private void convolveAndRelease(
Beagle beagle,
int[] firstConvolutionBuffers,
int[] secondConvolutionBuffers,
int[] resultConvolutionBuffers,
int operationsCount) {
if (RUN_IN_SERIES) {
if (operationsCount > 1) {
throw new RuntimeException("Unable to convolve matrices in series");
}
}
beagle.convolveTransitionMatrices(
firstConvolutionBuffers, // A
secondConvolutionBuffers, // B
resultConvolutionBuffers, // C
operationsCount // count
);
for (int i = 0; i < operationsCount; i++) {
if (firstConvolutionBuffers[i] >= matrixBufferHelper.getBufferCount()
&& firstConvolutionBuffers[i] != reserveBufferIndex) {
pushAvailableBuffer(firstConvolutionBuffers[i]);
}
if (secondConvolutionBuffers[i] >= matrixBufferHelper.getBufferCount()
&& secondConvolutionBuffers[i] != reserveBufferIndex) {
pushAvailableBuffer(secondConvolutionBuffers[i]);
}
}
} // END: convolveAndRelease
public SubstitutionModelDelegate(Tree tree, BranchModel branchModel, int bufferPoolSize) {
if (MEASURE_RUN_TIME) {
updateTime = 0;
convolveTime = 0;
}
this.tree = tree;
this.substitutionModelList = branchModel.getSubstitutionModels();
this.branchModel = branchModel;
eigenCount = substitutionModelList.size();
nodeCount = tree.getNodeCount();
// two eigen buffers for each decomposition for store and restore.
eigenBufferHelper = new BufferIndexHelper(eigenCount, 0);
// two matrices for each node less the root
matrixBufferHelper = new BufferIndexHelper(nodeCount, 0);
this.extraBufferCount =
branchModel.requiresMatrixConvolution()
? (bufferPoolSize > 0 ? bufferPoolSize : BUFFER_POOL_SIZE_DEFAULT)
: 0;
if (branchModel.requiresMatrixConvolution() && this.extraBufferCount < eigenCount) {
throw new RuntimeException(
"SubstitutionModelDelegate requires at least "
+ eigenCount
+ " extra buffers to convolve matrices");
}
for (int i = 0; i < extraBufferCount; i++) {
pushAvailableBuffer(i + matrixBufferHelper.getBufferCount());
}
// one extra created as a reserve
// which is used to free up buffers when the avail stack is empty.
reserveBufferIndex = matrixBufferHelper.getBufferCount() + extraBufferCount;
if (DEBUG) {
System.out.println("Creating reserve buffer with index: " + reserveBufferIndex);
}
} // END: Constructor
public int getMatrixBufferCount() {
// plus one for the reserve buffer
return matrixBufferHelper.getBufferCount() + extraBufferCount + 1;
}
public int getEigenBufferCount() {
return eigenBufferHelper.getBufferCount();
}