@SuppressWarnings("unchecked")
public void sync(int iPartition) {
if (parentInputs.size() > 0 && _input.get() != null) {
Input<?> input = parentInputs.get(iPartition);
if (bIsList) {
List<Object> list = (List<Object>) _input.get();
List<Object> targetList = ((List<Object>) input.get());
// targetList.clear();
// only clear former members
for (BEASTInterface plugin : startInputs) {
targetList.remove(plugin);
}
targetList.addAll(list);
// sync outputs of items in list
for (Object o : list) {
if (o instanceof BEASTInterface) {
((BEASTInterface) o).getOutputs().add(parentPlugins.get(iPartition));
}
}
} else {
try {
// System.err.println("sync " + parentPlugins.get(iPartition) + "[" + input.getName() + "]
// = " + _input.get());
input.setValue(_input.get(), parentPlugins.get(iPartition));
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
@Override
public void initAndValidate() {
scaleFactor = scaleFactorInput.get();
// determine taxon set to choose from
if (taxonsetInput.get() != null) {
List<String> taxaNames = new ArrayList<>();
for (String taxon : treeInput.get().getTaxaNames()) {
taxaNames.add(taxon);
}
List<String> set = taxonsetInput.get().asStringList();
int nrOfTaxa = set.size();
taxonIndices = new int[nrOfTaxa];
int k = 0;
for (String taxon : set) {
int taxonIndex = taxaNames.indexOf(taxon);
if (taxonIndex < 0) {
throw new IllegalArgumentException("Cannot find taxon " + taxon + " in tree");
}
taxonIndices[k++] = taxonIndex;
}
} else {
taxonIndices = new int[treeInput.get().getTaxaNames().length];
for (int i = 0; i < taxonIndices.length; i++) {
taxonIndices[i] = i;
}
}
}
public void initAndValidate() {
testCorrect = testCorrectInput.get();
paramList = paramListInput.get();
modelList = modelListInput.get();
freqsList = freqsListInput.get();
paramPointers = paramPointersInput.get();
modelPointers = modelPointersInput.get();
freqsPointers = freqsPointersInput.get();
pointerCount = paramPointers.getDimension();
dp = dpInput.get();
List<ParametricDistribution> distrs = dp.getBaseDistributions();
paramBaseDistr = distrs.get(0);
modelBaseDistr = distrs.get(1);
freqsBaseDistr = distrs.get(2);
tempLikelihood = tempLikelihoodInput.get();
dpTreeLikelihood = dpTreeLikelihoodInput.get();
modelNetworkMap.put(1.0, new double[] {3.0});
modelNetworkMap.put(2.0, new double[] {3.0});
modelNetworkMap.put(3.0, new double[] {1.0, 2.0, 4.0});
modelNetworkMap.put(4.0, new double[] {3.0, 5.0});
modelNetworkMap.put(5.0, new double[] {4.0});
// System.out.println("is null? "+(modelNetworkMap.get(5.0) == null));
}
private void calcPatternPoints(int nPatterns) {
patternPoints = new int[threadCount + 1];
if (proportionsInput.get() == null) {
int range = nPatterns / threadCount;
for (int i = 0; i < threadCount - 1; i++) {
patternPoints[i + 1] = range * (i + 1);
}
patternPoints[threadCount] = nPatterns;
} else {
String[] strs = proportionsInput.get().split("\\s+");
double[] proportions = new double[threadCount];
for (int i = 0; i < threadCount; i++) {
proportions[i] = Double.parseDouble(strs[i % strs.length]);
}
// normalise
double sum = 0;
for (double d : proportions) {
sum += d;
}
for (int i = 0; i < threadCount; i++) {
proportions[i] /= sum;
}
// cummulative
for (int i = 1; i < threadCount; i++) {
proportions[i] += proportions[i - 1];
}
// calc ranges
for (int i = 0; i < threadCount; i++) {
patternPoints[i + 1] = (int) (proportions[i] * nPatterns + 0.5);
}
}
}
/**
* Calculate probability of choosing region affected by the given conversion under the
* ClonalOrigin model.
*
* @param conv conversion region is associated with
* @return log probability density
*/
public double getAffectedRegionProb(Conversion conv) {
double logP = 0.0;
// Total effective number of possible start sites
double alpha =
acg.getTotalSequenceLength() + acg.getLoci().size() * deltaInput.get().getValue();
// Calculate probability of converted region.
if (conv.getStartSite() == 0) logP += Math.log((deltaInput.get().getValue() + 1) / alpha);
else logP += Math.log(1.0 / alpha);
// Probability of end site:
double probEnd =
Math.pow(1.0 - 1.0 / deltaInput.get().getValue(), conv.getEndSite() - conv.getStartSite())
/ deltaInput.get().getValue();
// Include probability of going past the end:
if (conv.getEndSite() == conv.getLocus().getSiteCount() - 1)
probEnd +=
Math.pow(
1.0 - 1.0 / deltaInput.get().getValue(),
conv.getLocus().getSiteCount() - conv.getStartSite());
logP += Math.log(probEnd);
return logP;
}
/**
* Choose region to be affected by this conversion.
*
* @param conv Conversion object where these sites are stored.
* @return log probability density of chosen attachment.
*/
public double drawAffectedRegion(Conversion conv) {
double logP = 0.0;
// Total effective number of possible start sites
double alpha =
acg.getTotalSequenceLength() + acg.getLoci().size() * deltaInput.get().getValue();
// Draw location of converted region.
int startSite = -1;
int endSite;
Locus locus = null;
double u = Randomizer.nextDouble() * alpha;
for (Locus thisLocus : acg.getLoci()) {
if (u < deltaInput.get().getValue() + thisLocus.getSiteCount()) {
locus = thisLocus;
if (u < deltaInput.get().getValue()) {
startSite = 0;
logP += Math.log(deltaInput.get().getValue() / alpha);
} else {
startSite = (int) (u - deltaInput.get().getValue());
logP += Math.log(1.0 / alpha);
}
break;
}
u -= deltaInput.get().getValue() + thisLocus.getSiteCount();
}
if (locus == null)
throw new IllegalStateException(
"Programmer error: " + "loop in drawAffectedRegion() fell through.");
endSite = startSite + (int) Randomizer.nextGeometric(1.0 / deltaInput.get().getValue());
endSite = Math.min(endSite, locus.getSiteCount() - 1);
// Probability of end site:
double probEnd =
Math.pow(1.0 - 1.0 / deltaInput.get().getValue(), endSite - startSite)
/ deltaInput.get().getValue();
// Include probability of going past the end:
if (endSite == locus.getSiteCount() - 1)
probEnd +=
Math.pow(1.0 - 1.0 / deltaInput.get().getValue(), locus.getSiteCount() - startSite);
logP += Math.log(probEnd);
conv.setLocus(locus);
conv.setStartSite(startSite);
conv.setEndSite(endSite);
return logP;
}
@Override
public void initAndValidate() {
meanRate = meanRateInput.get();
speciesTreeRatesX = speciesTreeRatesInput.get();
geneTree = geneTreeInput.get();
geneNodeCount = geneTree.getNodeCount();
branchRates = new double[geneNodeCount];
storedBranchRates = new double[geneNodeCount];
needsUpdate = true;
}
/**
* Evaluate rate multiplier expression for the given variable values.
*
* @param scalarVarNames Names of scalar variables in expression
* @param scalarVarVals Values of scalar variables in expression
* @param vectorVarNames Names of vector variables in expression
* @param vectorVarVals Values of vector variables in expression
* @param functions
* @return result of evaluating the expression
*/
public double evaluate(
List<String> scalarVarNames,
int[] scalarVarVals,
List<String> vectorVarNames,
List<Double[]> vectorVarVals,
Map<String, Function> functions) {
if (visitor == null) {
// Parse predicate expression
ANTLRInputStream input = new ANTLRInputStream(expInput.get());
MASTERGrammarLexer lexer = new MASTERGrammarLexer(input);
CommonTokenStream tokens = new CommonTokenStream(lexer);
MASTERGrammarParser parser = new MASTERGrammarParser(tokens);
ParseTree parseTree = parser.expression();
visitor = new ExpressionEvaluator(parseTree, scalarVarNames, functions);
}
for (int i = 0; i < vectorVarNames.size(); i++)
visitor.setVectorVar(vectorVarNames.get(i), vectorVarVals.get(i));
Double[] res = visitor.evaluate(scalarVarVals);
if (res.length != 1) {
throw new IllegalArgumentException("Reaction rate multiplier must be scalar!");
}
return res[0];
}
/** convert plain text string to JSON string, replacing some entities * */
private String normalise(Input<?> input, String str) {
str = str.replaceAll("\\\\", "\\\\\\\\");
str = str.replaceAll("/", "\\\\/");
str = str.replaceAll("\b", "\\\\b");
str = str.replaceAll("\f", "\\\\f");
str = str.replaceAll("\t", "\\\\t");
str = str.replaceAll("\\r", "\\\\r");
str = str.replaceAll("\"", "\\\\\"");
str = str.replaceAll("\n", "\\\\n");
if (input != null
&& !input.getType().equals(Double.class)
&& !input.getType().equals(Integer.class)
&& !input.getType().equals(Boolean.class)) {
str = "\"" + str + "\"";
}
return str;
}
/**
* @param newick a string representing a tree in newick format
* @param adjustTipHeights true if the tip heights should be adjusted to 0 (i.e. contemporaneous)
* after reading in tree.
* @param allowSingleChildNodes true if internal nodes with single children are allowed
* @param isLabeled true if nodes are labeled with taxa labels
* @param offset if isLabeled == false and node labeling starts with x then offset should be x.
* When isLabeled == true offset should be 1 as by default.
* @throws Exception
*/
public TreeParser(
final String newick,
final boolean adjustTipHeights,
final boolean allowSingleChildNodes,
final boolean isLabeled,
final int offset)
throws Exception {
newickInput.setValue(newick, this);
isLabelledNewickInput.setValue(isLabeled, this);
adjustTipHeightsInput.setValue(adjustTipHeights, this);
allowSingleChildInput.setValue(allowSingleChildNodes, this);
offsetInput.setValue(offset, this);
initAndValidate();
}
@Override
public void init(PrintStream out) throws Exception {
final Tree tree = treeInput.get();
if (getID() == null || getID().matches("\\s*")) {
out.print(tree.getID() + ".SAcount\t");
} else {
out.print(getID() + "\t");
}
}
/**
* Create a tree from the given newick format
*
* @param taxaNames a list of taxa names to use, or null. If null then IsLabelledNewick will be
* set to true
* @param newick the newick of the tree
* @param offset the offset to map node numbers in newick format to indices in taxaNames. so,
* name(node with nodeNumber) = taxaNames[nodeNumber-offset]
* @param adjustTipHeightsWhenMissingDateTraits true if tip heights should be adjusted to zero
* @throws Exception
*/
public TreeParser(
final List<String> taxaNames,
final String newick,
final int offset,
final boolean adjustTipHeightsWhenMissingDateTraits)
throws Exception {
if (taxaNames == null) {
isLabelledNewickInput.setValue(true, this);
} else {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(taxaNames)), this);
}
newickInput.setValue(newick, this);
offsetInput.setValue(offset, this);
adjustTipHeightsInput.setValue(adjustTipHeightsWhenMissingDateTraits, this);
labels = taxaNames;
initAndValidate();
}
@Override
public void initAndValidate() {
interpreter = new Interpreter();
NamedFunction.evalFunctionInputs(interpreter, functionInputs.get());
String script = valueInput.get();
try {
interpreter.eval(script);
} catch (EvalError e) {
throw new RuntimeException(e);
}
}
/**
* create new instance of src object, connecting all inputs from src object Note if input is a
* SubstModel, it is duplicated as well.
*
* @param src object to be copied
* @param i index used to extend ID with.
* @return copy of src object
*/
private Object duplicate(BEASTInterface src, int i) {
if (src == null) {
return null;
}
BEASTInterface copy;
try {
copy = src.getClass().newInstance();
copy.setID(src.getID() + "_" + i);
} catch (InstantiationException | IllegalAccessException e) {
e.printStackTrace();
throw new RuntimeException(
"Programmer error: every object in the model should have a default constructor that is publicly accessible: "
+ src.getClass().getName());
}
for (Input<?> input : src.listInputs()) {
if (input.get() != null) {
if (input.get() instanceof List) {
// handle lists
// ((List)copy.getInput(input.getName())).clear();
for (Object o : (List<?>) input.get()) {
if (o instanceof BEASTInterface) {
// make sure it is not already in the list
copy.setInputValue(input.getName(), o);
}
}
} else if (input.get() instanceof SubstitutionModel) {
// duplicate subst models
BEASTInterface substModel = (BEASTInterface) duplicate((BEASTInterface) input.get(), i);
copy.setInputValue(input.getName(), substModel);
} else {
// it is some other value
copy.setInputValue(input.getName(), input.get());
}
}
}
copy.initAndValidate();
return copy;
}
public double proposal() {
double logq = 0.0;
// Pick two indcies at random
int index1 = Randomizer.nextInt(pointerCount);
int index2 = index1;
while (index2 == index1) {
index2 = Randomizer.nextInt(pointerCount);
}
int clusterIndex1 = paramPointers.indexInList(index1, paramList);
int clusterIndex2 = paramPointers.indexInList(index2, paramList);
// If the randomly draw sites are from the same cluster, perform a split-move.
if (clusterIndex1 == clusterIndex2) {
int[] clusterSites = dpValuableInput.get().getClusterSites(clusterIndex1);
double temp = split(index1, index2, clusterIndex1, clusterSites);
// System.out.println("split: "+temp);
logq += temp;
// System.out.println("split: "+temp);
} else {
// If the the two randomly drawn sites are not from the same cluster, perform a merge-move.
int[] cluster1Sites = dpValuableInput.get().getClusterSites(clusterIndex1);
int[] cluster2Sites = dpValuableInput.get().getClusterSites(clusterIndex2);
// logq = merge(index1, index2,clusterIndex1,clusterIndex2,cluster1Sites,cluster2Sites);
double temp =
merge(index1, index2, clusterIndex1, clusterIndex2, cluster1Sites, cluster2Sites);
// System.out.println("merge: "+temp);
logq = temp;
}
return logq;
}
@Override
public void initAndValidate() throws Exception {
sPathComponents = sPathInput.get().split("/");
if (sPathComponents[0].equals("")) {
sPathComponents = new String[0];
}
sConditionalAttribute = new String[sPathComponents.length];
sConditionalValue = new String[sPathComponents.length];
for (int i = 0; i < sPathComponents.length; i++) {
int j = sPathComponents[i].indexOf('[');
if (j >= 0) {
String sConditionalComponents =
sPathComponents[i].substring(j + 1, sPathComponents[i].lastIndexOf(']'));
String[] sStrs = sConditionalComponents.split("=");
sConditionalAttribute[i] = sStrs[0];
sConditionalValue[i] = sStrs[1].substring(1, sStrs[1].length() - 1);
sPathComponents[i] = sPathComponents[i].substring(0, j);
}
}
inputs = new ArrayList<BEASTInterface>();
startInputs = new ArrayList<BEASTInterface>();
BEASTObjectPanel.getID(this);
}
@Override
public void initAndValidate() {
threadCount = BeastMCMC.m_nThreads;
if (maxNrOfThreadsInput.get() > 0) {
threadCount = Math.min(maxNrOfThreadsInput.get(), BeastMCMC.m_nThreads);
}
String instanceCount = System.getProperty("beast.instance.count");
if (instanceCount != null && instanceCount.length() > 0) {
threadCount = Integer.parseInt(instanceCount);
}
logPByThread = new double[threadCount];
// sanity check: alignment should have same #taxa as tree
if (dataInput.get().getTaxonCount() != treeInput.get().getLeafNodeCount()) {
throw new IllegalArgumentException(
"The number of nodes in the tree does not match the number of sequences");
}
treelikelihood = new TreeLikelihood[threadCount];
if (dataInput.get().isAscertained) {
Log.warning.println(
"Note, can only use single thread per alignment because the alignment is ascertained");
threadCount = 1;
}
if (threadCount <= 1) {
treelikelihood[0] = new TreeLikelihood();
treelikelihood[0].setID(getID() + "0");
treelikelihood[0].initByName(
"data",
dataInput.get(),
"tree",
treeInput.get(),
"siteModel",
siteModelInput.get(),
"branchRateModel",
branchRateModelInput.get(),
"useAmbiguities",
useAmbiguitiesInput.get(),
"scaling",
scalingInput.get() + "");
treelikelihood[0].getOutputs().add(this);
likelihoodsInput.get().add(treelikelihood[0]);
} else {
pool = Executors.newFixedThreadPool(threadCount);
calcPatternPoints(dataInput.get().getSiteCount());
for (int i = 0; i < threadCount; i++) {
Alignment data = dataInput.get();
String filterSpec = (patternPoints[i] + 1) + "-" + (patternPoints[i + 1]);
if (data.isAscertained) {
filterSpec +=
data.excludefromInput.get() + "-" + data.excludetoInput.get() + "," + filterSpec;
}
treelikelihood[i] = new TreeLikelihood();
treelikelihood[i].setID(getID() + i);
treelikelihood[i].getOutputs().add(this);
likelihoodsInput.get().add(treelikelihood[i]);
FilteredAlignment filter = new FilteredAlignment();
if (i == 0
&& dataInput.get() instanceof FilteredAlignment
&& ((FilteredAlignment) dataInput.get()).constantSiteWeightsInput.get() != null) {
filter.initByName(
"data",
dataInput.get() /*, "userDataType", m_data.get().getDataType()*/,
"filter",
filterSpec,
"constantSiteWeights",
((FilteredAlignment) dataInput.get()).constantSiteWeightsInput.get());
} else {
filter.initByName(
"data",
dataInput.get() /*, "userDataType", m_data.get().getDataType()*/,
"filter",
filterSpec);
}
treelikelihood[i].initByName(
"data",
filter,
"tree",
treeInput.get(),
"siteModel",
duplicate((BEASTInterface) siteModelInput.get(), i),
"branchRateModel",
duplicate(branchRateModelInput.get(), i),
"useAmbiguities",
useAmbiguitiesInput.get(),
"scaling",
scalingInput.get() + "");
likelihoodCallers.add(new TreeLikelihoodCaller(treelikelihood[i], i));
}
}
}
public TreeParser(final Alignment alignment, final String newick) throws Exception {
dataInput.setValue(alignment, this);
newickInput.setValue(newick, this);
initAndValidate();
}
public Partition hasPartition() {
return bHasPartitionsInput.get();
}
@Override
public double getArrayValue(int iDim) {
return treeInput.get().getDirectAncestorNodeCount();
}
/** Find the input associated with this panel based on the path Input. */
@SuppressWarnings("unchecked")
public Input<?> resolveInput(BeautiDoc doc, int iPartition) {
try {
// if (parentPlugins != null && parentPlugins.size() > 0 && _input != null)
// System.err.println("sync " + parentPlugins.get(iPartition) + "[?] = " +
// _input.get());
List<BEASTInterface> plugins;
if (bHasPartitionsInput.get() == Partition.none) {
plugins = new ArrayList<BEASTInterface>();
plugins.add(doc.mcmc.get());
} else {
plugins = doc.getPartitions(bHasPartitionsInput.get().toString());
}
parentPlugins = new ArrayList<BEASTInterface>();
parentInputs = new ArrayList<Input<?>>();
parentPlugins.add(doc);
parentInputs.add(doc.mcmc);
type = doc.mcmc.getType();
bIsList = false;
for (int i = 0; i < sPathComponents.length; i++) {
List<BEASTInterface> oldPlugins = plugins;
plugins = new ArrayList<BEASTInterface>();
parentPlugins = new ArrayList<BEASTInterface>();
parentInputs = new ArrayList<Input<?>>();
for (BEASTInterface plugin : oldPlugins) {
Input<?> namedInput = plugin.getInput(sPathComponents[i]);
type = namedInput.getType();
if (namedInput.get() instanceof List<?>) {
bIsList = true;
List<?> list = (List<?>) namedInput.get();
if (sConditionalAttribute[i] == null) {
for (Object o : list) {
BEASTInterface plugin2 = (BEASTInterface) o;
plugins.add(plugin2);
parentPlugins.add(plugin);
parentInputs.add(namedInput);
}
// throw new Exception ("Don't know which element to pick from the list. List
// component should come with a condition. " + m_sPathComponents[i]);
} else {
int nMatches = 0;
for (int j = 0; j < list.size(); j++) {
BEASTInterface plugin2 = (BEASTInterface) list.get(j);
if (matches(plugin2, sConditionalAttribute[i], sConditionalValue[i])) {
plugins.add(plugin2);
parentPlugins.add(plugin);
parentInputs.add(namedInput);
nMatches++;
break;
}
}
if (nMatches == 0) {
parentInputs.add(namedInput);
parentPlugins.add(plugin);
}
}
} else if (namedInput.get() instanceof BEASTInterface) {
bIsList = false;
if (sConditionalAttribute[i] == null) {
plugins.add((BEASTInterface) namedInput.get());
parentPlugins.add(plugin);
parentInputs.add(namedInput);
} else {
if (matches(plugin, sConditionalAttribute[i], sConditionalValue[i])) {
// if ((m_sConditionalAttribute[i].equals("id") &&
// plugin.getID().equals(m_sConditionalValue[i])) ||
// (m_sConditionalAttribute[i].equals("type") &&
// plugin.getClass().getName().equals(m_sConditionalValue[i]))) {
plugins.add(plugin);
parentPlugins.add(plugin);
parentInputs.add(namedInput);
}
}
} else {
throw new Exception("input " + sPathComponents[i] + " is not a plugin or list");
}
}
}
if (sTypeInput.get() != null) {
type = Class.forName(sTypeInput.get());
}
// sanity check
if (!bIsList && (bHasPartitionsInput.get() == Partition.none) && plugins.size() > 1) {
System.err.println("WARNING: multiple plugins match, but hasPartitions=none");
// this makes sure that all mathing plugins are available in one go
bIsList = true;
// this suppresses syncing
parentInputs.clear();
}
inputs.clear();
startInputs.clear();
for (BEASTInterface plugin : plugins) {
inputs.add(plugin);
startInputs.add(plugin);
}
if (!bIsList) {
_input = new FlexibleInput<BEASTInterface>();
} else {
_input = new FlexibleInput<ArrayList<BEASTInterface>>(new ArrayList<BEASTInterface>());
}
_input.setRule(Validate.REQUIRED);
syncTo(iPartition);
// if (parentPlugins != null && parentPlugins.size() > 0)
// System.err.println("sync " + parentPlugins.get(iPartition) + "[?] = " +
// _input.get());
if (bIsList) {
checkForDups((List<Object>) _input.get());
}
return _input;
} catch (Exception e) {
System.err.println(
"Warning: could not find objects in path " + Arrays.toString(sPathComponents));
}
return null;
} // resolveInputs
public InputEditor.ExpandOption forceExpansion() {
return forceExpansionInput.get();
}
public String getTipText() {
return sTipTextInput.get();
}
public String getIcon() {
return sIconInput.get();
}
@Override
public void log(int nSample, PrintStream out) {
final Tree tree = treeInput.get();
out.print(tree.getDirectAncestorNodeCount() + "\t");
}
@Override
public boolean requiresRecalculation() {
needsUpdate =
geneTreeInput.isDirty() || speciesTreeRatesInput.isDirty() || meanRateInput.isDirty();
return needsUpdate;
}
public double merge(
int index1,
int index2,
int clusterIndex1,
int clusterIndex2,
int[] cluster1Sites,
int[] cluster2Sites) {
double logqMerge = 0.0;
HashMap<Integer, Integer> siteMap = new HashMap<Integer, Integer>();
// The value of the merged cluster will have that of cluster 2 before the merge.
QuietRealParameter mergedParam = paramList.getParameter(clusterIndex2);
QuietRealParameter mergedModel = modelList.getParameter(clusterIndex2);
QuietRealParameter mergedFreqs = freqsList.getParameter(clusterIndex2);
QuietRealParameter mergedRates = ratesList.getParameter(clusterIndex2);
// Create a vector that combines the site indices of the two clusters
int[] mergedClusterSites = new int[cluster1Sites.length + cluster2Sites.length - 2];
int k = 0;
for (int i = 0; i < cluster1Sites.length; i++) {
// Point every member in cluster 1 to cluster 2
// paramPointers.point(cluster1Sites[i],mergedParam);
// modelPointers.point(cluster1Sites[i],mergedModel);
// freqsPointers.point(cluster1Sites[i],mergedFreqs);
// ratesPointers.point(cluster1Sites[i],mergedRates);
if (cluster1Sites[i] != index1) {
// For all members that are not index 1,
// record the cluster in which they have been before the merge,
// and assign them to the combined vector.
siteMap.put(cluster1Sites[i], clusterIndex1);
mergedClusterSites[k++] = cluster1Sites[i];
}
}
for (int i = 0; i < cluster2Sites.length; i++) {
// All members in cluster 2 remains in cluster2 so no new pointer assignments
if (cluster2Sites[i] != index2) {
// For all members that are not index 2,
// record the cluster in which they have been before the merge,
// and assign them to the combined vector.
siteMap.put(cluster2Sites[i], clusterIndex2);
mergedClusterSites[k++] = cluster2Sites[i];
}
}
try {
// Create a weight vector of patterns to inform the temporary tree likelihood
// which set of pattern likelihoods are to be computed.
// int[] tempWeights = dpTreeLikelihood.getClusterWeights(clusterIndex1);
/*int[] tempWeights = new int[tempLikelihood.m_data.get().getPatternCount()];
for(int i = 0; i < cluster1Sites.length; i++){
int patIndex = tempLikelihood.m_data.get().getPatternIndex(cluster1Sites[i]);
tempWeights[patIndex] = 1;
}
tempLikelihood.setPatternWeights(tempWeights);
double[] cluster1SitesCluster2ParamLogLik = tempLikelihood.calculateLogP(
mergedParam,
mergedModel,
mergedFreqs,
mergedRates,
cluster1Sites,
index1
); */
k = 0;
int[] sCluster1Sites = new int[cluster1Sites.length - 1];
for (int i = 0; i < cluster1Sites.length; i++) {
if (cluster1Sites[i] != index1) {
sCluster1Sites[k++] = cluster1Sites[i];
}
}
tempLikelihood.setupPatternWeightsFromSites(sCluster1Sites);
double[] cluster1SitesCluster2ParamLogLik =
tempLikelihood.calculateLogP(
mergedParam, mergedModel, mergedFreqs, mergedRates, sCluster1Sites);
// tempWeights = dpTreeLikelihood.getClusterWeights(clusterIndex2);
/*tempWeights = new int[tempLikelihood.m_data.get().getPatternCount()];
for(int i = 0; i < cluster2Sites.length; i++){
int patIndex = tempLikelihood.m_data.get().getPatternIndex(cluster2Sites[i]);
tempWeights[patIndex] = 1;
}
tempLikelihood.setPatternWeights(tempWeights);
RealParameter removedParam = paramList.getParameter(clusterIndex1);
RealParameter removedModel = modelList.getParameter(clusterIndex1);
RealParameter removedFreqs = freqsList.getParameter(clusterIndex1);
RealParameter removedRates = ratesList.getParameter(clusterIndex1);
double[] cluster2SitesCluster1ParamLogLik = tempLikelihood.calculateLogP(
removedParam,
removedModel,
removedFreqs,
removedRates,
cluster2Sites,
index2
);*/
k = 0;
int[] sCluster2Sites = new int[cluster2Sites.length - 1];
for (int i = 0; i < cluster2Sites.length; i++) {
if (cluster2Sites[i] != index2) {
sCluster2Sites[k++] = cluster2Sites[i];
}
}
tempLikelihood.setupPatternWeightsFromSites(sCluster2Sites);
RealParameter removedParam = paramList.getParameter(clusterIndex1);
RealParameter removedModel = modelList.getParameter(clusterIndex1);
RealParameter removedFreqs = freqsList.getParameter(clusterIndex1);
RealParameter removedRates = ratesList.getParameter(clusterIndex1);
double[] cluster2SitesCluster1ParamLogLik =
tempLikelihood.calculateLogP(
removedParam, removedModel, removedFreqs, removedRates, sCluster2Sites);
// System.out.println("populate logLik1:");
double[] logLik1 = new double[mergedClusterSites.length];
for (int i = 0; i < (cluster1Sites.length - 1); i++) {
// System.out.println(clusterIndex1+" "+mergedClusterSites[i]);
logLik1[i] = dpTreeLikelihood.getSiteLogLikelihood(clusterIndex1, mergedClusterSites[i]);
}
System.arraycopy(
cluster2SitesCluster1ParamLogLik,
0,
logLik1,
cluster1Sites.length - 1,
cluster2SitesCluster1ParamLogLik.length);
double[] logLik2 = new double[mergedClusterSites.length];
System.arraycopy(
cluster1SitesCluster2ParamLogLik, 0, logLik2, 0, cluster1SitesCluster2ParamLogLik.length);
// System.out.println("populate logLik2:");
for (int i = cluster1SitesCluster2ParamLogLik.length; i < logLik2.length; i++) {
// System.out.println(clusterIndex2+"
// "+mergedClusterSites[i-cluster1SitesCluster2ParamLogLik.length]);
logLik2[i] = dpTreeLikelihood.getSiteLogLikelihood(clusterIndex2, mergedClusterSites[i]);
}
double[] lik1 = new double[logLik1.length];
double[] lik2 = new double[logLik2.length];
// scale it so it may be more accuate
double minLog;
/*for(int i = 0; i < logLik1.length; i++){
minLog = Math.min(logLik1[i],logLik2[i]);
if(minLog == logLik1[i]){
lik1[i] = 1.0;
lik2[i] = Math.exp(logLik2[i] - minLog);
}else{
lik1[i] = Math.exp(logLik1[i] - minLog);
lik2[i] = 1.0;
}
}*/
for (int i = 0; i < logLik1.length; i++) {
lik1[i] = Math.exp(logLik1[i]);
lik2[i] = Math.exp(logLik2[i]);
// System.out.println(lik1[i]+" "+lik2[i]);
}
// Create a set of indices for random permutation
int[] shuffle = new int[mergedClusterSites.length];
for (int i = 0; i < shuffle.length; i++) {
shuffle[i] = i;
}
Randomizer.shuffle(shuffle);
int cluster1Count = 1;
int cluster2Count = 1;
int cluster;
double psi1, psi2, cluster1Prob;
for (int i = 0; i < mergedClusterSites.length; i++) {
cluster = siteMap.get(mergedClusterSites[shuffle[i]]);
psi1 = cluster1Count * lik1[shuffle[i]];
psi2 = cluster2Count * lik2[shuffle[i]];
/*testCorrectness(i,cluster,
clusterIndex1,clusterIndex2,shuffle, mergedClusterSites,
lik1,lik2);*/
cluster1Prob = psi1 / (psi1 + psi2);
// System.out.println(cluster1Prob);
if (cluster == clusterIndex1) {
logqMerge += Math.log(cluster1Prob);
cluster1Count++;
} else if (cluster == clusterIndex2) {
logqMerge += Math.log(1 - cluster1Prob);
cluster2Count++;
} else {
throw new RuntimeException("Something is wrong.");
}
}
logqMerge += // paramBaseDistr.calcLogP(removedParam)
mergeValue(removedParam, mergedParam, paramBaseDistr)
// + modelBaseDistr.calcLogP(removedModel)
+ mergeDiscreteValue(removedModel, mergedModel, modelDistrInput.get())
+ freqsBaseDistr.calcLogP(removedFreqs)
// + ratesBaseDistr.calcLogP(removedRates);
+ mergeValueInLogSpace(removedRates, mergedRates, ratesBaseDistr);
if (logqMerge > Double.NEGATIVE_INFINITY) {
paramList.mergeParameter(clusterIndex1, clusterIndex2);
modelList.mergeParameter(clusterIndex1, clusterIndex2);
freqsList.mergeParameter(clusterIndex1, clusterIndex2);
ratesList.mergeParameter(clusterIndex1, clusterIndex2);
for (int i = 0; i < cluster1Sites.length; i++) {
// Point every member in cluster 1 to cluster 2
paramPointers.point(cluster1Sites[i], mergedParam);
modelPointers.point(cluster1Sites[i], mergedModel);
freqsPointers.point(cluster1Sites[i], mergedFreqs);
ratesPointers.point(cluster1Sites[i], mergedRates);
}
}
} catch (Exception e) {
throw new RuntimeException(e);
}
return logqMerge;
}
@Override
public void initStateNodes() throws Exception {
typeLabel = typeLabelInput.get();
// nTypes = nTypesInput.get();
BeastTreeFromMaster masterTree = masterTreeInput.get();
TraitSet typeTrait = new TraitSet();
TraitSet dateTrait = new TraitSet();
String types = "";
String dates = "";
for (Node beastNode : masterTree.getExternalNodes()) {
dates += beastNode.getID() + "=" + beastNode.getHeight() + ",";
types += beastNode.getID() + "=" + (int) beastNode.getMetaData("location") + ",";
}
dates = dates.substring(0, dates.length() - 1);
types = types.substring(0, types.length() - 1);
typeTrait.initByName("value", types, "taxa", m_taxonset.get(), "traitname", "type");
dateTrait.initByName("value", dates, "taxa", m_taxonset.get(), "traitname", "date-backward");
SCMigrationModel migModel = new SCMigrationModel();
Double[] temp = new Double[nTypes.get()];
Arrays.fill(temp, muInput.get());
migModel.setInputValue("rateMatrix", new RealParameter(temp));
Arrays.fill(temp, popSizeInput.get());
migModel.setInputValue("popSizes", new RealParameter(temp));
migModel.initAndValidate();
if (random.get()) {
tree = new StructuredCoalescentMultiTypeTree();
tree.setInputValue("migrationModel", migModel);
} else {
Node oldRoot = masterTree.getRoot();
MultiTypeNode newRoot = new MultiTypeNode();
newRoot.height = oldRoot.height;
newRoot.nTypeChanges = 0;
newRoot.changeTimes.addAll(new ArrayList<Double>());
newRoot.changeTypes.addAll(new ArrayList<Integer>());
newRoot.nodeType = 0;
newRoot.labelNr = oldRoot.labelNr;
newRoot.addChild(copyFromFlatNode(oldRoot.getLeft()));
newRoot.addChild(copyFromFlatNode(oldRoot.getRight()));
tree = new MultiTypeTree(newRoot);
}
tree.setInputValue("trait", typeTrait);
tree.setInputValue("trait", dateTrait);
tree.initAndValidate();
setInputValue("trait", dateTrait);
setInputValue("trait", typeTrait);
assignFromWithoutID(tree);
}
/** Ensure the class behaves properly, even when inputs are not specified. */
@Override
public void initAndValidate() throws Exception {
boolean sortNodesAlphabetically = false;
if (dataInput.get() != null) {
labels = dataInput.get().getTaxaNames();
} else if (m_taxonset.get() != null) {
if (labels == null) {
labels = m_taxonset.get().asStringList();
} else { // else labels were set by TreeParser c'tor
sortNodesAlphabetically = true;
}
} else {
if (isLabelledNewickInput.get()) {
if (m_initial.get() != null) {
labels = m_initial.get().getTaxonset().asStringList();
} else {
labels = new ArrayList<>();
createUnrecognizedTaxa = true;
sortNodesAlphabetically = true;
}
} else {
if (m_initial.get() != null) {
// try to pick up taxa from initial tree
final Tree tree = m_initial.get();
if (tree.m_taxonset.get() != null) {
labels = tree.m_taxonset.get().asStringList();
} else {
// m_sLabels = null;
}
} else {
// m_sLabels = null;
}
}
// m_bIsLabelledNewick = false;
}
final String newick = newickInput.get();
if (newick == null || newick.equals("")) {
// can happen while initalising Beauti
final Node dummy = new Node();
setRoot(dummy);
} else {
try {
setRoot(parseNewick(newickInput.get()));
} catch (ParseCancellationException e) {
throw new RuntimeException(
"TreeParser cannot make sense of the Newick string "
+ "provided. It gives the following clue:\n"
+ e.getMessage());
}
}
super.initAndValidate();
if (sortNodesAlphabetically) {
// correct for node ordering: ensure order is alphabetical
for (int i = 0; i < getNodeCount() && i < labels.size(); i++) {
m_nodes[i].setID(labels.get(i));
}
Node[] nodes = new Node[labels.size()];
System.arraycopy(m_nodes, 0, nodes, 0, labels.size());
Arrays.sort(nodes, (o1, o2) -> o1.getID().compareTo(o2.getID()));
for (int i = 0; i < labels.size(); i++) {
m_nodes[i] = nodes[i];
nodes[i].setNr(i);
}
}
if (m_initial.get() != null) processTraits(m_initial.get().m_traitList.get());
else processTraits(m_traitList.get());
if (timeTraitSet != null) {
adjustTreeNodeHeights(root);
} else if (adjustTipHeightsInput.get()) {
double treeLength = TreeUtils.getTreeLength(this, getRoot());
double extraTreeLength = 0.0;
double maxTipHeight = 0.0;
// all nodes should be at zero height if no date-trait is available
for (int i = 0; i < getLeafNodeCount(); i++) {
double height = getNode(i).getHeight();
if (maxTipHeight < height) {
maxTipHeight = height;
}
extraTreeLength += height;
getNode(i).setHeight(0);
}
double scaleFactor = (treeLength + extraTreeLength) / treeLength;
final double SCALE_FACTOR_THRESHOLD = 0.001;
// if the change in total tree length is more than 0.1% then give the user a warning!
if (scaleFactor > 1.0 + SCALE_FACTOR_THRESHOLD) {
DecimalFormat format = new DecimalFormat("#.##");
Log.info.println(
"WARNING: Adjust tip heights attribute set to 'true' in " + getClass().getSimpleName());
Log.info.println(
" has resulted in significant (>"
+ format.format(SCALE_FACTOR_THRESHOLD * 100.0)
+ "%) change in tree length.");
Log.info.println(
" Use "
+ adjustTipHeightsInput.getName()
+ "='false' to override this default.");
Log.info.printf(" original max tip age = %8.3f\n", maxTipHeight);
Log.info.printf(" new max tip age = %8.3f\n", 0.0);
Log.info.printf(" original tree length = %8.3f\n", treeLength);
Log.info.printf(" new tree length = %8.3f\n", treeLength + extraTreeLength);
Log.info.printf(" TL scale factor = %8.3f\n", scaleFactor);
}
}
if (m_taxonset.get() == null && labels != null && isLabelledNewickInput.get()) {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(labels)), this);
}
initStateNodes();
} // init
/** more elegant getters for resolving Input values* */
public String getName() {
return sNameInput.get();
}