/*
* NativeAminoAcidLikelihoodCore.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 NativeAminoAcidLikelihoodCore extends AbstractLikelihoodCore{
public NativeAminoAcidLikelihoodCore() {
super(20);
}
protected void calculateIntegratePartials(double[] inPartials,
double[] proportions, double[] outPartials) {
nativeIntegratePartials(inPartials, proportions, patternCount, matrixCount, outPartials);
}
protected void calculatePartialsPartialsPruning(double[] partials1,
double[] matrices1, double[] partials2, double[] matrices2,
double[] partials3) {
nativePartialsPartialsPruning(partials1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3);
}
protected void calculateStatesPartialsPruning(int[] states1,
double[] matrices1, double[] partials2, double[] matrices2,
double[] partials3) {
nativeStatesPartialsPruning(states1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3);
}
protected void calculateStatesStatesPruning(int[] states1,
double[] matrices1, int[] states2, double[] matrices2,
double[] partials3) {
nativeStatesStatesPruning(states1, matrices1, states2, matrices2, patternCount, matrixCount, partials3);
}
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 = frequencies[0] * partials[v]; v++;
sum += frequencies[1] * partials[v]; v++;
sum += frequencies[2] * partials[v]; v++;
sum += frequencies[3] * partials[v]; v++;
sum += frequencies[4] * partials[v]; v++;
sum += frequencies[5] * partials[v]; v++;
sum += frequencies[6] * partials[v]; v++;
sum += frequencies[7] * partials[v]; v++;
sum += frequencies[8] * partials[v]; v++;
sum += frequencies[9] * partials[v]; v++;
sum += frequencies[10] * partials[v]; v++;
sum += frequencies[11] * partials[v]; v++;
sum += frequencies[12] * partials[v]; v++;
sum += frequencies[13] * partials[v]; v++;
sum += frequencies[14] * partials[v]; v++;
sum += frequencies[15] * partials[v]; v++;
sum += frequencies[16] * partials[v]; v++;
sum += frequencies[17] * partials[v]; v++;
sum += frequencies[18] * partials[v]; v++;
sum += frequencies[19] * partials[v]; v++;
outLogLikelihoods[k] = Math.log(sum) + getLogScalingFactor(k);
}
}
public native void nativeIntegratePartials(double[] partials, double[] proportions,
int patternCount, int matrixCount,
double[] outPartials);
protected native void nativePartialsPartialsPruning(double[] partials1, double[] matrices1,
double[] partials2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
protected native void nativeStatesPartialsPruning(int[] states1, double[] matrices1,
double[] partials2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
protected native void nativeStatesStatesPruning(int[] states1, double[] matrices1,
int[] states2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
public static boolean isAvailable(){
return isNativeAvailable;
}
private static boolean isNativeAvailable = false;
static {
try {
System.loadLibrary("AminoAcidLikelihoodCore");
isNativeAvailable = true;
} catch (UnsatisfiedLinkError e) {
System.err.println("Using Java AminoAcid likelihood core " + e.toString());
System.err.println("Looking for AminoAcidLikelihoodCore in " + System.getProperty("java.library.path"));
}
}
}