protected BeagleTreeLikelihood createTreeLikelihood(
PatternList patternList, //
TreeModel treeModel, //
BranchModel branchModel, //
GammaSiteRateModel siteRateModel, //
BranchRateModel branchRateModel, //
TipStatesModel tipStatesModel, //
boolean useAmbiguities, //
PartialsRescalingScheme scalingScheme, //
Map<
Set<String>, //
Parameter>
partialsRestrictions, //
XMLObject xo //
) throws XMLParseException {
boolean integrateGainRate = xo.getBooleanAttribute(INTEGRATE_GAIN_RATE);
useAmbiguities = true; // TODO No effect
if (scalingScheme != PartialsRescalingScheme.NONE) {
throw new XMLParseException(
"No rescaling scheme is currently support by the mutation-death model " + xo.getId());
}
Parameter mu = ((MutationDeathModel) siteRateModel.getSubstitutionModel()).getDeathParameter();
Parameter lam;
if (!integrateGainRate) {
lam = (Parameter) xo.getElementFirstChild(IMMIGRATION_RATE);
} else {
lam = new Parameter.Default("gainRate", 1.0, 0.001, 1.999);
}
AbstractObservationProcess observationProcess = null;
Logger.getLogger("dr.evolution")
.info("\n ---------------------------------\nCreating a BEAGLE ALSTreeLikelihood model.");
for (int i = 0; i < xo.getChildCount(); ++i) {
Object cxo = xo.getChild(i);
if (cxo instanceof XMLObject && ((XMLObject) cxo).getName().equals(OBSERVATION_PROCESS)) {
if (((XMLObject) cxo).getStringAttribute(OBSERVATION_TYPE).equals("singleTip")) {
String taxonName = ((XMLObject) cxo).getStringAttribute(OBSERVATION_TAXON);
Taxon taxon = treeModel.getTaxon(treeModel.getTaxonIndex(taxonName));
observationProcess =
new SingleTipObservationProcess(
treeModel, patternList, siteRateModel, branchRateModel, mu, lam, taxon);
Logger.getLogger("dr.evolution").info("All traits are assumed extant in " + taxonName);
} else { // "anyTip" observation process
observationProcess =
new AnyTipObservationProcess(
ANY_TIP, treeModel, patternList, siteRateModel, branchRateModel, mu, lam);
Logger.getLogger("dr.evolution")
.info("Observed traits are assumed to be extant in at least one tip node.");
}
observationProcess.setIntegrateGainRate(integrateGainRate);
}
}
Logger.getLogger("dr.evolution")
.info(
"\tIf you publish results using Acquisition-Loss-Mutation (ALS) Model likelihood, please reference Alekseyenko, Lee and Suchard (2008) Syst. Biol 57: 772-784.\n---------------------------------\n");
return new ALSBeagleTreeLikelihood(
observationProcess,
patternList,
treeModel,
branchModel,
siteRateModel,
branchRateModel,
tipStatesModel,
useAmbiguities,
scalingScheme,
partialsRestrictions);
}
