/*
 * BinomialLikelihoodParser.java
 *
 * Copyright (c) 2002-2013 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.distribution;

import dr.inference.distribution.BinomialLikelihood;
import dr.inference.model.Likelihood;
import dr.inference.model.Parameter;
import dr.xml.*;

/**
 *
 */
public class BinomialLikelihoodParser extends AbstractXMLObjectParser {

    public static final String TRIALS = "trials";
    public static final String COUNTS = "counts";
    public static final String PROPORTION = "proportion";
    public static final String VALUES = "values";
    public static final String ON_LOGIT_SCALE = "onLogitScale";

    public String getParserName() {
        return BinomialLikelihood.BINOMIAL_LIKELIHOOD;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        final boolean onLogitScale = xo.getAttribute(ON_LOGIT_SCALE, false);

        XMLObject cxo = xo.getChild(TRIALS);
        Parameter trialsParam = (Parameter) cxo.getChild(Parameter.class);

        cxo = xo.getChild(PROPORTION);
        Parameter proportionParam = (Parameter) cxo.getChild(Parameter.class);

        if (proportionParam.getDimension() != 1 && proportionParam.getDimension() != trialsParam.getDimension()) {
            throw new XMLParseException("Proportion dimension (" + proportionParam.getDimension() + ") " +
            "must equal 1 or trials dimension (" + trialsParam.getDimension() + ")");
        }

        cxo = xo.getChild(COUNTS);
        Parameter counts;
        if (cxo.hasAttribute(VALUES)) {
            int[] tmp = cxo.getIntegerArrayAttribute(VALUES);
            double[] v = new double[tmp.length];
            for (int i = 0; i < tmp.length; ++i) {
                v[i] = tmp[i];
            }
            counts = new Parameter.Default(v);
        } else {
            counts = (Parameter) cxo.getChild(Parameter.class);
        }

        if (trialsParam.getDimension() != counts.getDimension()) {
            throw new XMLParseException("Trials dimension (" + trialsParam.getDimension()
                    + ") must equal counts dimension (" + counts.getDimension() + ")");
        }

        return new BinomialLikelihood(trialsParam, proportionParam, counts, onLogitScale);

    }

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

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

    private final XMLSyntaxRule[] rules = {
            AttributeRule.newBooleanRule(ON_LOGIT_SCALE, true),
            new ElementRule(TRIALS,
                    new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
            new ElementRule(PROPORTION,
                    new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
            new XORRule(
                    new ElementRule(COUNTS,
                            new XMLSyntaxRule[]{AttributeRule.newIntegerArrayRule(VALUES, false),})
                    ,
                    new ElementRule(COUNTS,
                            new XMLSyntaxRule[]{new ElementRule(Parameter.class)}
                    )),
    };

    public String getParserDescription() {
        return "Calculates the likelihood of some data given some parametric or empirical distribution.";
    }

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

@@ -1825,21 +1825,21 @@
 etChild(
-TRIAL
+COUNT
 S);%0A    
@@ -1852,21 +1852,21 @@
 rameter 
-trial
+count
 sParam =
@@ -2114,21 +2114,21 @@
 on() != 
-trial
+count
 sParam.g
@@ -2280,21 +2280,21 @@
 al 1 or 
-trial
+count
 s dimens
@@ -2294,37 +2294,37 @@
  dimension (%22 + 
-trial
+count
 sParam.getDimens
@@ -2366,37 +2366,37 @@
 o = xo.getChild(
-COUNT
+TRIAL
 S);%0A        Para
@@ -2401,22 +2401,27 @@
 rameter 
-counts
+trialsParam
 ;%0A      
@@ -2673,22 +2673,27 @@
         
-counts
+trialsParam
  = new P
@@ -2742,22 +2742,27 @@
         
-counts
+trialsParam
  = (Para
@@ -2854,24 +2854,29 @@
 () != counts
+Param
 .getDimensio
@@ -3036,16 +3036,21 @@
 + counts
+Param
 .getDime
@@ -3150,16 +3150,21 @@
 , counts
+Param
 , onLogi
@@ -3596,21 +3596,21 @@
 entRule(
-TRIAL
+COUNT
 S,%0A     
@@ -3849,37 +3849,37 @@
 new ElementRule(
-COUNT
+TRIAL
 S,%0A             
@@ -4015,37 +4015,37 @@
 new ElementRule(
-COUNT
+TRIAL
 S,%0A             

switch definition of 'trials' (now # of attempts) and 'counts' (now # of successes); should break many exisiting XMLs