use strict;
    use Bio::Index::Blast;
    my $index = new Bio::Index::Blast(-filename => $indexfile,
				      -write_flag => 1);
    $index->make_index($file1, $file2);

    my $data = $index->get_stream($id);

    my $bplite_report = $index->fetch_report($id);
    print "query is ", $bplite_report->query, "\n";
    while( my $sbjct = $bplite_report->nextSbjct ) {
	print $sbjct->name, "\n";
	while( my $hsp = $sbjct->nextHSP ) {
	    print "\t e-value ", $hsp->P,
	}
	print "\n";
    }

     $VERSION = 0.1;

    return $VERSION;

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

  my $self = $class->SUPER::new(@args);

    my ($self,$id) = @_;
    my $fh = $self->get_stream($id);
    my $report = new Bio::Tools::BPlite(-fh      => $fh,
					-noclose => 1);
    return $report;

    my( $self, $code ) = @_;
    
    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;

        if ($_[0] =~ /^\s*(\S+)/) {
        return $1;
    } else {
        return;
    }

    my( $self,
        $file, # File name
        $i,    # Index-number of file being indexed
        ) = @_;
    
    my( $begin,     # Offset from start of file of the start
                    # of the last found record.
        );

    open(BLAST, "<$file") or die("cannot open file $file\n");
    
    my (@data, @records);
    my $indexpoint = 0;
    my $lastline = 0;

    while(<BLAST> ) {	
	if( /(T)?BLAST[PNX]/ ) {
	    if( @data ) { 
		# if we have already read a report
		# then store the data for this report 
		# in the CURRENT index
		$self->_process_report($indexpoint, $i,join("",@data));
		
	    } # handle fencepost problem (beginning) 
	      # by skipping here when empty

	    # since we are at the beginning of a new report
	    # store this begin location for the next index	   
	    $indexpoint = $lastline;
	    @data = ();
	}
	push @data, $_;
	$lastline = tell(BLAST);
    }
    # handle fencepost problem (end)
    if( @data ) {
	$self->_process_report($indexpoint,$i,join("",@data));
    }

    my ($self,$begin,$i,$data) = @_;
    
    if( ! $data ) { 
	$self->warn("calling _process_report without a valid data string"); 
	return ; 
    }
    my $id_parser = $self->id_parser;

    my $datal = new IO::String($data);
    my $report = new Bio::Tools::BPlite(-fh      => $datal,
					-noclose => 1);
    
    my $query = $report->query;		
    foreach my $id (&$id_parser($query)) {
	print "id is $id, begin is $begin\n" if( $self->verbose > 0);
	$self->add_record($id, $i, $begin);
    }

  bioperl-l@bioperl.org            - General discussion
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  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

 Title   : filename
 Usage   : $value = $self->filename();
           $self->filename($value);
 Function: Gets or sets the name of the dbm index file.
 Returns : The current value of filename
 Args    : Value of filename if setting, or none if
           getting the value.

 Title   : write_flag
 Usage   : $value = $self->write_flag();
           $self->write_flag($value);
 Function: Gets or sets the value of write_flag, which
           is wether the dbm file should be opened with
           write access.
 Returns : The current value of write_flag (default 0)
 Args    : Value of write_flag if setting, or none if
           getting the value.

 Usage   : $value = $self->dbm_package();
           $self->dbm_package($value);

 Function: Gets or sets the name of the Perl dbm module used. 
           If the value is unset, then it returns the value of
           the package variable $USE_DBM_TYPE or if that is
           unset, then it chooses the best available dbm type,
           choosing 'DB_File' in preference to 'SDBM_File'. 
           Bio::Abstract::Index may work with other dbm file
           types.

 Returns : The current value of dbm_package
 Args    : Value of dbm_package if setting, or none if
           getting the value.

 Title   : get_stream
 Usage   : $stream = $index->get_stream( $id );
 Function: Returns a file handle with the file pointer
           at the approprite place

           This provides for a way to get the actual
           file contents and not an object 

           WARNING: you must parse the record deliminter
           *yourself*. Abstract wont do this for you 
           So this code

           $fh = $index->get_stream($myid);
           while( <$fh> ) {
              # do something
           }
           will parse the entire file if you don't put in
           a last statement in, like

           while( <$fh> ) {
              /^\/\// && last; # end of record
              # do something
           }

 Returns : A filehandle object
 Args    : string represents the accession number
 Notes   : This method should not be used without forethought

  Usage   : $index->open_dbm()
  Function: Opens the dbm file associated with the index
            object.  Write access is only given if explicitly
            asked for by calling new(-write => 1) or having set
            the write_flag(1) on the index object.  The type of
            dbm file opened is that returned by dbm_package(). 
            The name of the file to be is opened is obtained by
            calling the filename() method.

  Example : $index->_open_dbm()
  Returns : 1 on success

  Title   : _filename
  Usage   : $index->_filename( FILE INT )
  Function: Indexes the file
  Example : 
  Returns : 
  Args    :

  Title   : _file_handle
  Usage   : $fh = $index->_file_handle( INT )
  Function: Returns an open filehandle for the file
            index INT.  On opening a new filehandle it
            caches it in the @{$index->_filehandle} array.
            If the requested filehandle is already open,
            it simply returns it from the array.
  Example : $fist_file_indexed = $index->_file_handle( 0 );
  Returns : ref to a filehandle
  Args    : INT

  Title   : _file_count
  Usage   : $index->_file_count( INT )
  Function: Used by the index building sub in a sub class to
            track the number of files indexed.  Sets or gets
            the number of files indexed when called with or
            without an argument.
  Example : 
  Returns : INT
  Args    : INT

  Title   : add_record
  Usage   : $index->add_record( $id, @stuff );
  Function: Calls pack_record on @stuff, and adds the result
            of pack_record to the index database under key $id.
            If $id is a reference to an array, then a new entry
            is added under a key corresponding to each element
            of the array.
  Example : $index->add_record( $id, $fileNumber, $begin, $end )
  Returns : TRUE on success or FALSE on failure
  Args    : ID LIST

  Title   : pack_record
  Usage   : $packed_string = $index->pack_record( LIST )
  Function: Packs an array of scalars into a single string
            joined by ASCII 034 (which is unlikely to be used
            in any of the strings), and returns it. 
  Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
  Returns : STRING or undef
  Args    : LIST

  Title   : unpack_record
  Usage   : $index->unpack_record( STRING )
  Function: Splits the sting provided into an array,
            splitting on ASCII 034.
  Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} )
  Returns : A 3 element ARRAY
  Args    : STRING containing ASCII 034

 Title   : DESTROY
 Usage   : Called automatically when index goes out of scope
 Function: Closes connection to database and handles to
           sequence files
 Returns : NEVER
 Args    : NONE