();

            if (s/global\/.* score:\s*(\d+)\;?//) {
                $self->element(
                    {
                        'Name' => 'Hsp_sw-score',
                        'Data' => $1
                    }
                );
            }
            if (s/Smith-Waterman score:\s*(\d+)\;?//) {
                $self->element(
                    {
                        'Name' => 'Hsp_sw-score',
                        'Data' => $1
                    }
                );
            }
            if (
                / (\d*\.?\d+)\% \s* identity
                 (?:\s* \(\s*(\S+)\% \s* (?:ungapped|similar) \) )?
                 \s* in \s* (\d+) \s+ (?:aa|nt) \s+ overlap \s*
                 \( (\d+) \- (\d+) : (\d+) \- (\d+) \)
               /x
              )
            {
                my ( $identper, $gapper, $len, $querystart, $queryend,
                    $hitstart, $hitend )
                  = ( $1, $2, $3, $4, $5, $6, $7 );
                my $ident = sprintf( "%.0f", ( $identper / 100 ) * $len );
                my $positive = sprintf( "%.0f", ( $gapper / 100 ) * $len );

                $self->element(
                    {
                        'Name' => 'Hsp_identity',
                        'Data' => $ident
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hsp_positive',
                        'Data' => $positive
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hsp_align-len',
                        'Data' => $len
                    }
                );

                $self->element(
                    {
                        'Name' => 'Hsp_query-from',
                        'Data' => $querystart
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hsp_query-to',
                        'Data' => $queryend
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hsp_hit-from',
                        'Data' => $hitstart
                    }
                );
                $self->element(
                    {
                        'Name' => 'Hsp_hit-to',
                        'Data' => $hitend
                    }
                );

            }

            if ($v) {
                $self->element(
                    { 'Name' => 'Hsp_querygaps', 'Data' => $v->{qgaps} } )
                  if exists $v->{qgaps};
                $self->element(
                    { 'Name' => 'Hsp_hitgaps', 'Data' => $v->{lgaps} } )
                  if exists $v->{lgaps};

                if ( $self->{'_reporttype'} =~ m/^FAST[NXY]$/o ) {
                    if ( 8 == scalar grep { exists $v->{$_} }
                        qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) )
                    {
                        if ( $v->{ax0} < $v->{an0} ) {
                            $self->element(
                                {
                                    'Name' => 'Hsp_query-frame',
                                    'Data' =>
                                      "-@{[(($v->{px0} - $v->{ax0}) % 3) + 1]}"
                                }
                            );
                        }
                        else {
                            $self->element(
                                {
                                    'Name' => 'Hsp_query-frame',
                                    'Data' =>
                                      "+@{[(($v->{an0} - $v->{pn0}) % 3) + 1]}"
                                }
                            );
                        }
                        if ( $v->{ax1} < $v->{an1} ) {
                            $self->element(
                                {
                                    'Name' => 'Hsp_hit-frame',
                                    'Data' =>
                                      "-@{[(($v->{px1} - $v->{ax1}) % 3) + 1]}"
                                }
                            );
                        }
                        else {
                            $self->element(
                                {
                                    'Name' => 'Hsp_hit-frame',
                                    'Data' =>
                                      "+@{[(($v->{an1} - $v->{pn1}) % 3) + 1]}"
                                }
                            );
                        }
                    }
                    else {
                        $self->element(
                            {
                                'Name' => 'Hsp_query-frame',
                                'Data' => $v->{lframe}
                            }
                        );
                        $self->element(
                            { 'Name' => 'Hsp_hit-frame', 'Data' => 0 } );
                    }
                }
                else {
                    $self->element(
                        { 'Name' => 'Hsp_query-frame', 'Data' => 0 } );
                    $self->element(
                        { 'Name' => 'Hsp_hit-frame', 'Data' => $v->{lframe} } );
                }

            }
            else {
                $self->warn("unable to parse FASTA score line: $_");
            }
        }
        elsif (/\d+\s*residues\s*in\s*\d+\s*query\s*sequences/) {
            if ( $self->in_element('hsp') ) {
                $self->end_element( { 'Name' => 'Hsp' } );
            }
            if ( $self->in_element('hit') ) {
                $self->end_element( { 'Name' => 'Hit' } );
                shift @hit_signifs if @hit_signifs;

            }

           #       $_ = $self->_readline();
           #       my ( $liblen,$libsize) = /(\d+)\s+residues\s*in(\d+)\s*library/;
           # fast forward to the end of the file as there is
           # nothing else left to do with this file and want to be sure and
           # reset it
            while ( defined( $_ = $self->_readline() ) ) {
                last if (/^Function used was/);
                if (
                    /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?
           sequence/oxi || /(\S+)\s+compares\s+a/oi
                  )
                {
                    $self->_pushback($_);
                }
            }

            $self->_processHits(@hit_signifs) if @hit_signifs;
            
            $self->end_element( { 'Name' => 'FastaOutput' } );
            return $self->end_document();
        }
        elsif (/^\s*\d+\s*>>>/) {
            if ( $self->within_element('FastaOutput') ) {
                if ( $self->in_element('hsp') ) {
                    $self->end_element( { 'Name' => 'Hsp' } );
                }
                if ( $self->in_element('hit') ) {
                    $self->end_element( { 'Name' => 'Hit' } );
                    shift @hit_signifs if @hit_signifs;

                }

                $self->_processHits(@hit_signifs) if (@hit_signifs);
                
                $self->end_element( { 'Name' => 'FastaOutput' } );
                $self->_pushback($_);
                return $self->end_document();
            }
            else {
                $self->start_element( { 'Name' => 'FastaOutput' } );
                $self->{'_result_count'}++;
                $seentop = 1;
                $self->element(
                    {
                        'Name' => 'FastaOutput_program',
                        'Data' => $self->{'_reporttype'}
                    }
                );
                $self->element(
                    {
                        'Name' => 'FastaOutput_version',
                        'Data' => $self->{'_version'}
                    }
                );

                my ( $type, $querylen, $querytype, $querydef );

                if (/^\s*\d+\s*>>>(.*)/) {
                    $querydef = $1;
                    if ( $querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o )
                    {
                        ( $querydef, $querylen, $querytype ) = ( $1, $2, $3 );
                    }
                }

                if (   $self->{'_reporttype'}
                    && $self->{'_reporttype'} eq 'FASTA' )
                {
                    if ( $querytype eq 'nt' ) {
                        $self->{'_reporttype'} = 'FASTN';
                    }
                    elsif ( $querytype eq 'aa' ) {
                        $self->{'_reporttype'} = 'FASTP';
                    }
                }
                my ( $name, $descr ) =
                  ( $querydef =~ m/^(\S+)(?:\s+(.*))?\s*$/o );
                $self->element(
                    {
                        'Name' => 'FastaOutput_query-def',
                        'Data' => $name
                    }
                );
                $self->element(
                    {
                        'Name' => 'FastaOutput_querydesc',
                        'Data' => $descr
                    }
                );
                if ($querylen) {
                    $self->element(
                        {
                            'Name' => 'FastaOutput_query-len',
                            'Data' => $querylen
                        }
                    );
                }
                else {
                    $self->warn("unable to find and set query length");
                }
                if ( defined( $_ = $self->_readline() )
                    && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ ) )
                {
                    $self->element(
                        {
                            'Name' => 'FastaOutput_db',
                            'Data' => $1
                        }
                    );
                }

            }
        }
        elsif ( $self->in_element('hsp') ) {
            my @data  = ( [], [], [] );
            my $count = 0;
            my $len   = $self->idlength + 1;
            my ($seq1_id);
            while ( defined($_) ) {
                chomp;
                #$self->debug("$count $_\n");
                if (/residues in \d+\s+query\s+sequences/o) {
                    $self->_pushback($_);
                    last;
                }
                elsif (/^>>>\*\*\*/o) {
                    $self->end_element( { Name => "Hsp" } );
                    last;
                }
                elsif (/^>>/o) {
                    $self->_pushback($_);
                    last;
                }
                elsif (/^\s*\d+\s*>>>/o) {
                    $self->_pushback($_);
                    last;
                }
                if ( $count == 0 ) {
                    if (/^(\S+)\s+/) {
                        $self->_pushback($_);
                        $count = 2;
                    }
                    elsif ( /^\s+\d+/ || /^\s+$/ ) {

                        # do nothing, this is really a 0 line
                    }
                    elsif ( length($_) == 0 ) {
                        $count = -1;
                    }
                    else {
                        $self->_pushback($_);
                        $count = 0;
                    }
                }
                elsif ( $count == 1 || $count == 3 ) {
                    if (/^(\S+)\s+/) {
                        $len = CORE::length($1) if $len < CORE::length($1);
                        s/\s+$//;    # trim trailing spaces,we don't want them
                        push @{ $data[ $count - 1 ] }, substr( $_, $len );
                    }
                    elsif (/^\s+(\d+)/) {
                        $count = -1;
                        $self->_pushback($_);
                    }
                    elsif ( /^\s+$/ || length($_) == 0 ) {
                        $count = 5;

                        # going to skip these
                    }
                    elsif ( /\s+\S+fasta3\d\s+/) {
                        # this is something that looks like a path but contains
                        # the fasta3x executable string, such as:
                        # /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i test.fa ../other_mirs.fa -O test.fasta35
                        last;
                    }
                    else {
                        $self->throw(
                            "Unrecognized alignment line ($count) '$_'");
                    }
                }
                elsif ( $count == 2 ) {
                    if (/^\s+\d+\s+/) {
                        $self->warn("$_\n") if $self->verbose > 0;

                        # we are on a Subject part of the alignment
                        # but we THOUGHT we were on the Query
                        # move that last line to the proper place
                        push @{ $data[2] }, pop @{ $data[0] };
                        $count = 4;
                    }
                    else {

                        # toss the first IDLENGTH characters of the line
                        if ( length($_) >= $len ) {
                            push @{ $data[ $count - 1 ] }, substr( $_, $len );
                        }
                    }
                }
                last if ( $count++ >= 5 );
                $_ = $self->_readline();
            }
            if ( @{ $data[0] } || @{ $data[2] } ) {
                $self->characters(
                    {
                        'Name' => 'Hsp_qseq',
                        'Data' => join( '', @{ $data[0] } )
                    }
                );
                $self->characters(
                    {
                        'Name' => 'Hsp_midline',
                        'Data' => join( '', @{ $data[1] } )
                    }
                );
                $self->characters(
                    {
                        'Name' => 'Hsp_hseq',
                        'Data' => join( '', @{ $data[2] } )
                    }
                );
            }
        }
        else {
            if ( !$seentop ) {
                $self->debug($_);
                #$self->warn("unrecognized FASTA Family report file!");
                #return;
            }
        }
    }
    if ( $self->in_element('result') ) {
        if ( $self->in_element('hsp') ) {
            $self->end_element( { 'Name' => 'Hsp' } );
        }
        if ( $self->in_element('hit') ) {
            $self->end_element( { 'Name' => 'Hit' } );
            shift @hit_signifs if @hit_signifs;
        }
        $self->end_element( { 'Name' => 'FastaOutput' } );
    }
    return $self->end_document();

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

    # we currently don't care about attributes
    my $nm = $data->{'Name'};
    if ( my $type = $MODEMAP{$nm} ) {
        $self->_mode($type);
        if ( my $handler = $self->_will_handle($type) ) {
            my $func = sprintf( "start_%s", lc $type );
            $handler->$func( $data->{'Attributes'} );
        }
        unshift @{ $self->{'_elements'} }, $type;
    }
    if ( $nm eq 'FastaOutput' ) {
        $self->{'_values'} = {};
        $self->{'_result'} = undef;
        $self->{'_mode'}   = '';
    }

    my ( $self, $data ) = @_;
    my $nm = $data->{'Name'};
    my $rc;

    # Hsp 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)) {
            $self->element(
                {
                    'Name' => $_,
                    'Data' => $self->{'_last_hspdata'}->{$_}
                }
            );
        }
        $self->{'_last_hspdata'} = {};
    }

    if ( my $type = $MODEMAP{$nm} ) {
        if ( my $handler = $self->_will_handle($type) ) {
            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 ) {
            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->warn("unknown nm $nm, ignoring\n");
    }
    $self->{'_last_data'} = '';    # remove read data if we are at
                                   # end of an element
    $self->{'_result'} = $rc if ( $nm eq 'FastaOutput' );
    return $rc;

    my ( $self, $data ) = @_;
    $self->start_element($data);
    $self->characters($data);
    $self->end_element($data);

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

    return unless ( defined $data->{'Data'} );
    if ( $data->{'Data'} =~ /^\s+$/ ) {
        return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
    }

    if (   $self->in_element('hsp')
        && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ )
    {

        $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'};
    }

    $self->{'_last_data'} = $data->{'Data'};

    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_mode'} = $value;
    }
    return $self->{'_mode'};

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

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

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

    my ( $self, @args ) = @_;
    return $self->{'_result'};

    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_idlength'} = $value;
    }
    return $self->{'_idlength'} || $IDLENGTH;

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

    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, $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, @hit_signifs) = @_;

  # process remaining best hits
  for my $hit (@hit_signifs) {

    # Hsp_score Hsp_evalue Hsp_bit-score
    # Hsp_sw-score Hsp_gaps Hsp_identity Hsp_positive
    # Hsp_align-len Hsp_query-from Hsp_query-to
    # Hsp_hit-from Hsp_hit-to Hsp_qseq Hsp_midline

    $self->start_element( { 'Name' => 'Hit' } );
    $self->element(
		   {
		    'Name' => 'Hit_len',
		    'Data' => $hit->{hit_len}
		   }
		  ) if exists $hit->{hit_len};
    $self->element(
		   {
		    'Name' => 'Hit_id',
		    'Data' => $hit->{id}
		   }
		  ) if exists $hit->{id};
    $self->element(
		   {
		    'Name' => 'Hit_accession',
		    'Data' => $hit->{acc}
		   }
		  ) if exists $hit->{acc};
    $self->element(
		   {
		    'Name' => 'Hit_def',
		    'Data' => $hit->{desc}
		   }
		  ) if exists $hit->{desc};
    $self->element(
		   {
		    'Name' => 'Hit_signif',
		    'Data' => $hit->{evalue}
		   }
		  ) if exists $hit->{evalue};
    $self->element(
		   {
		    'Name' => 'Hit_score',
		    'Data' => $hit->{bits}
		   }
		  ) if exists $hit->{bits};

    for my $hsp (@{$hit->{HSPs}}) {

      $self->start_element( { 'Name' => 'Hsp' } );
      $self->element({'Name' => 'Hsp_score', 'Data' => $hsp->{'z-sc'}})
	if exists $hsp->{'z-sc'};
      $self->element({'Name' => 'Hsp_evalue', 'Data' => $hsp->{evalue} } )
	if exists $hsp->{evalue};
      $self->element({'Name' => 'Hsp_evalue2', 'Data' => $hsp->{evalue2} } )
	if exists $hsp->{evalue2};

      $self->element({'Name' => 'Hsp_bit-score', 'Data' => $hsp->{bits} } )
	if exists $hsp->{bits};
      $self->element({'Name' => 'Hsp_sw-score', 'Data' => $hsp->{'n-w'} } )
	if exists $hsp->{'n-w'};
      $self->element({'Name' => 'Hsp_sw-score', 'Data' => $hsp->{sw} } )
	if exists $hsp->{sw};
      $self->element({'Name' => 'Hsp_gaps', 'Data' => $hsp->{'%_gid'} } )
	if exists $hsp->{'%_gid'};
      $self->element({
		      'Name' => 'Hsp_identity',
		      'Data' =>
		      sprintf( "%.0f", $hsp->{'%_id'} * $hsp->{alen} )
		     }) if ( exists $hsp->{'%_id'} && exists $hsp->{alen} );

      if ( exists $hsp->{'%_gid'} ) {
	$self->element(
		       {
			'Name' => 'Hsp_positive',
			'Data' =>
			sprintf( "%.0f", $hsp->{'%_gid'} * $hsp->{alen} )
		       }
		      ) if exists $hsp->{'%_gid'} && exists $hsp->{alen};
      } else {
	$self->element(
		       {
			'Name' => 'Hsp_positive',
			'Data' =>
			sprintf( "%.0f", $hsp->{'%_id'} * $hsp->{alen} )
		       }
		      ) if ( exists $hsp->{'%_id'} && exists $hsp->{alen} );
      }

      $self->element(
		     {
		      'Name' => 'Hsp_align-len', 'Data' => $hsp->{alen} } )
	if exists $hsp->{alen};
      $self->element(
		     {
		      'Name' => 'Hsp_query-from', 'Data' => $hsp->{an0} } )
	if exists $hsp->{an0};
      $self->element(
		     {
		      'Name' => 'Hsp_query-to', 'Data' => $hsp->{ax0} } )
	if exists $hsp->{ax0};
      $self->element(
		     {
		      'Name' => 'Hsp_hit-from', 'Data' => $hsp->{an1} } )
	if exists $hsp->{an1};
      $self->element(
		     {
		      'Name' => 'Hsp_hit-to', 'Data' => $hsp->{ax1} } )
	if exists $hsp->{ax1};

      $self->element(
		     {
		      'Name' => 'Hsp_querygaps', 'Data' => $hsp->{qgaps} } )
	if exists $hsp->{qgaps};
      $self->element(
		     {
		      'Name' => 'Hsp_hitgaps', 'Data' => $hsp->{lgaps} } )
	if exists $hsp->{lgaps};

      if ( $self->{'_reporttype'} =~ m/^FAST[NXY]$/o ) {
	if ( 8 == scalar grep { exists $hsp->{$_} }
	     qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) {
	  if ( $hsp->{ax0} < $hsp->{an0} ) {
	    $self->element(
			   {
			    'Name' => 'Hsp_query-frame',
			    'Data' =>
			    "-@{[(($hsp->{px0} - $hsp->{ax0}) % 3) + 1]}"
			   }
			  );
	  } else {
	    $self->element(
			   {
			    'Name' => 'Hsp_query-frame',
			    'Data' =>
			    "+@{[(($hsp->{an0} - $hsp->{pn0}) % 3) + 1]}"
			   }
			  );
	  }
	  if ( $hsp->{ax1} < $hsp->{an1} ) {
	    $self->element(
			   {
			    'Name' => 'Hsp_hit-frame',
			    'Data' =>
			    "-@{[(($hsp->{px1} - $hsp->{ax1}) % 3) + 1]}"
			   }
			  );
	  } else {
	    $self->element(
			   {
			    'Name' => 'Hsp_hit-frame',
			    'Data' =>
			    "+@{[(($hsp->{an1} - $hsp->{pn1}) % 3) + 1]}"
			   }
		);
	  }
	} else {
	  $self->element(
			 {
			  'Name' => 'Hsp_query-frame',
			  'Data' => $hsp->{lframe}
			 }
			);
	  $self->element(
			 {
			  'Name' => 'Hsp_hit-frame', 'Data' => 0 } );
	}
      } else {
	$self->element(
		       {
			'Name' => 'Hsp_query-frame', 'Data' => 0 } );
	$self->element(
		       {
			'Name' => 'Hsp_hit-frame',
			'Data' => $hsp->{lframe}
		       }
		      );
      }

      $self->end_element( { 'Name' => 'Hsp' } );
    }

    $self->end_element( { 'Name' => 'Hit' } );

  }
}



1;

  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::fasta->new();
 Function: Builds a new Bio::SearchIO::fasta object 
 Returns : Bio::SearchIO::fasta
 Args    : -idlength - set ID length to something other 
                       than the default (6), this is only
                       necessary if you have compiled FASTA
                       with a new default id length to display
                       in the HSP alignment blocks