require Bio::Tools::SeqAnal;

    $hit = new Bio::Tools::SeqAnal ( -run   => \%runParams,
				     -parse => 1);

    $hit = new Bio::Tools::SeqAnal ( -file  => 'filename.data',
				     -parse => 1);

    $hit = new Bio::Tools::SeqAnal ( -run   => \%runParams
				     );

    $hit = new Bio::Tools::SeqAnal ( -file  => 'filename.data',
				     -read  => 1);

#------------------
    my( $self, $OUT) = @_;

    print $OUT scalar($self->read);
    1;

#--------------------
    my( $self, $OUT ) = @_;

    printf( $OUT "\n%-15s: %s\n", "QUERY NAME", $self->query ||'UNKNOWN' );
    printf( $OUT "%-15s: %s\n", "QUERY DESC", $self->query_desc || 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "LENGTH", $self->length || 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "FILE", $self->file || 'STDIN');
    printf( $OUT "%-15s: %s\n", "DATE", $self->date || 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "PROGRAM", $self->program || 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "VERSION", $self->program_version || 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "DB-NAME", $self->database || 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "DB-RELEASE", ($self->database_release || 'UNKNOWN'));
    printf( $OUT "%-15s: %s\n", "DB-LETTERS", ($self->database_letters) ? $self->database_letters : 'UNKNOWN');
    printf( $OUT "%-15s: %s\n", "DB-SEQUENCES", ($self->database_seqs) ? $self->database_seqs : 'UNKNOWN');
}


#####################################################################################
##                                 VIRTUAL METHODS                                 ##
#####################################################################################

#-----------------
    my( $self, %param ) = @_;

    my $make = $self->SUPER::_initialize(%param);

    my($read, $parse, $runparam) = (
	($param{-READ}||$param{'-read'}), ($param{-PARSE}||$param{'-parse'}),
	($param{-RUN}||$param{'-run'})
				    );

#	$self->_rearrange([qw(READ PARSE RUN)], @param);
	
    # Issue: How to keep all the arguments for running the analysis
    # separate from other arguments needed for parsing the results, etc?
    # Solution: place all the run arguments in a separate hash.

    $self->run(%$runparam) if ref $runparam eq 'HASH';

    if($parse) { $self->parse(%param); }
    elsif($read) { $self->read(%param) }

    $make;
}

#--------------

#-------------------
    my ($self, %param) = @_;

    $self->{'_db'}        ||= $param{-NAME}    || '';
    $self->{'_dbRelease'}   = $param{-RELEASE} || '';
    ($self->{'_dbLetters'}  = $param{-LETTERS} || 0)  =~ s/,//g;
    ($self->{'_dbSeqs'}     = $param{-SEQS}    || 0) =~ s/,//g;

#----------
    my $self = shift;
    if(@_) { $self->{'_best'} = shift; }
    $self->{'_best'};

#---------------
    my $self = shift;
    if(@_) { $self->{'_db'} = shift; }
    $self->{'_db'};

#----------------------
    my $self = shift;
    if(@_) { $self->{'_dbLetters'} = shift; }
    $self->{'_dbLetters'};

#-----------------------
    my $self = shift;
    if(@_) { $self->{'_dbRelease'} = shift; }
    $self->{'_dbRelease'};

#------------------
    my $self = shift;
    if(@_) { $self->{'_dbSeqs'} = shift; }
    $self->{'_dbSeqs'};

  my $self = shift;  $self->{'_date'};

#--------------
    my $self=shift;
    $DEBUG==2 && print STDERR "DESTROYING $self ${\$self->name}";
    undef $self->{'_rawData'};
    $self->SUPER::destroy;
}


###############################################################################
#                                 ACCESSORS
###############################################################################

# The mode of the SeqAnal object is no longer explicitly set.
# This simplifies the interface somewhat.

##----------------------------------------------------------------------
#=head2 mode()

# Usage     : $object->mode();
#	    :
# Purpose   : Set/Get the mode for the sequence analysis object.
#	    :
# Returns   : String
#	    :
# Argument  : n/a
#	    :
#	    :
# Comments  : The mode specifies how much detail to extract from the
#	    : sequence analysis report. There are three modes:
#	    :
#	    :    'parse' -- Parse the sequence analysis output data.
#	    :
#	    :     'read' -- Reads in the raw report but does not
#	    :               attempt to parse it. Useful when you just
#	    :               want to work with the output as-is
#	    :               (e.g., create HTML-formatted output).
#	    :
#	    :     'run'  -- Generates a new report.
#	    :
#	    : Allowable modes are defined by the exported package global array
#	    : @SeqAnal_modes.
#
#See Also   : _set_mode()
#=cut
##----------------------------------------------------------------------
#sub mode {
#    my $self = shift;
#    if(@_) { $self->{'_mode'} = lc(shift); }
#    $self->{'_mode'};
#}
#

#---------------
    my( $self, %param ) = @_;

    $self->SUPER::display(%param);

    my $OUT = $self->fh();
    $self->show =~ /file/i and $self->_display_file($OUT);
    1;

#------------
    my $self = shift;
    if(@_) { $self->{'_length'} = shift; }
    $self->{'_length'};

#---------
    my ($self, @param) = @_;

    $self->throw("Virtual method parse() not defined ${ref($self)} objects.");

    # The first step in parsing is reading in the data:
    $self->read(@param);

#-------------
    my $self = shift;
    if(@_) { $self->{'_prog'} = shift; }
    $self->{'_prog'};

#---------------------
    my $self = shift;
    if(@_) { $self->{'_progVersion'} = shift; }
    $self->{'_progVersion'};

 my $self = shift; $self->name;

#--------------
    my $self = shift;
    if(@_) { $self->{'_qDesc'} = shift; }
    $self->{'_qDesc'};

#--------
    my ($self, %param) = @_;
    $self->throw("Virtual method run() not defined ${ref($self)} objects.");
}


1;
__END__

#####################################################################################
#                                END OF CLASS                                       #
#####################################################################################

#---------------
    my $self = shift;
    my $date = shift;
    my ($file);

    if( !$date and ($file = $self->file)) {
	# If no date is passed and a file exists, determine date from the file.
	# (provided by superclass Bio::Root::Object.pm)
	eval {
	    $date = $self->SUPER::file_date(-FMT => 'd m y');
	};
	if($@) {
	    $date = 'UNKNOWN';
	    $self->warn("Can't set date of report.");
	}
    }
    $self->{'_date'} = $date;

   http://bio.perl.org/Core/Latest
   ftp://bio.perl.org/pub/DIST

  MODE      DESCRIPTION
  -----     -----------
  run       Run a new sequence analysis report. New results can then
            be parsed or saved for analysis later.

  parse     Parse the data from a sequence analysis report loading it
            into the SeqAnal.pm object.

  read      Read in data from an existing raw analysis report without
            parsing it. In the future, this may also permit persistent
            SeqAnal.pm objects. This mode is considered experimental.

    bioperl-l@bioperl.org          - General discussion
    http://bio.perl.org/MailList.html             - About the mailing lists

    bioperl-bugs@bio.perl.org
    http://bugzilla.bioperl.org/

 http://bio.perl.org/Projects/modules.html  - Online module documentation
 http://bio.perl.org/Projects/Blast/        - Bioperl Blast Project
 http://bio.perl.org/                       - Bioperl Project Homepage

 FIELD           VALUE
 --------------------------------------------------------------
  _file            Full path to file containing raw sequence analysis report.

  _mode            Affects how much detail to extract from the raw report.
 		   Future mode will also distinguish 'running' from 'parsing'

 THE FOLLOWING MAY BE EXTRACTABLE FROM THE RAW REPORT FILE:

  _prog            Name of the sequence analysis program.

  _progVersion     Version number of the program.

  _db              Database searched.

  _dbRelease       Version or date of the database searched.

  _dbLetters       Total number of letters in the database.

  _dbSequences     Total number of sequences in the database.

  _query           Name of query sequence.

  _length          Length of the query sequence.

  _date            Date on which the analysis was performed.

  INHERITED DATA MEMBERS

  _name            From Bio::Root::Object.pm. String representing the name of the query sequence.
 		   Typically obtained from the report file.

  _parent          From Bio::Root::Object.pm. This member contains a reference to the
 		   object to which this seq anal report belongs. Optional & experimenta.
                   (E.g., a protein object could create and own a Blast object.)