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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| /* | ||
| * CoalescentRescaler.java | ||
| * | ||
| * Copyright © 2002-2024 the BEAST Development Team | ||
| * http://beast.community/about | ||
| * | ||
| * 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.evomodel.coalescent; | ||
|
|
||
| import dr.evolution.coalescent.ConstantPopulation; | ||
| import dr.evolution.tree.Tree; | ||
| import dr.evomodel.bigfasttree.BigFastTreeIntervals; | ||
| import dr.evomodel.coalescent.demographicmodel.ConstantPopulationModel; | ||
| import dr.evomodel.coalescent.demographicmodel.RescaleAwareDemographic; | ||
| import dr.evomodel.tree.TreeModel; | ||
|
|
||
| /** | ||
| * Simulates a set of coalescent intervals given a demographic model. | ||
| * | ||
| * @author Xiang Ji | ||
| * @author Marc Suchard | ||
| * @author Filippo Monti | ||
| */ | ||
| public class CoalescentRescaler { | ||
|
|
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| private TreeModel tree; | ||
|
|
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| private ConstantPopulationModel constantPopulationModel; | ||
|
|
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| private RescaleAwareDemographic rescaleAwareDemographic; | ||
|
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| private BigFastTreeIntervals bigFastTreeIntervals; | ||
|
|
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| public CoalescentRescaler(TreeModel tree, ConstantPopulationModel constantPopulationModel, RescaleAwareDemographic rescaleAwareDemographic) { | ||
| this.tree = tree; | ||
| this.constantPopulationModel = constantPopulationModel; | ||
| this.rescaleAwareDemographic = rescaleAwareDemographic; | ||
| this.bigFastTreeIntervals = new BigFastTreeIntervals("constant.population.size.tree", tree); | ||
| } | ||
|
|
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| public TreeModel rescaleTree() { | ||
| double[] intensityTimeProducts = new double[bigFastTreeIntervals.getIntervalCount()]; | ||
| double[] intervals = new double[bigFastTreeIntervals.getIntervalCount()]; | ||
| for (int i = 0; i < bigFastTreeIntervals.getIntervalCount(); i++) { | ||
| intervals[i] = bigFastTreeIntervals.getInterval(i); | ||
| intensityTimeProducts[i] = intervals[i] / ((ConstantPopulation) constantPopulationModel.getDemographicFunction()).getN0(); | ||
| } | ||
| double[] scaledIntervals = rescaleAwareDemographic.rescaleInterval(intervals, intensityTimeProducts); | ||
|
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| double height = 0; | ||
| for (int i = 0; i < scaledIntervals.length; i++) { | ||
| height += scaledIntervals[i]; | ||
| int[] intervalNodeNumbers = bigFastTreeIntervals.getNodeNumbersForInterval(i); | ||
| tree.setNodeHeightQuietly(tree.getNode(intervalNodeNumbers[1]), height); | ||
| } | ||
| tree.pushTreeChangedEvent(); | ||
|
|
||
| return tree; | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -1418,4 +1418,4 @@ public List<Citation> getCitations() { | |
| ) | ||
| ); | ||
| } | ||
| } | ||
| } | ||
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34 changes: 34 additions & 0 deletions
34
src/dr/evomodel/coalescent/demographicmodel/RescaleAwareDemographic.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| /* | ||
| * RescaleAwareDemographic.java | ||
| * | ||
| * Copyright © 2002-2024 the BEAST Development Team | ||
| * http://beast.community/about | ||
| * | ||
| * 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 | ||
| * | ||
| */ | ||
|
|
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| package dr.evomodel.coalescent.demographicmodel; | ||
|
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| public interface RescaleAwareDemographic { | ||
|
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| double[] rescaleInterval(double[] intervals, double[] targetIntensityIntervalProducts); | ||
|
|
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| } |
83 changes: 83 additions & 0 deletions
83
src/dr/evomodelxml/coalescent/CoalescentRescalerParser.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| /* | ||
| * CoalescentRescalerParser.java | ||
| * | ||
| * Copyright © 2002-2024 the BEAST Development Team | ||
| * http://beast.community/about | ||
| * | ||
| * 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.ConstantPopulation; | ||
| import dr.evolution.tree.Tree; | ||
| import dr.evolution.util.TaxonList; | ||
| import dr.evomodel.coalescent.CoalescentRescaler; | ||
| import dr.evomodel.coalescent.demographicmodel.ConstantPopulationModel; | ||
| import dr.evomodel.coalescent.demographicmodel.DemographicModel; | ||
| import dr.evomodel.coalescent.demographicmodel.RescaleAwareDemographic; | ||
| import dr.evomodel.tree.DefaultTreeModel; | ||
| import dr.evomodel.tree.TreeModel; | ||
| import dr.xml.*; | ||
|
|
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| public class CoalescentRescalerParser extends AbstractXMLObjectParser { | ||
|
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| public static final String COALESCENT_RESCALER = "coalescentRescaler"; | ||
|
|
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| @Override | ||
| public Object parseXMLObject(XMLObject xo) throws XMLParseException { | ||
| TreeModel tree = (TreeModel) xo.getChild(TreeModel.class); | ||
| if (tree == null) { | ||
| tree = new DefaultTreeModel((Tree) xo.getChild(Tree.class)); | ||
| } | ||
| ConstantPopulationModel constantPopulation = (ConstantPopulationModel) xo.getChild(ConstantPopulationModel.class); | ||
| RescaleAwareDemographic rescaleAwareDemographic = (RescaleAwareDemographic) xo.getChild(RescaleAwareDemographic.class); | ||
| CoalescentRescaler coalescentRescaler = new CoalescentRescaler(tree, constantPopulation, rescaleAwareDemographic); | ||
| return coalescentRescaler.rescaleTree(); | ||
| } | ||
|
|
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| @Override | ||
| public XMLSyntaxRule[] getSyntaxRules() { | ||
| return rules; | ||
| } | ||
|
|
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| private final XMLSyntaxRule[] rules = { | ||
| new XORRule(new ElementRule(TreeModel.class), | ||
| new ElementRule(Tree.class)), | ||
| new ElementRule(ConstantPopulationModel.class, 0, Integer.MAX_VALUE), | ||
| new ElementRule(RescaleAwareDemographic.class, 0, Integer.MAX_VALUE), | ||
| }; | ||
|
|
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| @Override | ||
| public String getParserDescription() { | ||
| return ""; | ||
| } | ||
|
|
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| @Override | ||
| public Class getReturnType() { | ||
| return TreeModel.class; | ||
| } | ||
|
|
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| @Override | ||
| public String getParserName() { | ||
| return COALESCENT_RESCALER; | ||
| } | ||
| } |
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