/*
* NativeNucleotideLikelihoodCore.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;
import dr.app.util.OSType;
import java.io.File;
import java.net.URISyntaxException;
/**
* NativeNucleotideLikelihoodCore - An implementation of LikelihoodCore for nucleotides
* that calls native methods for maximum speed. The native methods should be in
* a shared library called "NucleotideLikelihoodCore" but the exact name will be system
* dependent (i.e. "libNucleotideLikelihoodCore.so" or "NucleotideLikelihoodCore.dll").
*
* @version $Id: NativeNucleotideLikelihoodCore.java,v 1.14 2006/08/31 14:57:24 rambaut Exp $
*
* @author Andrew Rambaut
*/
@Deprecated // Switching to BEAGLE
public class NativeNucleotideLikelihoodCore extends AbstractLikelihoodCore {
/**
* Constructor
*/
public NativeNucleotideLikelihoodCore() {
super(4);
}
protected void calculateStatesStatesPruning(int[] states1, double[] matrices1,
int[] states2, double[] matrices2,
double[] partials3) {
nativeStatesStatesPruning(states1, matrices1, states2, 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);
}
/*
private void out(PrintStream s, double[] a, String name) {
s.print("double " + name + "[" + a.length + "] = {");
for( double f : a ) s.print(f + ", ");
s.println("};");
}
*/
protected void calculatePartialsPartialsPruning(double[] partials1, double[] matrices1,
double[] partials2, double[] matrices2,
double[] partials3) {
/* if( false ) {
System.out.println("*//*nativePartialsPartialsPruning*//* int patternCount = " +
patternCount + "; int matrixCount = " + matrixCount);
out(System.out, partials1, "partials1");
out(System.out, partials2, "partials2");
out(System.out, partials2, "matrices1");
out(System.out, partials2, "matrices2");
}*/
nativePartialsPartialsPruning(partials1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3);
}
/**
* Calculates partial likelihoods at a node when both children have states.
*/
protected void calculateStatesStatesPruning(int[] states1, double[] matrices1,
int[] states2, double[] matrices2,
double[] partials3, int[] matrixMap)
{
throw new RuntimeException("calculateStatesStatesPruning not implemented using matrixMap");
}
/**
* Calculates partial likelihoods at a node when one child has states and one has partials.
*/
protected void calculateStatesPartialsPruning( int[] states1, double[] matrices1,
double[] partials2, double[] matrices2,
double[] partials3, int[] matrixMap)
{
throw new RuntimeException("calculateStatesStatesPruning not implemented using matrixMap");
}
/**
* Calculates partial likelihoods at a node when both children have partials.
*/
protected void calculatePartialsPartialsPruning(double[] partials1, double[] matrices1,
double[] partials2, double[] matrices2,
double[] partials3, int[] matrixMap)
{
throw new RuntimeException("calculateStatesStatesPruning not implemented using matrixMap");
}
protected void calculateIntegratePartials(double[] inPartials, double[] proportions, double[] outPartials)
{
nativeIntegratePartials(inPartials, proportions, patternCount, matrixCount, outPartials);
}
/**
* Calculates partial likelihoods at a node when both children have states.
*/
protected native void nativeStatesStatesPruning( int[] states1, double[] matrices1,
int[] states2, 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 nativePartialsPartialsPruning(double[] partials1, double[] matrices1,
double[] partials2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
public native void nativeIntegratePartials( double[] partials, double[] proportions,
int patternCount, int matrixCount,
double[] outPartials);
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++;
outLogLikelihoods[k] = Math.log(sum) + getLogScalingFactor(k);
}
}
public static boolean isAvailable() { return isNativeAvailable; }
private static boolean isNativeAvailable = false;
static {
String currentDir = null;
try {
currentDir = new File(NativeNucleotideLikelihoodCore.class.getProtectionDomain().getCodeSource().
getLocation().toURI()).getParent() + System.getProperty("file.separator")
+ "lib" + System.getProperty("file.separator"); // get path to find lib http://code.google.com/p/beast-mcmc/issues/detail?id=203
// System.out.println("currentDir = " + currentDir);
} catch (URISyntaxException e) {
e.printStackTrace();
}
try {
if (OSType.isWindows()) {
System.load(currentDir + "NucleotideLikelihoodCore.dll");
} else {
currentDir = System.getProperty("user.dir");
System.loadLibrary("NucleotideLikelihoodCore");
}
isNativeAvailable = true;
System.out.println("Loading native NucleotideLikelihoodCore successfully from " + currentDir);
} catch (UnsatisfiedLinkError e) {
System.err.println("Failed to load native NucleotideLikelihoodCore in : " + currentDir);
System.err.println("Using Java nucleotide likelihood core because " + e.toString());
// System.err.println("Looking for NucleotideLikelihoodCore in java.library.path : " + System.getProperty("java.library.path"));
// System.err.println("Looking for NucleotideLikelihoodCore in user.dir : " + System.getProperty("user.dir"));
}
}
}