package dr.inference.model;

import dr.xml.*;

/**
 * @author Marc Suchard
 */
public class DuplicatedParameter extends Parameter.Abstract implements VariableListener {

    public static final String DUPLICATED_PARAMETER = "duplicatedParameter";
    public static final String COPIES = "copies";

    public DuplicatedParameter(Parameter parameter) {
        this.parameter = parameter;
        parameter.addVariableListener(this);
        copies = 1;
        originalBounds = parameter.getBounds();
        bounds = originalBounds;
    }

    public void addDuplicationParameter(Parameter dupParameter) {
        this.dupParameter = dupParameter;
        dupParameter.addParameterListener(this);
        updateDuplication();
    }

    private void updateDuplication() {
        copies = (int) dupParameter.getParameterValue(0);
        final int originalLength = originalBounds.getBoundsDimension();
        double[] lowers = new double[getDimension()];
        double[] uppers = new double[getDimension()];
        for(int i=0; i<originalLength; i++) {
            lowers[i] = originalBounds.getLowerLimit(i);
            uppers[i] = originalBounds.getUpperLimit(i);
        }
        for(int i=1; i<copies; i++) {
            System.arraycopy(lowers,0,lowers,i*originalLength,originalLength);
            System.arraycopy(uppers,0,uppers,i*originalLength,originalLength);
        }
        bounds = new DefaultBounds(uppers,lowers);
    }

    public int getDimension() {
        return parameter.getDimension() * copies;
    }

    protected void storeValues() {
        parameter.storeParameterValues();
    }

    protected void restoreValues() {
        parameter.restoreParameterValues();
    }

    protected void acceptValues() {
        parameter.acceptParameterValues();
    }

    protected void adoptValues(Parameter source) {
        parameter.adoptParameterValues(source);
    }

    public double getParameterValue(int dim) {
        return parameter.getParameterValue(dim % parameter.getDimension());
    }

    public void setParameterValue(int dim, double value) {
        parameter.setParameterValue(dim % parameter.getDimension(), value);
        fireParameterChangedEvent(dim, Parameter.ChangeType.VALUE_CHANGED);
    }

    public void setParameterValueQuietly(int dim, double value) {
        parameter.setParameterValueQuietly(dim % parameter.getDimension(), value);
    }

    public String getParameterName() {
        if (getId() == null)
            return "duplicated" + parameter.getParameterName();
        return getId();
    }

    public void addBounds(Bounds bounds) {
        throw new RuntimeException("Not yet implemented.");
    }

    public Bounds<Double> getBounds() {
        return bounds;
    }

    public void addDimension(int index, double value) {
        throw new RuntimeException("Not yet implemented.");
    }

    public double removeDimension(int index) {
        throw new RuntimeException("Not yet implemented.");
    }

    public void variableChangedEvent(Variable variable, int index, ChangeType type) {
        if (variable == dupParameter) {
            updateDuplication();
        }
        // Values have changed, so notify listeners
        fireParameterChangedEvent();
    }

    public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {

        public Object parseXMLObject(XMLObject xo) throws XMLParseException {

            Parameter parameter = (Parameter) xo.getChild(Parameter.class);
            XMLObject cxo = xo.getChild(COPIES);
            Parameter dup = (Parameter) cxo.getChild(Parameter.class);

            DuplicatedParameter duplicatedParameter = new DuplicatedParameter(parameter);
            duplicatedParameter.addDuplicationParameter(dup);

            return duplicatedParameter;
        }

        public XMLSyntaxRule[] getSyntaxRules() {
            return rules;
        }

        private final XMLSyntaxRule[] rules = {
                new ElementRule(Parameter.class),
                new ElementRule(COPIES,
                        new XMLSyntaxRule[]{
                                new ElementRule(Parameter.class)
                        }),
        };

        public String getParserDescription() {
            return "A duplicated parameter.";
        }

        public Class getReturnType() {
            return Parameter.class;
        }

        public String getParserName() {
            return DUPLICATED_PARAMETER;
        }
    };

    private final Parameter parameter;
    private Parameter dupParameter;
    private int copies;
    private Bounds<Double> bounds;
    private final Bounds<Double> originalBounds;

}

@@ -2387,32 +2387,205 @@
  value);%0A    %7D%0A%0A
+    public void setParameterValueNotifyChangedAll(int dim, double value)%7B%0A        parameter.setParameterValueNotifyChangedAll(dim %25 parameter.getDimension(), value);%0A    %7D%0A%0A
     public Strin

add setParameterValueNotifyChangedAll method.