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# transforms the string of target cuis to an array
# input:  none
# output: an array ref of CUIs
sub _getTargetCuis {
    my $self = shift;
    my @targetCuis = split(',',$lbdOptions{'targetCuis'});
    return \@targetCuis;
}

# transforms the string of accept types or groups into a hash of accept TUIs
# input:  a string specifying whether linking or target types are being defined
# output: a hash of acceptable TUIs
sub _getAcceptTypes {
    my $self = shift;
    my $stepString = shift; #either 'linking' or 'target'

    #get the accept types 
    my %acceptTypes = ();

    #add all types for groups specified
    my $string = $stepString.'AcceptGroups';
    if (defined $lbdOptions{$string}) {
	#accept groups were specified
	my @acceptGroups = split(',',$lbdOptions{$string});

	#add all the types of each group
	foreach my $group(@acceptGroups) {
	    my $typesRef = Filters::getTypesOfGroup($group, $umls_interface);
	    foreach my $key(keys %{$typesRef}) {
		$acceptTypes{$key} = 1;
	    }
	}
    }

    #add all types specified
    $string = $stepString.'AcceptTypes';
    if (defined $lbdOptions{$string}) {
	#convert each type to a tui and add
	my $tui;
	my @acceptTypes = split(',',$lbdOptions{$string});
	foreach my $abr(@acceptTypes) {
	    $tui = uc $umls_interface->getStTui($abr);
	    $acceptTypes{$tui} = 1;
	}
    }
    
    return \%acceptTypes;
}



##############################################################################
#        function to produce output
##############################################################################
# outputs the implicit terms to string
# input:  $scoresRef <- a reference to a hash of scores (hash{CUI}=score)
#         $ranksRef <- a reference to an array of CUIs ranked by their score
#         $printTo <- optional, outputs the $printTo top ranked terms. If not
#                     specified, all terms are output
# output: a line seperated string containing ranked terms, scores, and thier
#         preferred terms
sub _rankedTermsToString {
    my $self = shift;
    my $scoresRef = shift;
    my $ranksRef = shift;
    my $printTo = shift;

    #set printTo
    if (!$printTo) {
	$printTo = scalar @{$ranksRef};
    }
    
    #construct the output string
    my $string = '';
    my $index;
    for (my $i = 0; $i < $printTo; $i++) {
	#add the rank
	$index = $i+1;
	$string .= "$index\t";
	#add the score
	$string .= sprintf "%.5f\t", "${$scoresRef}{${$ranksRef}[$i]}\t";
	#add the CUI
	$string .= "${$ranksRef}[$i]\t";
	#add the name
	my $name = $umls_interface->getPreferredTerm(${$ranksRef}[$i]);
	#if no preferred name, get anything
	if (!defined $name || $name eq '') {
	    my $termListRef = $umls_interface->getTermList('C0440102');
	    if (scalar @{$termListRef} > 0) {
		$name = '.**'.${$termListRef}[0];
	    }
	}

	$string .= "$name\n";
    }

    #return the string of ranked terms
    return $string;
}

# converts the current objects parameters to a string
# input : none
# output: a string of parameters that were used for LBD
sub _parametersToString {
    my $self = shift;
        
    #LBD options
    my $paramsString = "Parameters:\n";
    foreach my $key (sort keys %lbdOptions) {
	$paramsString .= "$key -> $lbdOptions{$key}\n";
    }
    $paramsString .= "\n";
    return $paramsString;
    #association options? TODO
    #interface options? TODO
}


# returns the version currently being used
# input : none
# output: the version number being used
sub version {
    my $self = shift;
    return $VERSION;
}

##############################################################################
#        functions for debugging
##############################################################################
=comment
sub debugLBD {
    my $self = shift;
    my $startingCuisRef = shift;

    print "Starting CUIs = ".(join(',', @{$startingCuisRef}))."\n";

#Get the Explicit Matrix
    my ($explicitMatrixRef, $cuiToIndexRef, $indexToCuiRef, $matrixSize) = 
	Discovery::tableToSparseMatrix('N_11', $cuiFinder);
    print "Explicit Matrix:\n";
    _printMatrix($explicitMatrixRef, $matrixSize, $indexToCuiRef);
    print "-----------------------\n";

#Get the Starting Matrix
    my $startingMatrixRef = 
	Discovery::getRows($startingCuisRef, $explicitMatrixRef);