/*
* MultivariateOUModelParser.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.glm;
//import dr.inference.glm.MultivariateOUModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.inference.glm.GeneralizedLinearModel;
import dr.inference.model.DesignMatrix;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.inferencexml.glm.GeneralizedLinearModelParser;
import dr.xml.*;
/**
*
*/
//public class MultivariateOUModelParser extends AbstractXMLObjectParser {
//
// public static final String MVOU_MODEL = "multivariateOUModel";
// public static final String MVOU_TYPE = "MVOU";
// public static final String DATA = "data";
// public static final String TIME = "times";
// public static final String DESIGN = "design";
//
// public String getParserName() {
// return MVOU_MODEL;
// }
//
// public Object parseXMLObject(XMLObject xo) throws XMLParseException {
//
// SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
// Parameter effectParameter = (Parameter) ((XMLObject) xo.getChild(DATA)).getChild(Parameter.class);
// Parameter timesParameter = (Parameter) ((XMLObject) xo.getChild(TIME)).getChild(Parameter.class);
// Parameter designParameter = (Parameter) ((XMLObject) xo.getChild(DESIGN)).getChild(Parameter.class);
// MatrixParameter gammaParameter = (MatrixParameter) xo.getChild(MatrixParameter.class);
//
// if (effectParameter.getDimension() != timesParameter.getDimension() ||
// effectParameter.getDimension() != designParameter.getDimension()) {
//// System.err.println("dim(effect) " +effectParameter.getDimension());
//// System.err.println("dim(times) "+timesParameter.getDimension());
//// System.err.println("dim(design) "+designParameter.getDimension());
// throw new XMLParseException("dim(" + effectParameter.getStatisticName() +
// ") != dim(" + timesParameter.getStatisticName() + ") != dim(" + designParameter.getStatisticName() +
// ") in " + xo.getName() + " element");
// }
//
// MultivariateOUModel glm = new MultivariateOUModel(substitutionModel, effectParameter, gammaParameter,
// timesParameter.getParameterValues(), designParameter.getParameterValues());
//
// addIndependentParameters(xo, glm, effectParameter);
//
// // todo Confirm that design vector is consistent with substitution model
// // todo Confirm that design vector is ordered 1,\ldots,K,1,\ldots,K, etc.
//
// return glm;
//
// }
//
// public void addIndependentParameters(XMLObject xo, GeneralizedLinearModel glm,
// Parameter dependentParam) throws XMLParseException {
// int totalCount = xo.getChildCount();
//
// for (int i = 0; i < totalCount; i++) {
// if (xo.getChildName(i).compareTo(GeneralizedLinearModelParser.INDEPENDENT_VARIABLES) == 0) {
// XMLObject cxo = (XMLObject) xo.getChild(i);
// Parameter independentParam = (Parameter) cxo.getChild(Parameter.class);
// DesignMatrix designMatrix = (DesignMatrix) cxo.getChild(DesignMatrix.class);
// checkDimensions(independentParam, dependentParam, designMatrix);
// glm.addIndependentParameter(independentParam, designMatrix, null);
// }
// }
// }
//
// private void checkDimensions(Parameter independentParam, Parameter dependentParam, DesignMatrix designMatrix)
// throws XMLParseException {
// if ((dependentParam.getDimension() != designMatrix.getRowDimension()) ||
// (independentParam.getDimension() != designMatrix.getColumnDimension())) {
// System.err.println(dependentParam.getDimension());
// System.err.println(independentParam.getDimension());
// System.err.println(designMatrix.getRowDimension() + " rows");
// System.err.println(designMatrix.getColumnDimension() + " cols");
// throw new XMLParseException(
// "dim(" + dependentParam.getId() + ") != dim(" + designMatrix.getId() + " %*% " + independentParam.getId() + ")"
// );
// }
// }
//
// //************************************************************************
// // AbstractXMLObjectParser implementation
// //************************************************************************
//
// public XMLSyntaxRule[] getSyntaxRules() {
// return rules;
// }
//
// private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
// new ElementRule(SubstitutionModel.class),
// new ElementRule(MatrixParameter.class),
// new ElementRule(DATA, new XMLSyntaxRule[]{
// new ElementRule(Parameter.class)}),
// new ElementRule(TIME, new XMLSyntaxRule[]{
// new ElementRule(Parameter.class)}),
// new ElementRule(DESIGN, new XMLSyntaxRule[]{
// new ElementRule(Parameter.class)}),
// new ElementRule(GeneralizedLinearModelParser.INDEPENDENT_VARIABLES,
// new XMLSyntaxRule[]{new ElementRule(MatrixParameter.class)}, 0, 3),
// };
//
// public String getParserDescription() {
// return "Describes a multivariate OU process";
// }
//
// public Class getReturnType() {
// return MultivariateOUModel.class;
// }
//}