Examples with Taxa dr.evolution.util.Taxa used on opensource projects

Example 71 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class OldCoalescentSimulatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    CoalescentSimulator simulator = new CoalescentSimulator();
    DemographicModel demoModel = (DemographicModel) xo.getChild(DemographicModel.class);
    List<TaxonList> taxonLists = new ArrayList<TaxonList>();
    List<Tree> subtrees = new ArrayList<Tree>();
    double rootHeight = xo.getAttribute(ROOT_HEIGHT, -1.0);
    if (xo.hasAttribute(RESCALE_HEIGHT)) {
        rootHeight = xo.getDoubleAttribute(RESCALE_HEIGHT);
    }
    // should have one child that is node
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        // AER - swapped the order of these round because Trees are TaxonLists...
        if (child instanceof Tree) {
            subtrees.add((Tree) child);
        } else if (child instanceof TaxonList) {
            taxonLists.add((TaxonList) child);
        } else if (xo.getChildName(i).equals(CONSTRAINED_TAXA)) {
            XMLObject constrainedTaxa = (XMLObject) child;
            // all taxa
            final TaxonList taxa = (TaxonList) constrainedTaxa.getChild(TaxonList.class);
            List<CoalescentSimulator.TaxaConstraint> constraints = new ArrayList<CoalescentSimulator.TaxaConstraint>();
            final String setsNotCompatibleMessage = "taxa sets not compatible";
            for (int nc = 0; nc < constrainedTaxa.getChildCount(); ++nc) {
                final Object object = constrainedTaxa.getChild(nc);
                if (object instanceof XMLObject) {
                    final XMLObject constraint = (XMLObject) object;
                    if (constraint.getName().equals(TMRCA_CONSTRAINT)) {
                        TaxonList taxaSubSet = (TaxonList) constraint.getChild(TaxonList.class);
                        ParametricDistributionModel dist = (ParametricDistributionModel) constraint.getChild(ParametricDistributionModel.class);
                        boolean isMono = constraint.getAttribute(IS_MONOPHYLETIC, true);
                        final CoalescentSimulator.TaxaConstraint taxaConstraint = new CoalescentSimulator.TaxaConstraint(taxaSubSet, dist, isMono);
                        int insertPoint;
                        for (insertPoint = 0; insertPoint < constraints.size(); ++insertPoint) {
                            // if new <= constraints[insertPoint] insert before insertPoint
                            final CoalescentSimulator.TaxaConstraint iConstraint = constraints.get(insertPoint);
                            if (iConstraint.isMonophyletic) {
                                if (!taxaConstraint.isMonophyletic) {
                                    continue;
                                }
                                final TaxonList taxonsip = iConstraint.taxons;
                                final int nIn = simulator.sizeOfIntersection(taxonsip, taxaSubSet);
                                if (nIn == taxaSubSet.getTaxonCount()) {
                                    break;
                                }
                                if (nIn > 0 && nIn != taxonsip.getTaxonCount()) {
                                    throw new XMLParseException(setsNotCompatibleMessage);
                                }
                            } else {
                                // reached non mono area
                                if (!taxaConstraint.isMonophyletic) {
                                    if (iConstraint.upper >= taxaConstraint.upper) {
                                        break;
                                    }
                                } else {
                                    break;
                                }
                            }
                        }
                        constraints.add(insertPoint, taxaConstraint);
                    }
                }
            }
            final int nConstraints = constraints.size();
            if (nConstraints == 0) {
                if (taxa != null) {
                    taxonLists.add(taxa);
                }
            } else {
                for (int nc = 0; nc < nConstraints; ++nc) {
                    CoalescentSimulator.TaxaConstraint cnc = constraints.get(nc);
                    if (!cnc.isMonophyletic) {
                        for (int nc1 = nc - 1; nc1 >= 0; --nc1) {
                            CoalescentSimulator.TaxaConstraint cnc1 = constraints.get(nc1);
                            int x = simulator.sizeOfIntersection(cnc.taxons, cnc1.taxons);
                            if (x > 0) {
                                Taxa combinedTaxa = new Taxa(cnc.taxons);
                                combinedTaxa.addTaxa(cnc1.taxons);
                                cnc = new CoalescentSimulator.TaxaConstraint(combinedTaxa, cnc.lower, cnc.upper, cnc.isMonophyletic);
                                constraints.set(nc, cnc);
                            }
                        }
                    }
                }
                // determine upper bound for each set.
                double[] upper = new double[nConstraints];
                for (int nc = nConstraints - 1; nc >= 0; --nc) {
                    final CoalescentSimulator.TaxaConstraint cnc = constraints.get(nc);
                    if (cnc.realLimits()) {
                        upper[nc] = cnc.upper;
                    } else {
                        upper[nc] = Double.POSITIVE_INFINITY;
                    }
                }
                for (int nc = nConstraints - 1; nc >= 0; --nc) {
                    final CoalescentSimulator.TaxaConstraint cnc = constraints.get(nc);
                    if (upper[nc] < Double.POSITIVE_INFINITY) {
                        for (int nc1 = nc - 1; nc1 >= 0; --nc1) {
                            final CoalescentSimulator.TaxaConstraint cnc1 = constraints.get(nc1);
                            if (simulator.contained(cnc1.taxons, cnc.taxons)) {
                                upper[nc1] = Math.min(upper[nc1], upper[nc]);
                                if (cnc1.realLimits() && cnc1.lower > upper[nc1]) {
                                    throw new XMLParseException(setsNotCompatibleMessage);
                                }
                                break;
                            }
                        }
                    }
                }
                // collect subtrees here
                List<Tree> st = new ArrayList<Tree>();
                for (int nc = 0; nc < constraints.size(); ++nc) {
                    final CoalescentSimulator.TaxaConstraint nxt = constraints.get(nc);
                    // collect all previously built subtrees which are a subset of taxa set to be added
                    List<Tree> subs = new ArrayList<Tree>();
                    Taxa newTaxons = new Taxa(nxt.taxons);
                    for (int k = 0; k < st.size(); ++k) {
                        final Tree stk = st.get(k);
                        int x = simulator.sizeOfIntersection(stk, nxt.taxons);
                        if (x == st.get(k).getTaxonCount()) {
                            final Tree tree = st.remove(k);
                            --k;
                            subs.add(tree);
                            newTaxons.removeTaxa(tree);
                        }
                    }
                    SimpleTree tree = simulator.simulateTree(newTaxons, demoModel);
                    final double lower = nxt.realLimits() ? nxt.lower : 0;
                    if (upper[nc] < Double.MAX_VALUE) {
                        simulator.attemptToScaleTree(tree, (lower + upper[nc]) / 2);
                    }
                    if (subs.size() > 0) {
                        if (tree.getTaxonCount() > 0)
                            subs.add(tree);
                        double h = -1;
                        if (upper[nc] < Double.MAX_VALUE) {
                            for (Tree t : subs) {
                                // protect against 1 taxa tree with height 0
                                final double rh = t.getNodeHeight(t.getRoot());
                                h = Math.max(h, rh > 0 ? rh : (lower + upper[nc]) / 2);
                            }
                            h = (h + upper[nc]) / 2;
                        }
                        tree = simulator.simulateTree(subs.toArray(new Tree[subs.size()]), demoModel, h, true);
                    }
                    st.add(tree);
                }
                // add a taxon list for remaining taxa
                if (taxa != null) {
                    final Taxa list = new Taxa();
                    for (int j = 0; j < taxa.getTaxonCount(); ++j) {
                        Taxon taxonj = taxa.getTaxon(j);
                        for (Tree aSt : st) {
                            if (aSt.getTaxonIndex(taxonj) >= 0) {
                                taxonj = null;
                                break;
                            }
                        }
                        if (taxonj != null) {
                            list.addTaxon(taxonj);
                        }
                    }
                    if (list.getTaxonCount() > 0) {
                        taxonLists.add(list);
                    }
                }
                if (st.size() > 1) {
                    final Tree t = simulator.simulateTree(st.toArray(new Tree[st.size()]), demoModel, -1, false);
                    subtrees.add(t);
                } else {
                    subtrees.add(st.get(0));
                }
            }
        }
    }
    if (taxonLists.size() == 0) {
        if (subtrees.size() == 1) {
            return subtrees.get(0);
        }
        throw new XMLParseException("Expected at least one taxonList or two subtrees in " + getParserName() + " element.");
    }
    try {
        Tree[] trees = new Tree[taxonLists.size() + subtrees.size()];
        // simulate each taxonList separately
        for (int i = 0; i < taxonLists.size(); i++) {
            trees[i] = simulator.simulateTree(taxonLists.get(i), demoModel);
        }
        // add the preset trees
        for (int i = 0; i < subtrees.size(); i++) {
            trees[i + taxonLists.size()] = subtrees.get(i);
        }
        return simulator.simulateTree(trees, demoModel, rootHeight, trees.length != 1);
    } catch (IllegalArgumentException iae) {
        throw new XMLParseException(iae.getMessage());
    }
}

Example 72 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class AncestralTraitTreeModelParser method parseAncestor.

private static AncestralTaxonInTree parseAncestor(MutableTreeModel tree, XMLObject xo, final int index) throws XMLParseException {
    Taxon ancestor = (Taxon) xo.getChild(Taxon.class);
    Parameter pseudoBranchLength = (Parameter) xo.getChild(Parameter.class);
    AncestralTaxonInTree ancestorInTree;
    NodeRef node = new NodeRef() {

        @Override
        public int getNumber() {
            return index;
        }

        @Override
        public void setNumber(int n) {
            throw new RuntimeException("Do not set");
        }
    };
    if (xo.hasChildNamed(MonophylyStatisticParser.MRCA)) {
        TaxonList descendants = MonophylyStatisticParser.parseTaxonListOrTaxa(xo.getChild(MonophylyStatisticParser.MRCA));
        try {
            ancestorInTree = new AncestralTaxonInTree(ancestor, tree, descendants, pseudoBranchLength, null, node, index, 0.0);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to find taxa for " + ancestor.getId());
        }
    } else {
        XMLObject cxo = xo.getChild(ANCESTRAL_PATH);
        Taxon taxon = (Taxon) cxo.getChild(Taxon.class);
        Parameter time = (Parameter) cxo.getChild(Parameter.class);
        boolean relativeHeight = cxo.getAttribute(RELATIVE_HEIGHT, false);
        double offset = 0;
        if (relativeHeight) {
            Object date = taxon.getAttribute("date");
            if (date != null && date instanceof Date) {
                offset = taxon.getHeight();
            } else {
                throw new XMLParseException("Taxon '" + taxon.getId() + "' has no specified date");
            }
        } else {
            if (time.getParameterValue(0) <= taxon.getHeight()) {
                throw new XMLParseException("Ancestral path time must be > sampling time for taxon '" + taxon.getId() + "'");
            }
        }
        Taxa descendent = new Taxa();
        descendent.addTaxon(taxon);
        try {
            ancestorInTree = new AncestralTaxonInTree(ancestor, tree, descendent, pseudoBranchLength, time, node, index, // TODO Refactor into separate class from MRCA version
            offset);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to find taxa for " + ancestor.getId());
        }
    }
    return ancestorInTree;
}

Example 73 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class ExternalLengthStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    TaxonList taxa = (TaxonList) xo.getChild(Taxa.class);
    try {
        return new ExternalLengthStatistic(name, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 74 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class AncestralStateTreeLikelihoodTest method testJointLikelihood.

public void testJointLikelihood() {
    TreeModel treeModel = new DefaultTreeModel("treeModel", tree);
    Sequence[] sequence = new Sequence[3];
    sequence[0] = new Sequence(new Taxon("0"), "A");
    sequence[1] = new Sequence(new Taxon("1"), "C");
    sequence[2] = new Sequence(new Taxon("2"), "C");
    Taxa taxa = new Taxa();
    for (Sequence s : sequence) {
        taxa.addTaxon(s.getTaxon());
    }
    SimpleAlignment alignment = new SimpleAlignment();
    for (Sequence s : sequence) {
        alignment.addSequence(s);
    }
    Parameter mu = new Parameter.Default(1, 1.0);
    Parameter kappa = new Parameter.Default(1, 1.0);
    double[] pi = { 0.25, 0.25, 0.25, 0.25 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    AncestralStateTreeLikelihood treeLikelihood = new AncestralStateTreeLikelihood(alignment, treeModel, new GammaSiteModel(hky), new StrictClockBranchRates(mu), false, true, Nucleotides.INSTANCE, "state", false, // useMap = true
    true, false);
    double logLike = treeLikelihood.getLogLikelihood();
    StringBuffer buffer = new StringBuffer();
    TreeUtils.newick(treeModel, treeModel.getRoot(), false, TreeUtils.BranchLengthType.LENGTHS_AS_TIME, null, null, new TreeTraitProvider[] { treeLikelihood }, null, buffer);
    System.out.println(buffer);
    System.out.println("t_CA(2) = " + t(false, 2.0));
    System.out.println("t_CC(1) = " + t(true, 1.0));
    double trueValue = 0.25 * t(false, 2.0) * Math.pow(t(true, 1.0), 3.0);
    assertEquals(logLike, Math.log(trueValue), 1e-6);
}

Example 75 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class MsatFullLikelihoodTest method setUpExample3.

private void setUpExample3() throws Exception {
    // taxa
    ArrayList<Taxon> taxonList3 = new ArrayList<Taxon>();
    Collections.addAll(taxonList3, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"), new Taxon("taxon6"), new Taxon("taxon7"));
    Taxa taxa3 = new Taxa(taxonList3);
    // msat datatype
    Microsatellite msat = new Microsatellite(1, 4);
    Patterns msatPatterns = new Patterns(msat, taxa3);
    // pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 3, 1, 2, 3, 0, 1 });
    // create tree
    NewickImporter importer = new NewickImporter("(((taxon1:0.3,taxon2:0.3):0.6,taxon3:0.9):0.9,((taxon4:0.5,taxon5:0.5):0.3,(taxon6:0.7,taxon7:0.7):0.1):1.0);");
    Tree tree = importer.importTree(null);
    // treeModel
    TreeModel treeModel = new DefaultTreeModel(tree);
    // msatsubstModel
    AsymmetricQuadraticModel aqm3 = new AsymmetricQuadraticModel(msat, null);
    // siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm3);
    // treeLikelihood
    treeLikelihood3 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}