private void computeNodeToRestrictionMap() {
Arrays.fill(partialsMap, null);
for (Set<String> taxonNames : partialsRestrictions.keySet()) {
NodeRef node = Tree.Utils.getCommonAncestorNode(treeModel, taxonNames);
partialsMap[node.getNumber()] = partialsRestrictions.get(taxonNames);
}
}
public AncestralTrait(String name, TreeTrait ancestralTrait, Tree tree, TaxonList taxa)
throws Tree.MissingTaxonException {
this.name = name;
this.tree = tree;
this.ancestralTrait = ancestralTrait;
this.leafSet = Tree.Utils.getLeavesForTaxa(tree, taxa);
}
@Override
public List<Integer> getDescendantLeaves(int i, boolean b) {
List<Integer> descendants = new ArrayList<Integer>();
if (!b) descendants.add(i);
for (NodeRef n : Tree.Utils.getExternalNodes(tree, tree.getNode(i)))
descendants.add(n.getNumber());
return descendants;
}
public double[] getSummaryStatistic(Tree tree) {
if (taxonList == null) {
return new double[] {1.0};
}
double TL = Tree.Utils.getTreeLength(tree, tree.getRoot());
double betaDiversity = (TL - getUniqueBranches(tree, tree.getRoot())) / TL;
return new double[] {betaDiversity};
}
private boolean isUnique(TaxonList taxonList, Tree tree, NodeRef node) {
Set<String> taxa = Tree.Utils.getDescendantLeaves(tree, node);
int count = 0;
for (String taxon : taxa) {
count += (taxonList.getTaxonIndex(taxon) >= 0 ? 1 : 0);
// System.out.print(taxon + "\t");
}
boolean unique = (count == 0) || (count == taxa.size());
// System.out.println(count + "\t" + unique);
return unique;
}
@Override
public int getLCA(int i, int j) {
return Tree.Utils.getCommonAncestor(tree, tree.getNode(i), tree.getNode(j)).getNumber();
}
@Override
public String toString() {
return Tree.Utils.newick(tree);
}
public static void main(String[] arg) throws IOException {
// READ DEMOGRAPHIC FUNCTION
String filename = arg[0];
BufferedReader reader = new BufferedReader(new FileReader(filename));
double popSizeScale = 1.0;
double generationTime = 1.0;
if (arg.length > 2) {
popSizeScale = Double.parseDouble(arg[2]);
}
if (arg.length > 3) {
generationTime = Double.parseDouble(arg[3]);
}
PrintWriter populationFuncLogger = null;
if (arg.length > 5) {
String logFileName = arg[5];
if (logFileName.equals("-")) {
populationFuncLogger = new PrintWriter(System.out);
} else {
populationFuncLogger = new PrintWriter(new FileWriter(logFileName));
}
}
List<Double> times = new ArrayList<Double>();
String line = reader.readLine();
String[] tokens = line.trim().split("[\t ]+");
if (tokens.length < 2) throw new RuntimeException();
ArrayList<ArrayList> popSizes = new ArrayList<ArrayList>();
while (line != null) {
double time = Double.parseDouble(tokens[0]) / generationTime;
times.add(time);
for (int i = 1; i < tokens.length; i++) {
popSizes.add(new ArrayList<Double>());
popSizes.get(i - 1).add(Double.parseDouble(tokens[i]));
}
line = reader.readLine();
if (line != null) {
tokens = line.trim().split("[\t ]+");
if (tokens.length != popSizes.size() + 1) throw new RuntimeException();
}
}
reader.close();
// READ SAMPLE TIMES
String samplesFilename = arg[1];
reader = new BufferedReader(new FileReader(samplesFilename));
line = reader.readLine();
Taxa taxa = new Taxa();
int id = 0;
while (line != null) {
if (!line.startsWith("#")) {
tokens = line.split("[\t ]+");
if (tokens.length == 4) {
double t0 = Double.parseDouble(tokens[0]);
double t1 = Double.parseDouble(tokens[1]);
double dt = Double.parseDouble(tokens[2]);
int k = Integer.parseInt(tokens[3]);
for (double time = t0; time <= t1; time += dt) {
double sampleTime = time / generationTime;
for (int i = 0; i < k; i++) {
Taxon taxon = new Taxon("t" + id);
taxon.setAttribute(
dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
taxa.addTaxon(taxon);
id += 1;
}
}
} else {
// sample times are in the same units as simulation
double sampleTime = Double.parseDouble(tokens[0]) / generationTime;
int count = Integer.parseInt(tokens[1]);
for (int i = 0; i < count; i++) {
Taxon taxon = new Taxon(id + "");
taxon.setAttribute(
dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
taxa.addTaxon(taxon);
id += 1;
}
}
}
line = reader.readLine();
}
double minTheta = Double.MAX_VALUE;
double maxTheta = 0.0;
PrintWriter out;
if (arg.length > 4) {
out = new PrintWriter(new FileWriter(arg[4]));
} else {
out = new PrintWriter(System.out);
}
int pp = 0;
for (List<Double> popSize : popSizes) {
double[] thetas = new double[popSize.size()];
double[] intervals = new double[times.size() - 1];
if (populationFuncLogger != null) {
populationFuncLogger.println("# " + pp);
++pp;
}
// must reverse the direction of the model
for (int j = intervals.length; j > 0; j--) {
intervals[intervals.length - j] = times.get(j) - times.get(j - 1);
final double theta = popSize.get(j) * popSizeScale;
thetas[intervals.length - j] = theta;
if (theta < minTheta) {
minTheta = theta;
}
if (theta > maxTheta) {
maxTheta = theta;
}
final double t = times.get(intervals.length) - times.get(j);
if (populationFuncLogger != null) {
populationFuncLogger.println(t + "\t" + theta);
}
}
if (debug != null) {
debug.println("min theta = " + minTheta);
debug.println("max theta = " + maxTheta);
}
PiecewiseLinearPopulation demo =
new PiecewiseLinearPopulation(intervals, thetas, Units.Type.GENERATIONS);
CoalescentSimulator simulator = new CoalescentSimulator();
Tree tree = simulator.simulateTree(taxa, demo);
out.println(Tree.Utils.newick(tree));
if (debug != null) {
debug.println(Tree.Utils.newick(tree));
}
}
if (populationFuncLogger != null) {
populationFuncLogger.flush();
populationFuncLogger.close();
}
out.flush();
out.close();
}
/** @return the ancestral state of the MRCA node. */
public String getAncestralState() {
NodeRef node = Tree.Utils.getCommonAncestorNode(tree, leafSet);
if (node == null) throw new RuntimeException("No node found that is MRCA of " + leafSet);
return ancestralTrait.getTraitString(tree, node);
}