public static void checkTree(TreeModel treeModel) {
// todo Should only be run if there exists a zero-length interval
// TreeModel treeModel = (TreeModel) tree;
for (int i = 0; i < treeModel.getInternalNodeCount(); i++) {
NodeRef node = treeModel.getInternalNode(i);
if (node != treeModel.getRoot()) {
double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
double childHeight0 = treeModel.getNodeHeight(treeModel.getChild(node, 0));
double childHeight1 = treeModel.getNodeHeight(treeModel.getChild(node, 1));
double maxChild = childHeight0;
if (childHeight1 > maxChild) maxChild = childHeight1;
double newHeight = maxChild + MathUtils.nextDouble() * (parentHeight - maxChild);
treeModel.setNodeHeight(node, newHeight);
}
}
treeModel.pushTreeChangedEvent();
}
/** Constructor. */
public CenancestorTreeLikelihood(
PatternList patternList,
TreeModel treeModel,
SiteModel siteModel,
CenancestorBranchRateModel branchRateModel,
TipStatesModel tipStatesModel,
Parameter cenancestorHeight,
Parameter cenancestorBranch,
// Parameter asStatistic,
boolean useAmbiguities,
boolean allowMissingTaxa,
boolean storePartials,
boolean forceJavaCore,
boolean forceRescaling) {
super(CenancestorTreeLikelihoodParser.TREE_LIKELIHOOD, patternList, treeModel);
this.storePartials = storePartials;
nodeCount = treeModel.getNodeCount() + 1;
updateNode = new boolean[nodeCount];
for (int i = 0; i < nodeCount; i++) {
updateNode[i] = true;
}
try {
this.siteModel = siteModel;
addModel(siteModel);
this.frequencyModel = siteModel.getFrequencyModel();
addModel(frequencyModel);
this.tipStatesModel = tipStatesModel;
integrateAcrossCategories = siteModel.integrateAcrossCategories();
this.categoryCount = siteModel.getCategoryCount();
this.cenancestorHeight = cenancestorHeight;
addVariable(cenancestorHeight);
cenancestorHeight.addBounds(
new Parameter.DefaultBounds(
Double.POSITIVE_INFINITY,
0.0,
1)); // TODO The lower bound should be the maximum leaf height
this.cenancestorBranch = cenancestorBranch;
cenancestorBranch.addBounds(
new Parameter.DefaultBounds(
Double.POSITIVE_INFINITY,
0.0,
1)); // TODO The upper bound should be the maximum leaf height
addVariable(cenancestorBranch);
// if (asStatistic == cenancestorHeight){
// this.branchRules=true;
// }
// if (branchRules==true){
updateCenancestorHeight(); // Trying to avoid improper initial values
// }
// else{
// updateCenancestorBranch();
// }
final Logger logger = Logger.getLogger("dr.evomodel");
String coreName = "Java general";
/** TODO: Check if is worthy to implement other datatypes. */
final DataType dataType = patternList.getDataType();
if (dataType instanceof dr.evolution.datatype.TwoStates) {
coreName = "Java cenancestor binary";
cenancestorlikelihoodCore =
new GeneralCenancestorLikelihoodCore(patternList.getStateCount());
} else if (dataType instanceof dr.evolution.datatype.GeneralDataType) {
coreName = "Java cenancestor CNV";
cenancestorlikelihoodCore =
new GeneralCenancestorLikelihoodCore(patternList.getStateCount());
}
/* if (integrateAcrossCategories) {
final DataType dataType = patternList.getDataType();
if (dataType instanceof dr.evolution.datatype.Nucleotides) {
if (!forceJavaCore && NativeNucleotideLikelihoodCore.isAvailable()) {
coreName = "native nucleotide";
likelihoodCore = new NativeNucleotideLikelihoodCore();
} else {
coreName = "Java nucleotide";
likelihoodCore = new NucleotideLikelihoodCore();
}
} else if (dataType instanceof dr.evolution.datatype.AminoAcids) {
if (!forceJavaCore && NativeAminoAcidLikelihoodCore.isAvailable()) {
coreName = "native amino acid";
likelihoodCore = new NativeAminoAcidLikelihoodCore();
} else {
coreName = "Java amino acid";
likelihoodCore = new AminoAcidLikelihoodCore();
}
// The codon core was out of date and did nothing more than the general core...
} else if (dataType instanceof dr.evolution.datatype.Codons) {
if (!forceJavaCore && NativeGeneralLikelihoodCore.isAvailable()) {
coreName = "native general";
likelihoodCore = new NativeGeneralLikelihoodCore(patternList.getStateCount());
} else {
coreName = "Java general";
likelihoodCore = new GeneralLikelihoodCore(patternList.getStateCount());
}
useAmbiguities = true;
} else {
if (!forceJavaCore && NativeGeneralLikelihoodCore.isAvailable()) {
coreName = "native general";
likelihoodCore = new NativeGeneralLikelihoodCore(patternList.getStateCount());
} else {
coreName = "Java general";
likelihoodCore = new GeneralLikelihoodCore(patternList.getStateCount());
}
}
} else {
likelihoodCore = new GeneralLikelihoodCore(patternList.getStateCount());
}*/
{
final String id = getId();
logger.info(
"TreeLikelihood("
+ ((id != null) ? id : treeModel.getId())
+ ") using "
+ coreName
+ " likelihood core");
logger.info(
" " + (useAmbiguities ? "Using" : "Ignoring") + " ambiguities in tree likelihood.");
logger.info(" With " + patternList.getPatternCount() + " unique site patterns.");
}
if (branchRateModel != null) {
this.branchRateModel = branchRateModel;
logger.info("Branch rate model used: " + branchRateModel.getModelName());
} else {
this.branchRateModel = new DefaultCenancestorBranchRateModel();
}
addModel(this.branchRateModel);
probabilities = new double[stateCount * stateCount];
cenancestorlikelihoodCore.initialize(
nodeCount, patternCount, categoryCount, integrateAcrossCategories);
int extNodeCount = treeModel.getExternalNodeCount();
int intNodeCount = treeModel.getInternalNodeCount();
if (tipStatesModel != null) {
tipStatesModel.setTree(treeModel);
tipPartials = new double[patternCount * stateCount];
for (int i = 0; i < extNodeCount; i++) {
// Find the id of tip i in the patternList
String id = treeModel.getTaxonId(i);
int index = patternList.getTaxonIndex(id);
if (index == -1) {
throw new TaxonList.MissingTaxonException(
"Taxon, "
+ id
+ ", in tree, "
+ treeModel.getId()
+ ", is not found in patternList, "
+ patternList.getId());
}
tipStatesModel.setStates(patternList, index, i, id);
cenancestorlikelihoodCore.createNodePartials(i);
}
addModel(tipStatesModel);
} else {
for (int i = 0; i < extNodeCount; i++) {
// Find the id of tip i in the patternList
String id = treeModel.getTaxonId(i);
int index = patternList.getTaxonIndex(id);
if (index == -1) {
if (!allowMissingTaxa) {
throw new TaxonList.MissingTaxonException(
"Taxon, "
+ id
+ ", in tree, "
+ treeModel.getId()
+ ", is not found in patternList, "
+ patternList.getId());
}
if (useAmbiguities) {
setMissingPartials((LikelihoodCore) cenancestorlikelihoodCore, i);
} else {
setMissingStates((LikelihoodCore) cenancestorlikelihoodCore, i);
}
} else {
if (useAmbiguities) {
setPartials(
(LikelihoodCore) cenancestorlikelihoodCore, patternList, categoryCount, index, i);
} else {
setStates((LikelihoodCore) cenancestorlikelihoodCore, patternList, index, i);
}
}
}
}
for (int i = 0; i <= intNodeCount; i++) { // Added one step for the cenancestor
cenancestorlikelihoodCore.createNodePartials(extNodeCount + i);
}
if (forceRescaling) {
cenancestorlikelihoodCore.setUseScaling(true);
logger.info(" Forcing use of partials rescaling.");
}
} catch (TaxonList.MissingTaxonException mte) {
throw new RuntimeException(mte.toString());
}
addStatistic(new SiteLikelihoodsStatistic());
}