/* * NativeGeneralLikelihoodCore.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.oldevomodel.treelikelihood; @Deprecated // Switching to BEAGLE public class NativeGeneralLikelihoodCore extends AbstractLikelihoodCore { public NativeGeneralLikelihoodCore(int stateCount) { super(stateCount); } protected void calculateIntegratePartials(double[] inPartials, double[] proportions, double[] outPartials) { nativeIntegratePartials(inPartials, proportions, patternCount, matrixCount, outPartials, stateCount); } protected void calculatePartialsPartialsPruning(double[] partials1, double[] matrices1, double[] partials2, double[] matrices2, double[] partials3) { nativePartialsPartialsPruning(partials1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3, stateCount); } protected void calculateStatesPartialsPruning(int[] states1, double[] matrices1, double[] partials2, double[] matrices2, double[] partials3) { nativeStatesPartialsPruning(states1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3, stateCount); } protected void calculateStatesStatesPruning(int[] states1, double[] matrices1, int[] states2, double[] matrices2, double[] partials3) { nativeStatesStatesPruning(states1, matrices1, states2, matrices2, patternCount, matrixCount, partials3, stateCount); } protected void calculatePartialsPartialsPruning(double[] partials1, double[] matrices1, double[] partials2, double[] matrices2, double[] partials3, int[] matrixMap) { throw new RuntimeException("not implemented using matrixMap"); } protected void calculateStatesStatesPruning(int[] states1, double[] matrices1, int[] states2, double[] matrices2, double[] partials3, int[] matrixMap) { throw new RuntimeException("not implemented using matrixMap"); } protected void calculateStatesPartialsPruning(int[] states1, double[] matrices1, double[] partials2, double[] matrices2, double[] partials3, int[] matrixMap) { throw new RuntimeException("not implemented using matrixMap"); } public void calculateLogLikelihoods(double[] partials, double[] frequencies, double[] outLogLikelihoods) { int v = 0; for (int k = 0; k < patternCount; k++) { double sum = 0.0; for (int i = 0; i < stateCount; i++) { sum += frequencies[i] * partials[v]; v++; } outLogLikelihoods[k] = Math.log(sum) + getLogScalingFactor(k); } } public native void nativeIntegratePartials(double[] partials, double[] proportions, int patternCount, int matrixCount, double[] outPartials, int stateCount); protected native void nativePartialsPartialsPruning(double[] partials1, double[] matrices1, double[] partials2, double[] matrices2, int patternCount, int matrixCount, double[] partials3, int stateCount); protected native void nativeStatesPartialsPruning(int[] states1, double[] matrices1, double[] partials2, double[] matrices2, int patternCount, int matrixCount, double[] partials3, int stateCount); protected native void nativeStatesStatesPruning(int[] states1, double[] matrices1, int[] states2, double[] matrices2, int patternCount, int matrixCount, double[] partials3, int stateCount); protected native void setMode(int mode); public static boolean isAvailable() { return isNativeAvailable; } private static boolean isNativeAvailable = false; static { try { System.loadLibrary("GeneralLikelihoodCore"); isNativeAvailable = true; } catch (UnsatisfiedLinkError e) { System.err.println("Unable to load general core"); } } }