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/**
*
*/
package beagle;
import java.util.*;
import java.util.logging.Logger;
/**
* @author Marc Suchard
* @author Andrew Rambaut
*
*/
public class BeagleFactory {
private static Map<Integer, ResourceDetails> resourceDetailsMap = new HashMap<Integer, ResourceDetails>();
public static String getVersionInformation() {
getBeagleJNIWrapper();
if (BeagleJNIWrapper.INSTANCE != null) {
try {
return BeagleJNIWrapper.INSTANCE.getCitation();
} catch (UnsatisfiedLinkError ule) {
// If this method is not available then we must be linked to a v1.x BEAGLE library
return "Using BEAGLE library v1.x for accelerated, parallel likelihood evaluation\n" +
"2009-2013, BEAGLE Working Group - http://beagle-lib.googlecode.com/\n" +
"Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100";
}
}
return "BEAGLE not installed/found";
}
public static String getVersion() {
getBeagleJNIWrapper();
if (BeagleJNIWrapper.INSTANCE != null) {
try {
return BeagleJNIWrapper.INSTANCE.getVersion();
} catch (UnsatisfiedLinkError ule) {
// If this method is not available then we must be linked to a v1.x BEAGLE library
return "1.x";
}
}
return "BEAGLE not installed/found";
}
public static List<ResourceDetails> getResourceDetails() {
getBeagleJNIWrapper();
return new ArrayList<ResourceDetails>(resourceDetailsMap.values());
}
public static ResourceDetails getResourceDetails(int resourceNumber) {
getBeagleJNIWrapper();
// System.err.println("resourceNumber = "+resourceNumber);
return resourceDetailsMap.get(resourceNumber);
}
public static Beagle loadBeagleInstance(
int tipCount,
int partialsBufferCount,
int compactBufferCount,
int stateCount,
int patternCount,
int eigenBufferCount,
int matrixBufferCount,
int categoryCount,
int scaleBufferCount,
int[] resourceList,
long preferenceFlags,
long requirementFlags
) {
boolean forceJava = Boolean.valueOf(System.getProperty("java.only"));
// boolean forceHybrid = Boolean.valueOf(System.getProperty("force.hybrid"));
getBeagleJNIWrapper();
if (!forceJava && BeagleJNIWrapper.INSTANCE != null) {
try {
Beagle beagle = new BeagleJNIImpl(
tipCount,
partialsBufferCount,
compactBufferCount,
stateCount,
patternCount,
eigenBufferCount,
matrixBufferCount,
categoryCount,
scaleBufferCount,
resourceList,
preferenceFlags,
requirementFlags
);
// In order to know that it was a CPU instance created, we have to let BEAGLE
// to make the instance and then override it...
InstanceDetails details = beagle.getDetails();
if (details != null) // If resourceList/requirements not met, details == null here
return beagle;
} catch (BeagleException beagleException) {
Logger.getLogger("beagle").info(" "+beagleException.getMessage());
}
}
if (!forceJava) {
throw new RuntimeException("No acceptable BEAGLE library plugins found. " +
"Make sure that BEAGLE is properly installed or try changing resource requirements.");
}
return new GeneralBeagleImpl(tipCount,
partialsBufferCount,
compactBufferCount,
stateCount,
patternCount,
eigenBufferCount,
matrixBufferCount,
categoryCount,
scaleBufferCount
);
}
private static BeagleJNIWrapper getBeagleJNIWrapper() {
if (BeagleJNIWrapper.INSTANCE == null) {
try {
BeagleJNIWrapper.loadBeagleLibrary();
// System.err.println("BEAGLE library loaded");
} catch (UnsatisfiedLinkError ule) {
System.err.println("Failed to load BEAGLE library: " + ule.getMessage());
}
if (BeagleJNIWrapper.INSTANCE != null) {
for (ResourceDetails details : BeagleJNIWrapper.INSTANCE.getResourceList()) {
resourceDetailsMap.put(details.getNumber(), details);
}
}
}
return BeagleJNIWrapper.INSTANCE;
}
// Code and constants for test main()
private final static String human = "AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA";
private final static String chimp = "AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA";
private final static String gorilla = "AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA";
private static int[] getStates(String sequence) {
int[] states = new int[sequence.length()];
for (int i = 0; i < sequence.length(); i++) {
switch (sequence.charAt(i)) {
case 'A':
states[i] = 0;
break;
case 'C':
states[i] = 1;
break;
case 'G':
states[i] = 2;
break;
case 'T':
states[i] = 3;
break;
default:
states[i] = 4;
break;
}
}
return states;
}
private static double[] getPartials(String sequence) {
double[] partials = new double[sequence.length() * 4];
int k = 0;
for (int i = 0; i < sequence.length(); i++) {
switch (sequence.charAt(i)) {
case 'A':
partials[k++] = 1;
partials[k++] = 0;
partials[k++] = 0;
partials[k++] = 0;
break;
case 'C':
partials[k++] = 0;
partials[k++] = 1;
partials[k++] = 0;
partials[k++] = 0;
break;
case 'G':
partials[k++] = 0;
partials[k++] = 0;
partials[k++] = 1;
partials[k++] = 0;
break;
case 'T':
partials[k++] = 0;
partials[k++] = 0;
partials[k++] = 0;
partials[k++] = 1;
break;
default:
partials[k++] = 1;
partials[k++] = 1;
partials[k++] = 1;
partials[k++] = 1;
break;
}
}
return partials;
}
public static void main(String[] argv) {
// is nucleotides...
int stateCount = 4;
// get the number of site patterns
int nPatterns = human.length();
BeagleInfo.printVersionInformation();
BeagleInfo.printResourceList();
System.setProperty("java.only", "true");
// create an instance of the BEAGLE library
Beagle instance = loadBeagleInstance(
3, /**< Number of tip data elements (input) */
5, /**< Number of partials buffers to create (input) */
3, /**< Number of compact state representation buffers to create (input) */
stateCount, /**< Number of states in the continuous-time Markov chain (input) */
nPatterns, /**< Number of site patterns to be handled by the instance (input) */
1, /**< Number of rate matrix eigen-decomposition buffers to allocate (input) */
4, /**< Number of rate matrix buffers (input) */
1, /**< Number of rate categories (input) */
3, /**< Number of scale buffers (input) */
new int[] {1, 0},
0,
// BeagleFlag.PROCESSOR_GPU.getMask(),
0
);
if (instance == null) {
System.err.println("Failed to obtain BEAGLE instance");
System.exit(1);
}
StringBuilder sb = new StringBuilder();
for (BeagleFlag flag : BeagleFlag.values()) {
if (flag.isSet(instance.getDetails().getFlags())) {
sb.append(" ").append(flag.name());
}
}
System.out.println("Instance on resource #" + instance.getDetails().getResourceNumber() + " flags:" + sb.toString());
double[] patternWeights = new double[nPatterns];
for (int i = 0; i < nPatterns; i++) {
patternWeights[i] = 1.0;
}
instance.setPatternWeights(patternWeights);
instance.setTipStates(0, getStates(human));
instance.setTipStates(1, getStates(chimp));
instance.setTipStates(2, getStates(gorilla));
// set the sequences for each tip using partial likelihood arrays
// instance.setPartials(0, getPartials(human));
// instance.setPartials(1, getPartials(chimp));
// instance.setPartials(2, getPartials(gorilla));
final double[] rates = { 1.0 };
instance.setCategoryRates(rates);
// create an array containing site category weights
final double[] weights = { 1.0 };
instance.setCategoryWeights(0, weights);
// create base frequency array
final double[] freqs = { 0.25, 0.25, 0.25, 0.25 };
instance.setStateFrequencies(0, freqs);
// an eigen decomposition for the JC69 model
final double[] evec = {
1.0, 2.0, 0.0, 0.5,
1.0, -2.0, 0.5, 0.0,
1.0, 2.0, 0.0, -0.5,
1.0, -2.0, -0.5, 0.0
};
final double[] ivec = {
0.25, 0.25, 0.25, 0.25,
0.125, -0.125, 0.125, -0.125,
0.0, 1.0, 0.0, -1.0,
1.0, 0.0, -1.0, 0.0
};
double[] eval = { 0.0, -1.3333333333333333, -1.3333333333333333, -1.3333333333333333 };
// set the Eigen decomposition
instance.setEigenDecomposition(0, evec, ivec, eval);
// a list of indices and edge lengths
int[] nodeIndices = { 0, 1, 2, 3 };
double[] edgeLengths = { 0.1, 0.1, 0.2, 0.1 };
// tell BEAGLE to populate the transition matrices for the above edge lengths
instance.updateTransitionMatrices(
0, // eigenIndex
nodeIndices, // probabilityIndices
null, // firstDerivativeIndices
null, // secondDervativeIndices
edgeLengths, // edgeLengths
4); // count
instance.resetScaleFactors(2);
// create a list of partial likelihood update operations
// the order is [dest, writeScale, readScale, source1, matrix1, source2, matrix2]
int[] operations = {
3, 0, 0, 0, 0, 1, 1,
4, 1, 1, 2, 2, 3, 3
};
int[] rootIndices = { 4 };
// update the partials
instance.updatePartials(
operations, // eigenIndex
2, // operationCount
2); // rescale ?
int[] scalingFactorsIndices = {2}; // internal nodes
// TODO Need to call accumulateScaleFactors if scaling is enabled
int[] weightIndices = { 0 };
int[] freqIndices = { 0 };
double[] sumLogLik = new double[1];
// calculate the site likelihoods at the root node
instance.calculateRootLogLikelihoods(
rootIndices, // bufferIndices
weightIndices, // weights
freqIndices, // stateFrequencies
scalingFactorsIndices,
1,
sumLogLik); // outLogLikelihoods
System.out.println("logL = " + sumLogLik[0] + " (PAUP logL = -1574.63623)");
}
}
|
