/*
 * DiagonalMatrixParser.java
 *
 * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.inferencexml.model;

import dr.inference.model.DiagonalMatrix;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.xml.*;

/**
 *
 */
public class DiagonalMatrixParser extends AbstractXMLObjectParser {

    public final static String MATRIX_PARAMETER = "diagonalMatrix";

    public String getParserName() {
        return MATRIX_PARAMETER;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {


        Parameter diagonalParameter = (Parameter) xo.getChild(Parameter.class);

        return new DiagonalMatrix(diagonalParameter);
    }

    //************************************************************************
    // AbstractXMLObjectParser implementation
    //************************************************************************

    public String getParserDescription() {
        return "A diagonal matrix parameter constructed from its diagonals.";
    }

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

    private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
            new ElementRule(Parameter.class, 1, 1),
    };

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

@@ -1051,16 +1051,62 @@
 del;%0D%0A%0D%0A
+import dr.inference.model.CompoundParameter;%0D%0A
 import d
@@ -1140,16 +1140,16 @@
 atrix;%0D%0A
-
 import d
@@ -1395,16 +1395,73 @@
 atrix%22;%0D
+%0A    public final static String DIMENSION = %22dimension%22;%0D
 %0A%0D%0A    p
@@ -1693,24 +1693,521 @@
 .class);%0D%0A%0D%0A
+        final int dim = xo.getAttribute(DIMENSION, diagonalParameter.getDimension());%0D%0A        if (dim %3E diagonalParameter.getDimension() && diagonalParameter.getDimension() == 1) %7B%0D%0A            CompoundParameter newDiagonalParameter = new CompoundParameter(diagonalParameter.getParameterName());%0D%0A            for (int i = 0; i %3C dim; i++) %7B%0D%0A                newDiagonalParameter.addParameter(diagonalParameter);%0D%0A            %7D%0D%0A            diagonalParameter = newDiagonalParameter;%0D%0A        %7D%0D%0A%0D%0A
         retu
@@ -2736,16 +2736,16 @@
 ule%5B%5D%7B%0D%0A
-
         
@@ -2789,16 +2789,75 @@
 1, 1),%0D%0A
+            AttributeRule.newIntegerRule(DIMENSION, true)%0D%0A
     %7D;%0D%0A

allow DiagonalMatrixParser to construct single parameter diagonal matrix to match up old setup