use of dr.evomodel.treelikelihood.AbstractTreeLikelihood in project beast-mcmc by beast-dev.
the class BalancedBeagleTreeLikelihoodParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean useAmbiguities = xo.getAttribute(BeagleTreeLikelihoodParser.USE_AMBIGUITIES, false);
/*int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
if (instanceCount < 1) {
instanceCount = 1;
}
String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
if (ic != null && ic.length() > 0) {
instanceCount = Integer.parseInt(ic);
}*/
PatternList patternList = (PatternList) xo.getChild(PatternList.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
GammaSiteRateModel siteRateModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
if (branchModel == null) {
SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
if (substitutionModel == null) {
substitutionModel = siteRateModel.getSubstitutionModel();
}
if (substitutionModel == null) {
throw new XMLParseException("No substitution model available for TreeLikelihood: " + xo.getId());
}
branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
}
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
// if (xo.getChild(TipStatesModel.class) != null) {
// throw new XMLParseException("Sequence Error Models are not supported under BEAGLE yet. Please use Native BEAST Likelihood.");
// }
PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
if (xo.hasAttribute(BeagleTreeLikelihoodParser.SCALING_SCHEME)) {
// scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(BeagleTreeLikelihoodParser.SCALING_SCHEME));
if (scalingScheme == null)
throw new XMLParseException("Unknown scaling scheme '" + xo.getStringAttribute(BeagleTreeLikelihoodParser.SCALING_SCHEME) + "' in " + "OldBeagleTreeLikelihood object '" + xo.getId());
}
boolean delayScaling = true;
Map<Set<String>, Parameter> partialsRestrictions = null;
if (xo.hasChildNamed(PARTIALS_RESTRICTION)) {
XMLObject cxo = xo.getChild(PARTIALS_RESTRICTION);
TaxonList taxonList = (TaxonList) cxo.getChild(TaxonList.class);
// Parameter parameter = (Parameter) cxo.getChild(Parameter.class);
try {
TreeUtils.getLeavesForTaxa(treeModel, taxonList);
} catch (TreeUtils.MissingTaxonException e) {
throw new XMLParseException("Unable to parse taxon list: " + e.getMessage());
}
throw new XMLParseException("Restricting internal nodes is not yet implemented. Contact Marc");
}
/*if (instanceCount == 1 || patternList.getPatternCount() < instanceCount) {
return createTreeLikelihood(
patternList,
treeModel,
branchModel,
siteRateModel,
branchRateModel,
tipStatesModel,
useAmbiguities,
scalingScheme,
partialsRestrictions,
xo
);
}*/
//first run a test for instanceCount == 1
System.err.println("\nTesting instanceCount == 1");
Likelihood baseLikelihood = createTreeLikelihood(patternList, treeModel, branchModel, siteRateModel, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
double start = System.nanoTime();
for (int i = 0; i < TEST_RUNS; i++) {
baseLikelihood.makeDirty();
baseLikelihood.getLogLikelihood();
}
double end = System.nanoTime();
double baseResult = end - start;
System.err.println("Evaluation took: " + baseResult);
if (!(patternList instanceof SitePatterns)) {
throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with BEAUti-selected codon partitioning.");
}
if (tipStatesModel != null) {
throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
}
//List<Likelihood> likelihoods = new ArrayList<Likelihood>();
List<Likelihood> likelihoods = null;
CompoundLikelihood compound = null;
int instanceCount = 2;
boolean optimal = false;
while (optimal == false) {
System.err.println("\nCreating instanceCount == " + instanceCount);
likelihoods = new ArrayList<Likelihood>();
for (int i = 0; i < instanceCount; i++) {
Patterns subPatterns = new Patterns((SitePatterns) patternList, 0, 0, 1, i, instanceCount);
AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(subPatterns, treeModel, branchModel, siteRateModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
treeLikelihood.setId(xo.getId() + "_" + instanceCount);
likelihoods.add(treeLikelihood);
}
//construct compoundLikelihood
compound = new CompoundLikelihood(instanceCount, likelihoods);
//test timings
System.err.println("\nTesting instanceCount == " + instanceCount);
start = System.nanoTime();
for (int i = 0; i < TEST_RUNS; i++) {
compound.makeDirty();
compound.getLogLikelihood();
}
end = System.nanoTime();
double newResult = end - start;
System.err.println("Evaluation took: " + newResult);
if (baseResult / newResult > TEST_CUTOFF) {
instanceCount++;
baseResult = newResult;
} else {
optimal = true;
instanceCount--;
System.err.println("\nCreating final BeagleTreeLikelihood with instanceCount: " + instanceCount);
likelihoods = new ArrayList<Likelihood>();
for (int i = 0; i < instanceCount; i++) {
Patterns subPatterns = new Patterns((SitePatterns) patternList, 0, 0, 1, i, instanceCount);
AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(subPatterns, treeModel, branchModel, siteRateModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
treeLikelihood.setId(xo.getId() + "_" + instanceCount);
likelihoods.add(treeLikelihood);
}
//construct compoundLikelihood
compound = new CompoundLikelihood(instanceCount, likelihoods);
}
}
return compound;
/*for (int i = 0; i < instanceCount; i++) {
Patterns subPatterns = new Patterns((SitePatterns)patternList, 0, 0, 1, i, instanceCount);
AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(
subPatterns,
treeModel,
branchModel,
siteRateModel,
branchRateModel,
null,
useAmbiguities,
scalingScheme,
partialsRestrictions,
xo);
treeLikelihood.setId(xo.getId() + "_" + instanceCount);
likelihoods.add(treeLikelihood);
}
return new CompoundLikelihood(likelihoods);*/
}
use of dr.evomodel.treelikelihood.AbstractTreeLikelihood in project beast-mcmc by beast-dev.
the class BeagleTreeLikelihoodParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean useAmbiguities = xo.getAttribute(USE_AMBIGUITIES, false);
int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
if (instanceCount < 1) {
instanceCount = 1;
}
String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
if (ic != null && ic.length() > 0) {
instanceCount = Integer.parseInt(ic);
}
PatternList patternList = (PatternList) xo.getChild(PatternList.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
GammaSiteRateModel siteRateModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
if (branchModel == null) {
SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
if (substitutionModel == null) {
substitutionModel = siteRateModel.getSubstitutionModel();
}
if (substitutionModel == null) {
throw new XMLParseException("No substitution model available for TreeLikelihood: " + xo.getId());
}
branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
}
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
// if (xo.getChild(TipStatesModel.class) != null) {
// throw new XMLParseException("Sequence Error Models are not supported under BEAGLE yet. Please use Native BEAST Likelihood.");
// }
PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
boolean delayScaling = true;
if (xo.hasAttribute(SCALING_SCHEME)) {
scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(SCALING_SCHEME));
if (scalingScheme == null)
throw new XMLParseException("Unknown scaling scheme '" + xo.getStringAttribute(SCALING_SCHEME) + "' in " + "OldBeagleTreeLikelihood object '" + xo.getId());
}
if (xo.hasAttribute(DELAY_SCALING)) {
delayScaling = xo.getBooleanAttribute(DELAY_SCALING);
}
Map<Set<String>, Parameter> partialsRestrictions = null;
if (xo.hasChildNamed(PARTIALS_RESTRICTION)) {
XMLObject cxo = xo.getChild(PARTIALS_RESTRICTION);
TaxonList taxonList = (TaxonList) cxo.getChild(TaxonList.class);
// Parameter parameter = (Parameter) cxo.getChild(Parameter.class);
try {
TreeUtils.getLeavesForTaxa(treeModel, taxonList);
} catch (TreeUtils.MissingTaxonException e) {
throw new XMLParseException("Unable to parse taxon list: " + e.getMessage());
}
throw new XMLParseException("Restricting internal nodes is not yet implemented. Contact Marc");
}
if (instanceCount == 1 || patternList.getPatternCount() < instanceCount) {
return createTreeLikelihood(patternList, treeModel, branchModel, siteRateModel, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
}
if (tipStatesModel != null) {
throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
}
List<Likelihood> likelihoods = new ArrayList<Likelihood>();
for (int i = 0; i < instanceCount; i++) {
Patterns subPatterns = new Patterns(patternList, i, instanceCount);
AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(subPatterns, treeModel, branchModel, siteRateModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, xo);
treeLikelihood.setId(xo.getId() + "_" + instanceCount);
likelihoods.add(treeLikelihood);
}
return new CompoundLikelihood(likelihoods);
}
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