public String asText(int indentlen) { StringBuilder s = new StringBuilder(); Formatter formatter = new Formatter(s, Locale.US); if (lft < 0) { formatter.format("%s ", taxon.getId()); } else { formatter.format("%s ", "+"); } while (s.length() < 20 - indentlen) { formatter.format("%s", " "); } formatter.format("%s ", AlloppMisc.nonnegIn8Chars(height)); formatter.format("%20s ", AlloppMisc.FixedBitSetasText(union)); formatter.format("%3d ", nlineages); for (int c = 0; c < coalheights.size(); c++) { formatter.format(AlloppMisc.nonnegIn8Chars(coalheights.get(c)) + ","); } return s.toString(); }
public PopsIOSpeciesTreeModel( PopsIOSpeciesBindings piosb, Parameter popPriorScale, PriorComponent[] priorComponents) { super(PopsIOSpeciesTreeModelParser.PIO_SPECIES_TREE); this.piosb = piosb; this.popPriorScale = popPriorScale; addVariable(popPriorScale); popPriorScale.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1)); this.priorComponents = priorComponents; PopsIOSpeciesBindings.SpInfo[] species = piosb.getSpecies(); int nTaxa = species.length; int nNodes = 2 * nTaxa - 1; pionodes = new PopsIONode[nNodes]; for (int n = 0; n < nNodes; n++) { pionodes[n] = new PopsIONode(n); } ArrayList<Integer> tojoin = new ArrayList<Integer>(nTaxa); for (int n = 0; n < nTaxa; n++) { pionodes[n].setTaxon(species[n].name); pionodes[n].setHeight(0.0); pionodes[n].setUnion(piosb.tipUnionFromTaxon(pionodes[n].getTaxon())); tojoin.add(n); } double rate = 1.0; double treeheight = 0.0; for (int i = 0; i < nTaxa - 1; i++) { int numtojoin = tojoin.size(); int j = MathUtils.nextInt(numtojoin); Integer child0 = tojoin.get(j); tojoin.remove(j); int k = MathUtils.nextInt(numtojoin - 1); Integer child1 = tojoin.get(k); tojoin.remove(k); pionodes[nTaxa + i].addChildren(pionodes[child0], pionodes[child1]); pionodes[nTaxa + i].setHeight(treeheight + randomnodeheight(numtojoin * rate)); treeheight = pionodes[nTaxa + i].getHeight(); tojoin.add(nTaxa + i); } rootn = pionodes.length - 1; double scale = 0.99 * piosb.initialMinGeneNodeHeight() / pionodes[rootn].height; scaleAllHeights(scale); pionodes[rootn].fillinUnionsInSubtree(piosb.getSpecies().length); stree = makeSimpleTree(); Logger.getLogger("dr.evomodel.speciation.popsio") .info( "\tConstructing a PopsIO Species Tree Model, please cite:\n" + Citable.Utils.getCitationString(this)); }
private void copyNonTopologyFields(PopsIONode node) { height = node.height; taxon = new Taxon(node.taxon.getId()); nlineages = node.nlineages; if (node.union == null) { union = null; } else { union = new FixedBitSet(node.union); } coalheights = new ArrayList<Double>(); for (int i = 0; i < node.coalheights.size(); i++) { coalheights.add(node.coalheights.get(i)); } }