/*
 * OldGLMSubstitutionModelParser.java
 *
 * Copyright (c) 2002-2016 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.evomodelxml.substmodel;

import dr.evolution.datatype.DataType;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.OldGLMSubstitutionModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evoxml.util.DataTypeUtils;
import dr.inference.distribution.GeneralizedLinearModel;
import dr.inference.distribution.LogLinearModel;
import dr.xml.*;

/**
 */
@Deprecated // This uses the old (deprecated) GLM stuff and is here for XML compatibility for now
// Only one of OldGLMSubstitutionModelParser and GLMSubstitutionModelParser should be in the parser list.
public class OldGLMSubstitutionModelParser extends AbstractXMLObjectParser {

    public static final String GLM_SUBSTITUTION_MODEL = "glmSubstitutionModel";


    public String getParserName() {
        return GLM_SUBSTITUTION_MODEL;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        DataType dataType = DataTypeUtils.getDataType(xo);

        if (dataType == null) dataType = (DataType) xo.getChild(DataType.class);

        int rateCount = (dataType.getStateCount() - 1) * dataType.getStateCount();

        LogLinearModel glm = (LogLinearModel) xo.getChild(GeneralizedLinearModel.class);

        int length = glm.getXBeta().length;

        if (length != rateCount) {
            throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + (rateCount) + " dimensions.  However GLM dimension is " + length);
        }

        XMLObject cxo = xo.getChild(dr.oldevomodelxml.substmodel.ComplexSubstitutionModelParser.ROOT_FREQUENCIES);
        FrequencyModel rootFreq = (FrequencyModel) cxo.getChild(FrequencyModel.class);

        if (dataType != rootFreq.getDataType()) {
            throw new XMLParseException("Data type of " + getParserName() + " element does not match that of its rootFrequencyModel.");
        }

        return new OldGLMSubstitutionModel(xo.getId(), dataType, rootFreq, glm);
    }

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

    public String getParserDescription() {
        return "A general model of sequence substitution for any data type where the rates come from the generalized linear model.";
    }

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

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

    private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
            new XORRule(
                    new StringAttributeRule(DataType.DATA_TYPE, "The type of sequence data",
                            DataType.getRegisteredDataTypeNames(), false),
                    new ElementRule(DataType.class)
            ),
            new ElementRule(ComplexSubstitutionModelParser.ROOT_FREQUENCIES, FrequencyModel.class),
            new ElementRule(GeneralizedLinearModel.class),
    };

}