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sub thread_summary($$) {
  my ($self,$seqID,$s,$secondaryStructure,$templateSet,$templates,$alignmentType,$calculateZscores) = @_;

  my $opts = &_parseOptions($templateSet,$templates,$alignmentType,$calculateZscores);

  # use LocalClient to do the work
  my $LocalClient = new Bio::Prospect::LocalClient( {options=>$opts} );
  my $seq = new Bio::Seq( -display_id => $seqID, -seq => $s );
  my @threads = $LocalClient->thread_summary( $seq );

  return( \@threads );
}


#-------------------------------------------------------------------------------
# xml()
#-------------------------------------------------------------------------------

=head2 thread()

 Name:      xml()
 Purpose:   thread a sequence using Bio::Prospect::LocalClient
 Arguments: comma-separated list:
    0 - string containing sequence id
    1 - string, contains protein sequence (or '' if secondary structure is
        defined in #2)
    2 - string, contains secondary structure information in phd format
        (or '' if sequence is defined in #1)
    3 - string, one of 'scop', 'fssp', 'all' (or '' if templates is defined in #4)
        to define a template set
    4 - string, contains a space-separated list of templates (or '' if
        template set is defined in #3)
    5 - string, one of 'global' or 'global_local' for alignment type
    6 - string, either '0' (false) or '1' (true) for calculating zscores
 Returns:   XML string containing prospect results

=cut

sub xml($$) {
  my ($self,$seqID,$s,$secondaryStructure,$templateSet,$templates,$alignmentType,$calculateZscores) = @_;

  my $opts = &_parseOptions($templateSet,$templates,$alignmentType,$calculateZscores);

  # use LocalClient to do the work
  my $LocalClient = new Bio::Prospect::LocalClient( {options=>$opts} );
  my $seq = new Bio::Seq( -display_id => $seqID, -seq => $s );
  my $xml = $LocalClient->xml( $seq );

  return( $xml );
}


#-------------------------------------------------------------------------------
# ping()
#-------------------------------------------------------------------------------

=head2 ping()

 Name:      ping()
 Purpose:   return whether alive or not
 Arguments: none
 Returns:   0 - dead, 1 - alive

=cut

sub ping {
  return 1;
}


#-------------------------------------------------------------------------------
# INTERNAL METHODS: not intended for use outside this module
#-------------------------------------------------------------------------------

=pod

=head1 INTERNAL METHODS & ROUTINES

The following functions are documented for developers' benefit.  THESE
SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE.  YOU'VE BEEN WARNED.

=cut

#-------------------------------------------------------------------------------
# _parseOption()
#-------------------------------------------------------------------------------

=head2 _parseOption()

 Name:      _parseOption()
 Purpose:   parse arguments to the thread, thread_summary, and xml() methods
 Arguments: comma-separated list:
    1 - string, one of 'scop', 'fssp', 'all' (or '' if templates is defined in #4)
        to define a template set
    2 - string, contains a space-separated list of templates (or '' if
        template set is defined in #3)
    3 - string, one of 'global' or 'global_local' for alignment type
    4 - string, either '0' (false) or '1' (true) for calculating zscores
 Returns:   Bio::Prospect::Options object

=cut

sub _parseOptions {
  my ($templateSet,$templates,$alignmentType,$calculateZscores) = @_;

  # build Bio::Prospect::Options.  howto handle caching???
  my $opts = new Bio::Prospect::Options;

  $opts->{'templates'} = [ split /,/,$templates ] if defined $templates;
  $opts->{'zscore'} = $calculateZscores if defined $calculateZscores;
  $opts->{'global_local'} = ( defined $alignmentType ) ?  $alignmentType : '-global';
  $opts->{'svm'} = 1;
  $opts->{'seq'} = 1;

  return( $opts );
}


1;