Parser for MultilocusNonparametricCoalescentLikelihood

src/dr/app/beast/development_parsers.properties

@@ -95,6 +95,7 @@ dr.evomodelxml.coalescent.operators.GaussianProcessSkytrackBlockUpdateOperatorPa
 dr.evomodelxml.coalescent.operators.GaussianProcessSkytrackTreeOperatorParser
 dr.inferencexml.distribution.GeneralizedAdditiveGaussianProcessModelParser
 dr.inferencexml.distribution.GaussianProcessBasisApproximationParser
+dr.evomodelxml.coalescent.MultilocusNonParametricCoalescentLikelihoodParser
 
 
 # TREE SUMMARY STATISTICS

src/dr/evomodelxml/coalescent/MultilocusNonParametricCoalescentLikelihoodParser.java

@@ -0,0 +1,154 @@
+/*
+ * GMRFSkyrideLikelihoodParser.java
+ *
+ * Copyright (c) 2002-2024 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.coalescent;
+
+import dr.evolution.coalescent.TreeIntervals;
+import dr.evomodel.coalescent.MultilocusNonparametricCoalescentLikelihood;
+import dr.evomodel.coalescent.smooth.SkyGlideLikelihood;
+import dr.evomodel.tree.TreeModel;
+import dr.evomodelxml.coalescent.smooth.SmoothSkygridLikelihoodParser;
+import dr.inference.model.Parameter;
+import dr.xml.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class MultilocusNonParametricCoalescentLikelihoodParser extends AbstractXMLObjectParser {
+
+    private static final String PARSER_NAME = "multiLocusNPCoalescentLikelihood";
+    private static final String POPULATION_TREE = GMRFSkyrideLikelihoodParser.POPULATION_TREE;
+    private static final String POPULATION_PARAMETER = GMRFSkyrideLikelihoodParser.POPULATION_PARAMETER;
+    //    public static final String PRECISION_PARAMETER = "precisionParameter";
+
+    public static final String PLOIDY = "ploidy";
+
+    private static final String GRID_POINTS = GMRFSkyrideLikelihoodParser.GRID_POINTS;
+    private static final String NUM_GRID_POINTS = GMRFSkyrideLikelihoodParser.NUM_GRID_POINTS;
+    private static final String CUT_OFF = GMRFSkyrideLikelihoodParser.CUT_OFF;
+
+    @Override
+    public Object parseXMLObject(XMLObject xo) throws XMLParseException {
+
+        Parameter logPopSizes = (Parameter) xo.getElementFirstChild(POPULATION_PARAMETER);
+        Parameter gridPoints = SmoothSkygridLikelihoodParser.getGridPoints(xo); //TODO should I call this parser?
+        int nGridPoints = gridPoints.getDimension();
+
+        //        cxo = xo.getChild(PRECISION_PARAMETER);
+        //        Parameter precParameter = (Parameter) cxo.getChild(Parameter.class);
+
+        List<TreeModel> trees = new ArrayList<>();
+        XMLObject cxo = xo.getChild(POPULATION_TREE);
+        for (int i = 0; i < cxo.getChildCount(); i++) {
+            trees.add((TreeModel) cxo.getChild(i));
+        }
+
+        List<TreeIntervals> intervalLists = new ArrayList<>();
+        for (int i = 0; i < trees.size(); i++) {
+            TreeIntervals treeIntervals = new TreeIntervals(trees.get(i));
+            intervalLists.add(treeIntervals);
+        }
+        //        List<BigFastTreeIntervals> intervalLists = new ArrayList<>();
+        //        for (int i = 0; i < trees.size(); i++) {
+        //            BigFastTreeIntervals treeIntervals = new BigFastTreeIntervals(trees.get(i));
+        //            intervalLists.add((BigFastTreeIntervals) treeIntervals);
+        //        }
+
+        Parameter ploidyFactors = parsePloidyFactors(xo, trees, nGridPoints);
+
+        MultilocusNonparametricCoalescentLikelihood likelihood = new MultilocusNonparametricCoalescentLikelihood(intervalLists, logPopSizes, gridPoints, ploidyFactors);
+        return likelihood;
+    }
+
+    protected Parameter parsePloidyFactors(XMLObject xo, List<TreeModel> trees, int nGridPoints) {
+        Parameter ploidyFactors = null;
+        if (xo.getChild(PLOIDY) != null) {
+            XMLObject cxo = xo.getChild(PLOIDY);
+            ploidyFactors = (Parameter) cxo.getChild(Parameter.class);
+        } else {
+            ploidyFactors = new Parameter.Default(PLOIDY, trees.size());
+            for (int i = 0; i < trees.size(); i++) {
+                ploidyFactors.setParameterValue(i, 1.0);
+            }
+//            if (nGridPoints != 0) {
+//                ploidyFactors = new Parameter.Default(PLOIDY, nGridPoints);
+//                for(int i = 0; i < nGridPoints; i++){
+//                    ploidyFactors.setParameterValue(i, 1.0);
+//                }
+//            } else {
+//                ploidyFactors = new Parameter.Default(PLOIDY, trees.size());
+//                for (int i = 0; i < trees.size(); i++) {
+//                    ploidyFactors.setParameterValue(i, 1.0);
+//                }
+//            }
+        }
+        return ploidyFactors;
+    }
+
+    @Override
+    public XMLSyntaxRule[] getSyntaxRules() {
+        return new XMLSyntaxRule[0];
+    }
+
+    private final XMLSyntaxRule[] rules = {
+            new ElementRule(POPULATION_TREE, new XMLSyntaxRule[]{
+                    new ElementRule(TreeModel.class, 1, Integer.MAX_VALUE)
+            }),
+
+            new ElementRule(POPULATION_PARAMETER, new XMLSyntaxRule[]{
+                    new ElementRule(Parameter.class)
+            }),
+
+            new XORRule(
+                    new ElementRule(GRID_POINTS, new XMLSyntaxRule[]{
+                            new ElementRule(Parameter.class)
+                    }),
+                    new AndRule(
+                            new ElementRule(CUT_OFF, new XMLSyntaxRule[]{
+                                    new ElementRule(Parameter.class)
+                            }),
+                            new ElementRule(NUM_GRID_POINTS, new XMLSyntaxRule[]{
+                                    new ElementRule(Parameter.class)
+                            })
+                    )
+            ),
+
+    };
+
+    @Override
+    public String getParserDescription() {
+        return null;
+    }
+
+    @Override
+    public Class getReturnType() {
+        return SkyGlideLikelihood.class;
+    }
+
+    @Override
+    public String getParserName() {
+        return PARSER_NAME;
+    }
+}