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/*
* BeagleJNIjava
*
*/
package beagle;
/*
* BeagleJNIjava
*
* @author Andrew Rambaut
* @author Marc Suchard
*
*/
public class BeagleJNIImpl implements Beagle {
private int instance = -1;
private InstanceDetails details = new InstanceDetails();
public BeagleJNIImpl(int tipCount,
int partialsBufferCount,
int compactBufferCount,
int stateCount,
int patternCount,
int eigenBufferCount,
int matrixBufferCount,
int categoryCount,
int scaleBufferCount,
final int[] resourceList,
long preferenceFlags,
long requirementFlags) {
instance = BeagleJNIWrapper.INSTANCE.createInstance(
tipCount,
partialsBufferCount,
compactBufferCount,
stateCount,
patternCount,
eigenBufferCount,
matrixBufferCount,
categoryCount,
scaleBufferCount,
resourceList,
(resourceList != null? resourceList.length: 0),
preferenceFlags,
requirementFlags,
details);
if (instance < 0) {
details = null; // To communicate that no instance has been created!
throw new BeagleException("create", instance);
}
}
public void finalize() throws Throwable {
super.finalize();
int errCode = BeagleJNIWrapper.INSTANCE.finalize(instance);
if (errCode != 0) {
throw new BeagleException("finalize", errCode);
}
}
public void setPatternWeights(final double[] patternWeights) {
int errCode = BeagleJNIWrapper.INSTANCE.setPatternWeights(instance, patternWeights);
if (errCode != 0) {
throw new BeagleException("setPatternWeights", errCode);
}
}
public void setTipStates(int tipIndex, final int[] states) {
int errCode = BeagleJNIWrapper.INSTANCE.setTipStates(instance, tipIndex, states);
if (errCode != 0) {
throw new BeagleException("setTipStates", errCode);
}
}
public void getTipStates(int tipIndex, final int[] states) {
int errCode = BeagleJNIWrapper.INSTANCE.getTipStates(instance, tipIndex, states);
if (errCode != 0) {
throw new BeagleException("getTipStates", errCode);
}
}
public void setTipPartials(int tipIndex, final double[] partials) {
int errCode = BeagleJNIWrapper.INSTANCE.setTipPartials(instance, tipIndex, partials);
if (errCode != 0) {
throw new BeagleException("setTipPartials", errCode);
}
}
public void setPartials(int bufferIndex, final double[] partials) {
int errCode = BeagleJNIWrapper.INSTANCE.setPartials(instance, bufferIndex, partials);
if (errCode != 0) {
throw new BeagleException("setPartials", errCode);
}
}
public void getPartials(int bufferIndex, int scaleIndex, final double []outPartials) {
int errCode = BeagleJNIWrapper.INSTANCE.getPartials(instance, bufferIndex, scaleIndex, outPartials);
if (errCode != 0) {
throw new BeagleException("getPartials", errCode);
}
}
public void setEigenDecomposition(int eigenIndex,
final double[] eigenVectors,
final double[] inverseEigenValues,
final double[] eigenValues) {
int errCode = BeagleJNIWrapper.INSTANCE.setEigenDecomposition(instance, eigenIndex, eigenVectors, inverseEigenValues, eigenValues);
if (errCode != 0) {
throw new BeagleException("setEigenDecomposition", errCode);
}
}
public void setStateFrequencies(int stateFrequenciesIndex,
final double[] stateFrequencies) {
int errCode = BeagleJNIWrapper.INSTANCE.setStateFrequencies(instance,
stateFrequenciesIndex, stateFrequencies);
if (errCode != 0) {
throw new BeagleException("setStateFrequencies", errCode);
}
}
public void setCategoryWeights( int categoryWeightsIndex,
final double[] categoryWeights) {
int errCode = BeagleJNIWrapper.INSTANCE.setCategoryWeights(instance,
categoryWeightsIndex, categoryWeights);
if (errCode != 0) {
throw new BeagleException("setCategoryWeights", errCode);
}
}
public void setCategoryRates(double[] inCategoryRates) {
int errCode = BeagleJNIWrapper.INSTANCE.setCategoryRates(instance, inCategoryRates);
if (errCode != 0) {
throw new BeagleException("setCategoryRates", errCode);
}
}
public void setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue) {
int errCode = BeagleJNIWrapper.INSTANCE.setTransitionMatrix(instance, matrixIndex, inMatrix, paddedValue);
if (errCode != 0) {
throw new BeagleException("setTransitionMatrix", errCode);
}
}
public void getTransitionMatrix(int matrixIndex, final double[] outMatrix) {
int errCode = BeagleJNIWrapper.INSTANCE.getTransitionMatrix(instance, matrixIndex, outMatrix);
if (errCode != 0) {
throw new BeagleException("getTransitionMatrix", errCode);
}
}
// /////////////////////////
// ---TODO: Epoch model---//
// /////////////////////////
public void convolveTransitionMatrices(final int[] firstIndices,
final int[] secondIndices,
final int[] resultIndices,
int matrixCount) {
int errCode = BeagleJNIWrapper.INSTANCE.convolveTransitionMatrices(instance,
firstIndices,
secondIndices,
resultIndices,
matrixCount);
if (errCode != 0) {
throw new BeagleException("convolveTransitionMatrices", errCode);
}
}//END: convolveTransitionMatrices
public void updateTransitionMatrices(int eigenIndex,
final int[] probabilityIndices,
final int[] firstDerivativeIndices,
final int[] secondDervativeIndices,
final double[] edgeLengths,
int count) {
int errCode = BeagleJNIWrapper.INSTANCE.updateTransitionMatrices(instance,
eigenIndex, probabilityIndices,
firstDerivativeIndices, secondDervativeIndices,
edgeLengths, count);
if (errCode != 0) {
throw new BeagleException("updateTransitionMatrices", errCode);
}
}
public void updatePartials(final int[] operations, final int operationCount, final int cumulativeScaleIndex) {
int errCode = BeagleJNIWrapper.INSTANCE.updatePartials(instance, operations, operationCount, cumulativeScaleIndex);
if (errCode != 0) {
throw new BeagleException("updatePartials", errCode);
}
}
public void accumulateScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) {
int errCode = BeagleJNIWrapper.INSTANCE.accumulateScaleFactors(instance, scaleIndices, count, cumulativeScaleIndex);
if (errCode != 0) {
throw new BeagleException("accumulateScaleFactors", errCode);
}
}
public void removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) {
int errCode = BeagleJNIWrapper.INSTANCE.removeScaleFactors(instance, scaleIndices, count, cumulativeScaleIndex);
if (errCode != 0) {
throw new BeagleException("removeScaleFactors", errCode);
}
}
public void copyScaleFactors(int destScalingIndex, int srcScalingIndex) {
int errCode = BeagleJNIWrapper.INSTANCE.copyScaleFactors(instance, destScalingIndex, srcScalingIndex);
if (errCode != 0) {
throw new BeagleException("copyScaleFactors", errCode);
}
}
public void resetScaleFactors(int cumulativeScaleIndex) {
int errCode = BeagleJNIWrapper.INSTANCE.resetScaleFactors(instance, cumulativeScaleIndex);
if (errCode != 0) {
throw new BeagleException("resetScaleFactors", errCode);
}
}
public void calculateRootLogLikelihoods(int[] bufferIndices,
final int[] categoryWeightsIndices,
final int[] stateFrequenciesIndices,
final int[] cumulativeScaleIndices,
int count,
final double[] outSumLogLikelihood) {
int errCode = BeagleJNIWrapper.INSTANCE.calculateRootLogLikelihoods(instance,
bufferIndices,
categoryWeightsIndices,
stateFrequenciesIndices,
cumulativeScaleIndices,
count,
outSumLogLikelihood);
// We probably don't want the Floating Point error to throw an exception...
if (errCode != 0 && errCode != BeagleErrorCode.FLOATING_POINT_ERROR.getErrCode()) {
throw new BeagleException("calculateRootLogLikelihoods", errCode);
}
}
public void calculateEdgeLogLikelihoods(final int[] parentBufferIndices,
final int[] childBufferIndices,
final int[] probabilityIndices,
final int[] firstDerivativeIndices,
final int[] secondDerivativeIndices,
final int[] categoryWeightsIndices,
final int[] stateFrequenciesIndices,
final int[] cumulativeScaleIndices,
int count,
final double[] outSumLogLikelihood,
final double[] outSumFirstDerivative,
final double[] outSumSecondDerivative) {
int errCode = BeagleJNIWrapper.INSTANCE.calculateEdgeLogLikelihoods(instance,
parentBufferIndices,
childBufferIndices,
probabilityIndices,
firstDerivativeIndices,
secondDerivativeIndices,
categoryWeightsIndices,
stateFrequenciesIndices,
cumulativeScaleIndices,
count,
outSumLogLikelihood,
outSumFirstDerivative,
outSumSecondDerivative);
if (errCode != 0) {
throw new BeagleException("calculateEdgeLogLikelihoods", errCode);
}
}
public void getSiteLogLikelihoods(final double[] outLogLikelihoods) {
int errCode = BeagleJNIWrapper.INSTANCE.getSiteLogLikelihoods(instance,
outLogLikelihoods);
if (errCode != 0) {
throw new BeagleException("getSiteLogLikelihoods", errCode);
}
}
public InstanceDetails getDetails() {
return details;
}
}
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