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/*
* BeagleJNIjava
*
*/
package beagle;
/*
* BeagleJNIjava
*
* @author Andrew Rambaut
* @author Marc Suchard
*
*/
public class BeagleJNIWrapper {
private static final String LIBRARY_NAME = getPlatformSpecificLibraryName();
/**
* private constructor to enforce singleton instance
*/
private BeagleJNIWrapper() {
}
public native String getVersion();
public native String getCitation();
public native ResourceDetails[] getResourceList();
public native BenchmarkedResourceDetails[] getBenchmarkedResourceList(
int tipCount,
int compactBufferCount,
int stateCount,
int patternCount,
int categoryCount,
final int[] resourceList,
int resourceCount,
long preferenceFlags,
long requirementFlags,
int eigenModelCount,
int partitionCount,
int calculateDerivatives,
long benchmarkFlags);
public native int createInstance(
int tipCount,
int partialsBufferCount,
int compactBufferCount,
int stateCount,
int patternCount,
int eigenBufferCount,
int matrixBufferCount,
int categoryCount,
int scaleBufferCount,
final int[] resourceList,
int resourceCount,
long preferenceFlags,
long requirementFlags,
InstanceDetails returnInfo);
public native int finalize(int instance);
public native int setCPUThreadCount(int instance, int threadCount);
public native int setPatternWeights(int instance, final double[] patternWeights);
public native int setPatternPartitions(int instance, int partitionCount, final int[] patternPartitions);
public native int setTipStates(int instance, int tipIndex, final int[] inStates);
public native int getTipStates(int instance, int tipIndex, final int[] inStates);
public native int setTipPartials(int instance, int tipIndex, final double[] inPartials);
public native int setRootPrePartials(int instance, final int[] inbufferIndices, final int[] instateFrequenciesIndices, int count);
public native int setPartials(int instance, int bufferIndex, final double[] inPartials);
public native int getPartials(int instance, int bufferIndex, int scaleIndex,
final double[] outPartials);
public native int getLogScaleFactors(int stance, int scaleIndex, final double[] outFactors);
public native int setEigenDecomposition(int instance,
int eigenIndex,
final double[] eigenVectors,
final double[] inverseEigenValues,
final double[] eigenValues);
public native int setStateFrequencies(int instance,
int stateFrequenciesIndex,
final double[] stateFrequencies);
public native int setCategoryWeights(int instance,
int categoryWeightsIndex,
final double[] categoryWeights);
public native int setCategoryRates(int instance,
final double[] inCategoryRates);
public native int setCategoryRatesWithIndex(int instance,
int categoryRatesIndex,
final double[] inCategoryRates);
public native int setTransitionMatrix(int instance, int matrixIndex, final double[] inMatrix, double paddedValue);
public native int setDifferentialMatrix(int instance, int matrixIndex, final double[] inMatrix);
public native int getTransitionMatrix(int instance, int matrixIndex, final double[] outMatrix);
public native int convolveTransitionMatrices(int instance,
final int[] firstIndices,
final int[] secondIndices,
final int[] resultIndices,
int matrixCount);
public native int addTransitionMatrices(int instance,
final int[] firstIndices,
final int[] secondIndices,
final int[] resultIndices,
int matrixCount);
public native int transposeTransitionMatrices(int instance,
final int[] inIndices,
final int[] outIndices,
int matrixCount);
public native int updateTransitionMatrices(int instance, int eigenIndex,
final int[] probabilityIndices,
final int[] firstDerivativeIndices,
final int[] secondDervativeIndices,
final double[] edgeLengths,
int count);
public native int updateTransitionMatricesWithMultipleModels(
int instance,
final int[] eigenIndices,
final int[] categoryRateIndices,
final int[] probabilityIndices,
final int[] firstDerivativeIndices,
final int[] secondDervativeIndices,
final double[] edgeLengths,
int count);
public native int updatePrePartials(final int instance,
final int[] operations,
int operationCount,
int cumulativeScalingIndex);
public native int updatePrePartialsByPartition(final int instance,
final int[] operations,
int operationCount);
public native int updatePartials(final int instance,
final int[] operations,
int operationCount,
int cumulativeScalingIndex);
public native int updatePartialsByPartition(final int instance,
final int[] operations,
int operationCount);
public native int waitForPartials(final int instance,
final int[] destinationPartials,
int destinationPartialsCount);
public native int accumulateScaleFactors(final int instance,
final int[] scaleIndices,
final int count,
final int cumulativeScalingIndex);
public native int accumulateScaleFactorsByPartition(final int instance,
final int[] scaleIndices,
int count,
int cumulativeScaleIndex,
int partitionIndex);
public native int removeScaleFactors(final int instance,
final int[] scaleIndices,
final int count,
final int cumulativeScalingIndex);
public native int removeScaleFactorsByPartition(final int instance,
final int[] scaleIndices,
final int count,
final int cumulativeScalingIndex,
final int partitionIndex);
public native int resetScaleFactors(final int instance,
final int cumulativeScalingIndex);
public native int resetScaleFactorsByPartition(final int instance,
final int cumulativeScalingIndex,
final int partitionIndex);
public native int copyScaleFactors(final int instance,
final int destScalingIndex,
final int srcScalingIndex);
public native int calculateRootLogLikelihoods(int instance,
final int[] bufferIndices,
final int[] categoryWeightsIndices,
final int[] stateFrequenciesIndices,
final int[] cumulativeScaleIndices,
int count,
final double[] outSumLogLikelihood);
public native int calculateRootLogLikelihoodsByPartition(int instance,
final int[] bufferIndices,
final int[] categoryWeightsIndices,
final int[] stateFrequenciesIndices,
final int[] cumulativeScaleIndices,
final int[] partitionIndices,
int partitionCount,
int count,
final double[] outSumLogLikelihoodByPartition,
final double[] outSumLogLikelihood);
/*public native int calculateEdgeLogLikelihoods(int instance,
final int[] parentBufferIndices,
final int[] childBufferIndices,
final int[] probabilityIndices,
final int[] firstDerivativeIndices,
final int[] secondDerivativeIndices,
final int[] categoryWeightsIndices,
final int[] stateFrequenciesIndices,
final int[] scalingFactorsIndices,
int count,
final double[] outSumLogLikelihood,
final double[] outSumFirstDerivative,
final double[] outSumSecondDerivative);*/
public native int getSiteLogLikelihoods(final int instance,
final double[] outLogLikelihoods);
public native int calculateEdgeDifferentials(final int instance,
final int[] postBufferIndices,
final int[] preBufferIndices,
final int[] derivativeMatrixIndices,
final int[] categoryWeightsIndices,
int count,
double[] outDerivatives,
double[] outSumDerivatives,
double[] outSumSquaredDerivatives);
public native int calculateCrossProductDifferentials(final int instance,
final int[] postBufferIndices,
final int[] preBufferIndices,
final int[] categoryRateIndices,
final int[] categoryWeightsIndices,
final double[] edgeLengths,
int count,
double[] outSumDerivatives,
double[] outSumSquaredDerivatives);
public native int calculateEdgeDerivative(int instance,
final int[] postBufferIndices,
final int[] preBufferIndices,
final int rootBufferIndex,
final int[] firstDerivativeIndices,
final int[] secondDerivativeIndices,
final int categoryWeightsIndex,
final int categoryRatesIndex,
final int stateFrequenciesIndex,
final int[] cumulativeScaleIndices,
int count,
double[] outFirstDerivative,
double[] outDiagonalSecondDerivative);
/* Library loading routines */
private static String getPlatformSpecificLibraryName()
{
String osName = System.getProperty("os.name").toLowerCase();
String osArch = System.getProperty("os.arch").toLowerCase();
if (osName.startsWith("windows")) {
if(osArch.equals("x86")||osArch.equals("i386")) return "hmsbeagle32";
if(osArch.startsWith("amd64")||osArch.startsWith("x86_64")) return "hmsbeagle64";
}
return "hmsbeagle-jni";
}
public static void loadBeagleLibrary() throws UnsatisfiedLinkError {
String path = "";
if (System.getProperty("beagle.library.path") != null) {
path = System.getProperty("beagle.library.path");
if (path.length() > 0 && !path.endsWith("/")) {
path += "/";
}
}
System.loadLibrary(path + LIBRARY_NAME);
/// XJ: you may need to add the java.library.path in your JRE
/// e.g. in IntelliJ you can add VM options: -Djava.library.path=/usr/local/lib
INSTANCE = new BeagleJNIWrapper();
}
public static BeagleJNIWrapper INSTANCE;
}
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