Examples with Tree dr.evolution.tree.Tree used on opensource projects

Example 91 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class GaussianProcessSkytrackLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(POPULATION_PARAMETER);
    Parameter popParameter = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(PRECISION_PARAMETER);
    Parameter precParameter = (Parameter) cxo.getChild(Parameter.class);
    //        cxo = xo.getChild(LAMBDA_BOUND_PARAMETER);
    //        Parameter lambda_bound = (Parameter) cxo.getChild(Parameter.class);
    //
    //        cxo = xo.getChild(LAMBDA_PARAMETER);
    //        Parameter lambda_parameter = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(POPULATION_TREE);
    List<Tree> treeList = new ArrayList<Tree>();
    for (int i = 0; i < cxo.getChildCount(); i++) {
        Object testObject = cxo.getChild(i);
        if (testObject instanceof Tree) {
            treeList.add((TreeModel) testObject);
        }
    }
    //        TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
    //        cxo = xo.getChild(GROUP_SIZES);
    //        Parameter groupParameter = null;
    //        if (cxo != null) {
    //            groupParameter = (Parameter) cxo.getChild(Parameter.class);
    //
    //            if (popParameter.getDimension() != groupParameter.getDimension())
    //                throw new XMLParseException("Population and group size parameters must have the same length");
    //        }
    Parameter lambda_parameter;
    if (xo.getChild(LAMBDA_PARAMETER) != null) {
        cxo = xo.getChild(LAMBDA_PARAMETER);
        lambda_parameter = (Parameter) cxo.getChild(Parameter.class);
    } else {
        lambda_parameter = new Parameter.Default(1.0);
    }
    Parameter GPtype;
    if (xo.getChild(GPTYPE) != null) {
        cxo = xo.getChild(GPTYPE);
        GPtype = (Parameter) cxo.getChild(Parameter.class);
    } else {
        GPtype = new Parameter.Default(1.0);
    }
    Parameter Tmrca;
    if (xo.getChild(TMRCA) != null) {
        cxo = xo.getChild(TMRCA);
        Tmrca = (Parameter) cxo.getChild(Parameter.class);
    } else {
        Tmrca = new Parameter.Default(1.0);
    }
    Parameter numPoints;
    if (xo.getChild(NUMBER_POINTS) != null) {
        cxo = xo.getChild(NUMBER_POINTS);
        numPoints = (Parameter) cxo.getChild(Parameter.class);
    } else {
        numPoints = new Parameter.Default(1.0);
    }
    Parameter CoalCounts;
    if (xo.getChild(COALCOUNT) != null) {
        cxo = xo.getChild(COALCOUNT);
        CoalCounts = (Parameter) cxo.getChild(Parameter.class);
    } else {
        CoalCounts = new Parameter.Default(1.0);
    }
    Parameter GPcounts;
    if (xo.getChild(GPCOUNTS) != null) {
        cxo = xo.getChild(GPCOUNTS);
        GPcounts = (Parameter) cxo.getChild(Parameter.class);
    } else {
        GPcounts = new Parameter.Default(1.0);
    }
    Parameter coalfactor;
    if (xo.getChild(COALFACTOR) != null) {
        cxo = xo.getChild(COALFACTOR);
        coalfactor = (Parameter) cxo.getChild(Parameter.class);
    } else {
        coalfactor = new Parameter.Default(1.0);
    }
    Parameter lambda_bound;
    if (xo.getChild(LAMBDA_BOUND_PARAMETER) != null) {
        cxo = xo.getChild(LAMBDA_BOUND_PARAMETER);
        lambda_bound = (Parameter) cxo.getChild(Parameter.class);
    } else {
        lambda_bound = new Parameter.Default(1.0);
    }
    Parameter alpha_parameter;
    if (xo.getChild(ALPHA_PARAMETER) != null) {
        cxo = xo.getChild(ALPHA_PARAMETER);
        alpha_parameter = (Parameter) cxo.getChild(Parameter.class);
    } else {
        alpha_parameter = new Parameter.Default(0.001);
    }
    Parameter beta_parameter;
    if (xo.getChild(BETA_PARAMETER) != null) {
        cxo = xo.getChild(BETA_PARAMETER);
        beta_parameter = (Parameter) cxo.getChild(Parameter.class);
    } else {
        beta_parameter = new Parameter.Default(0.001);
    }
    Parameter change_points;
    if (xo.getChild(CHANGE_POINTS) != null) {
        cxo = xo.getChild(CHANGE_POINTS);
        change_points = (Parameter) cxo.getChild(Parameter.class);
    } else {
        change_points = new Parameter.Default(0, 1);
    }
    if (xo.getAttribute(RANDOMIZE_TREE, false)) {
        for (Tree tree : treeList) {
            if (tree instanceof TreeModel) {
                GaussianProcessSkytrackLikelihood.checkTree((TreeModel) tree);
            } else {
                throw new XMLParseException("Can not randomize a fixed tree");
            }
        }
    }
    //        XMLObject latentChild = xo.getChild(LATENT_PARAMETER);
    //        Parameter latentPoints = (Parameter) latentChild.getChild(Parameter.class);
    boolean rescaleByRootHeight = xo.getAttribute(RESCALE_BY_ROOT_ISSUE, true);
    if (treeList.size() == 1) {
        return new GaussianProcessSkytrackLikelihood(treeList, precParameter, rescaleByRootHeight, lambda_bound, lambda_parameter, popParameter, alpha_parameter, beta_parameter, change_points, GPtype, GPcounts, coalfactor, CoalCounts, numPoints, Tmrca);
    } else {
        return new GaussianProcessMultilocusSkytrackLikelihood(treeList, precParameter, rescaleByRootHeight, lambda_bound, lambda_parameter, popParameter, alpha_parameter, beta_parameter, change_points, GPtype, GPcounts, coalfactor, CoalCounts, numPoints, Tmrca);
    }
}

Example 92 with Tree

use of dr.evolution.tree.Tree 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 93 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class CoalescentSimulatorParser 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 height = xo.getAttribute(HEIGHT, Double.NaN);
    // 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);
        }
    }
    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.");
    }
    Taxa remainingTaxa = new Taxa();
    for (int i = 0; i < taxonLists.size(); i++) {
        remainingTaxa.addTaxa(taxonLists.get(i));
    }
    for (int i = 0; i < subtrees.size(); i++) {
        remainingTaxa.removeTaxa(subtrees.get(i));
    }
    try {
        Tree[] trees = new Tree[subtrees.size() + remainingTaxa.getTaxonCount()];
        // add the preset trees
        for (int i = 0; i < subtrees.size(); i++) {
            trees[i] = subtrees.get(i);
        }
        // add all the remaining taxa in as single tip trees...
        for (int i = 0; i < remainingTaxa.getTaxonCount(); i++) {
            Taxa tip = new Taxa();
            tip.addTaxon(remainingTaxa.getTaxon(i));
            trees[i + subtrees.size()] = simulator.simulateTree(tip, demoModel);
        }
        return simulator.simulateTree(trees, demoModel, height, trees.length != 1);
    } catch (IllegalArgumentException iae) {
        throw new XMLParseException(iae.getMessage());
    }
}

Example 94 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class GMRFSkyrideLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(POPULATION_PARAMETER);
    Parameter popParameter = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(PRECISION_PARAMETER);
    Parameter precParameter = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(POPULATION_TREE);
    List<Tree> treeList = new ArrayList<Tree>();
    for (int i = 0; i < cxo.getChildCount(); i++) {
        Object testObject = cxo.getChild(i);
        if (testObject instanceof Tree) {
            treeList.add((TreeModel) testObject);
        }
    }
    //        TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
    cxo = xo.getChild(GROUP_SIZES);
    Parameter groupParameter = null;
    if (cxo != null) {
        groupParameter = (Parameter) cxo.getChild(Parameter.class);
        if (popParameter.getDimension() != groupParameter.getDimension())
            throw new XMLParseException("Population and group size parameters must have the same length");
    }
    Parameter lambda;
    if (xo.getChild(LAMBDA_PARAMETER) != null) {
        cxo = xo.getChild(LAMBDA_PARAMETER);
        lambda = (Parameter) cxo.getChild(Parameter.class);
    } else {
        lambda = new Parameter.Default(LAMBDA_PARAMETER, 1.0);
    }
    Parameter gridPoints = null;
    if (xo.getChild(GRID_POINTS) != null) {
        cxo = xo.getChild(GRID_POINTS);
        gridPoints = (Parameter) cxo.getChild(Parameter.class);
    }
    Parameter numGridPoints = null;
    if (xo.getChild(NUM_GRID_POINTS) != null) {
        cxo = xo.getChild(NUM_GRID_POINTS);
        numGridPoints = (Parameter) cxo.getChild(Parameter.class);
    }
    Parameter cutOff = null;
    if (xo.getChild(CUT_OFF) != null) {
        cxo = xo.getChild(CUT_OFF);
        cutOff = (Parameter) cxo.getChild(Parameter.class);
    }
    Parameter phi = null;
    if (xo.getChild(PHI_PARAMETER) != null) {
        cxo = xo.getChild(PHI_PARAMETER);
        phi = (Parameter) cxo.getChild(Parameter.class);
    }
    List<Parameter> lastObservedIndex = null;
    if (xo.hasChildNamed(LAST_OBSERVED_INDEX)) {
        lastObservedIndex = new ArrayList<Parameter>();
        cxo = xo.getChild(LAST_OBSERVED_INDEX);
        final int numObsInd = cxo.getChildCount();
        for (int i = 0; i < numObsInd; ++i) {
            lastObservedIndex.add((Parameter) cxo.getChild(i));
        }
    }
    Parameter ploidyFactors = null;
    if (xo.getChild(PLOIDY) != null) {
        cxo = xo.getChild(PLOIDY);
        ploidyFactors = (Parameter) cxo.getChild(Parameter.class);
    } else {
        ploidyFactors = new Parameter.Default(PLOIDY, treeList.size());
        for (int i = 0; i < treeList.size(); i++) {
            ploidyFactors.setParameterValue(i, 1.0);
        }
    }
    Parameter betaParameter = null;
    if (xo.hasChildNamed(SINGLE_BETA)) {
        betaParameter = (Parameter) xo.getElementFirstChild(SINGLE_BETA);
    }
    List<Parameter> betaList = null;
    if (xo.getChild(BETA_PARAMETER) != null) {
        betaList = new ArrayList<Parameter>();
        cxo = xo.getChild(BETA_PARAMETER);
        final int numBeta = cxo.getChildCount();
        for (int i = 0; i < numBeta; ++i) {
            betaList.add((Parameter) cxo.getChild(i));
        }
    }
    MatrixParameter dMatrix = null;
    if (xo.getChild(COVARIATE_MATRIX) != null) {
        cxo = xo.getChild(COVARIATE_MATRIX);
        dMatrix = (MatrixParameter) cxo.getChild(MatrixParameter.class);
    }
    boolean timeAwareSmoothing = GMRFSkyrideLikelihood.TIME_AWARE_IS_ON_BY_DEFAULT;
    if (xo.hasAttribute(TIME_AWARE_SMOOTHING)) {
        timeAwareSmoothing = xo.getBooleanAttribute(TIME_AWARE_SMOOTHING);
    }
    if (dMatrix != null) {
        if (dMatrix.getRowDimension() != popParameter.getDimension())
            throw new XMLParseException("Design matrix row dimension must equal the population parameter length.");
        if (dMatrix.getColumnDimension() != betaParameter.getDimension())
            throw new XMLParseException("Design matrix column dimension must equal the regression coefficient length.");
    }
    List<Parameter> covPrecParam = null;
    if (xo.hasChildNamed(COV_PREC_PARAM)) {
        covPrecParam = new ArrayList<Parameter>();
        cxo = xo.getChild(COV_PREC_PARAM);
        final int numCovPrec = cxo.getChildCount();
        for (int i = 0; i < numCovPrec; ++i) {
            covPrecParam.add((Parameter) cxo.getChild(i));
        }
    }
    List<MatrixParameter> covariates = null;
    if (xo.hasChildNamed(COVARIATES)) {
        covariates = new ArrayList<MatrixParameter>();
        cxo = xo.getChild(COVARIATES);
        final int numCov = cxo.getChildCount();
        for (int i = 0; i < numCov; ++i) {
            covariates.add((MatrixParameter) cxo.getChild(i));
        }
    }
    if ((covariates != null && betaList == null) || (covariates == null && betaList != null))
        throw new XMLParseException("Must specify both a set of regression coefficients and a design matrix.");
    if (xo.getAttribute(RANDOMIZE_TREE, false)) {
        for (Tree tree : treeList) {
            if (tree instanceof TreeModel) {
                GMRFSkyrideLikelihood.checkTree((TreeModel) tree);
            } else {
                throw new XMLParseException("Can not randomize a fixed tree");
            }
        }
    }
    boolean rescaleByRootHeight = xo.getAttribute(RESCALE_BY_ROOT_ISSUE, true);
    Logger.getLogger("dr.evomodel").info("The " + SKYLINE_LIKELIHOOD + " has " + (timeAwareSmoothing ? "time aware smoothing" : "uniform smoothing"));
    if (xo.getAttribute(OLD_SKYRIDE, true) && xo.getName().compareTo(SKYGRID_LIKELIHOOD) != 0) {
        return new GMRFSkyrideLikelihood(treeList, popParameter, groupParameter, precParameter, lambda, betaParameter, dMatrix, timeAwareSmoothing, rescaleByRootHeight);
    } else {
        if (xo.getChild(GRID_POINTS) != null) {
            return new GMRFMultilocusSkyrideLikelihood(treeList, popParameter, groupParameter, precParameter, lambda, betaParameter, dMatrix, timeAwareSmoothing, gridPoints, covariates, ploidyFactors, lastObservedIndex, covPrecParam, betaList);
        } else {
            return new GMRFMultilocusSkyrideLikelihood(treeList, popParameter, groupParameter, precParameter, lambda, betaParameter, dMatrix, timeAwareSmoothing, cutOff.getParameterValue(0), (int) numGridPoints.getParameterValue(0), phi, ploidyFactors);
        }
    }
}

Example 95 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class DnDsLoggerParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String[] names = DnDsLogger.traitNames;
    TreeTrait[] foundTraits = new TreeTrait[names.length];
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object obj = xo.getChild(i);
        if (obj instanceof CodonPartitionedRobustCounting) {
            CodonPartitionedRobustCounting thisCount = (CodonPartitionedRobustCounting) obj;
            for (int j = 0; j < names.length; j++) {
                TreeTrait trait = thisCount.getTreeTrait(names[j]);
                if (trait != null) {
                    foundTraits[j] = trait;
                }
            }
        }
    }
    for (int i = 0; i < foundTraits.length; i++) {
        if (foundTraits[i] == null) {
            throw new XMLParseException("Unable to find trait '" + names[i] + "'");
        }
    }
    Tree tree = (Tree) xo.getChild(Tree.class);
    // Use AttributeRules for options here
    boolean useSmoothing = xo.getAttribute(USE_SMOOTHING, true);
    boolean useDnMinusDs = xo.getAttribute(USE_DNMINUSDS, false);
    boolean conditionalCounts = xo.getAttribute(COUNTS, false);
    boolean synonymous = xo.getAttribute(SYNONYMOUS, false);
    return new DnDsLogger(xo.getId(), tree, foundTraits, useSmoothing, useDnMinusDs, conditionalCounts, synonymous);
}