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

Example 46 with TaxonList

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

the class LocalClockModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    LocalClockModel localClockModel;
    if (xo.getElementFirstChild(RATE) instanceof BranchRateModel) {
        BranchRateModel globalBranchRates = (BranchRateModel) xo.getElementFirstChild(RATE);
        localClockModel = new LocalClockModel(tree, globalBranchRates);
    } else {
        Parameter globalRateParameter = (Parameter) xo.getElementFirstChild(RATE);
        localClockModel = new LocalClockModel(tree, globalRateParameter);
    }
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject xoc = (XMLObject) xo.getChild(i);
            Parameter rateParameter = null;
            BranchRateModel branchRates = (BranchRateModel) xoc.getChild(BranchRateModel.class);
            if (branchRates == null) {
                rateParameter = (Parameter) xoc.getChild(Parameter.class);
            }
            if (xoc.getName().equals(CLADE)) {
                boolean relative = xoc.getAttribute(RELATIVE, false);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                if (taxonList.getTaxonCount() == 1) {
                    throw new XMLParseException("A local clock for a clade must be defined by at least two taxa");
                }
                boolean excludeClade = false;
                double stemProportion = 0.0;
                if (xoc.hasAttribute(INCLUDE_STEM)) {
                    // if includeStem=true then assume it is the whole stem
                    stemProportion = xoc.getBooleanAttribute(INCLUDE_STEM) ? 1.0 : 0.0;
                }
                if (xoc.hasAttribute(STEM_PROPORTION)) {
                    stemProportion = xoc.getDoubleAttribute(STEM_PROPORTION);
                    if (stemProportion < 0.0 || stemProportion > 1.0) {
                        throw new XMLParseException("A stem proportion should be between 0, 1");
                    }
                }
                if (xoc.hasAttribute(EXCLUDE_CLADE)) {
                    excludeClade = xoc.getBooleanAttribute(EXCLUDE_CLADE);
                }
                try {
                    if (branchRates != null) {
                        localClockModel.addCladeClock(taxonList, branchRates, relative, stemProportion, excludeClade);
                    } else {
                        localClockModel.addCladeClock(taxonList, rateParameter, relative, stemProportion, excludeClade);
                    }
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            } else if (xoc.getName().equals(EXTERNAL_BRANCHES)) {
                boolean relative = xoc.getAttribute(RELATIVE, false);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                try {
                    if (branchRates != null) {
                        localClockModel.addExternalBranchClock(taxonList, branchRates, relative);
                    } else {
                        localClockModel.addExternalBranchClock(taxonList, rateParameter, relative);
                    }
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            } else if (xoc.getName().equals(TRUNK)) {
                boolean relative = xoc.getAttribute(RELATIVE, false);
                Parameter indexParameter = null;
                if (xoc.hasChildNamed(INDEX)) {
                    indexParameter = (Parameter) xoc.getElementFirstChild(INDEX);
                }
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                try {
                    if (branchRates != null) {
                        localClockModel.addTrunkClock(taxonList, branchRates, indexParameter, relative);
                    } else {
                        localClockModel.addTrunkClock(taxonList, rateParameter, indexParameter, relative);
                    }
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            }
        }
    }
    Logger.getLogger("dr.evomodel").info("\nUsing local clock branch rate model.");
    return localClockModel;
}

Example 47 with TaxonList

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

the class RestrictedPartialsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getId();
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    TaxonList taxa = MonophylyStatisticParser.parseTaxonListOrTaxa(xo.getChild(MonophylyStatisticParser.MRCA));
    Parameter meanParameter = (Parameter) xo.getElementFirstChild(MultivariateDistributionLikelihood.MVN_MEAN);
    Parameter priorSampleSize = (Parameter) xo.getElementFirstChild(AbstractMultivariateTraitLikelihood.PRIOR_SAMPLE_SIZE);
    RestrictedPartials rp = null;
    try {
        rp = new RestrictedPartials(name, tree, taxa, meanParameter, priorSampleSize);
    } catch (TreeUtils.MissingTaxonException e) {
        throw new XMLParseException("Unable to find taxa for " + xo.getId());
    }
    return rp;
}

Example 48 with TaxonList

use of dr.evolution.util.TaxonList 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);
    Tree constraintsTree = null;
    if (xo.hasChildNamed((CONSTRAINTS_TREE))) {
        XMLObject cxo = xo.getChild(CONSTRAINTS_TREE);
        constraintsTree = (Tree) cxo.getChild(Tree.class);
    }
    // should have one child that is node
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        if (child != constraintsTree) {
            // 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);
        }
        if (constraintsTree == null) {
            throw new XMLParseException("Expected at least one taxonList or two subtrees or a constraints tree 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));
    }
    if (constraintsTree != null) {
        remainingTaxa.removeTaxa(constraintsTree);
    }
    try {
        if (constraintsTree != null) {
            subtrees.add(simulator.simulateTree(constraintsTree, constraintsTree.getRoot(), demoModel));
        }
        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 49 with TaxonList

use of dr.evolution.util.TaxonList 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 50 with TaxonList

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

the class TreeModelParser method parseXMLObject.

/**
 * @return a tree object based on the XML element it was passed.
 */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Tree tree = (Tree) xo.getChild(Tree.class);
    boolean fixHeights = xo.getAttribute(FIX_HEIGHTS, false);
    boolean fixTree = xo.getAttribute(FIX_TREE, false);
    DefaultTreeModel treeModel = new DefaultTreeModel(xo.getId(), tree, fixHeights, fixTree);
    Logger.getLogger("dr.evomodel").info("\nCreating the tree model, '" + xo.getId() + "'");
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject cxo = (XMLObject) xo.getChild(i);
            if (cxo.getName().equals(ROOT_HEIGHT)) {
                ParameterParser.replaceParameter(cxo, treeModel.getRootHeightParameter());
            } else if (cxo.getName().equals(LEAF_HEIGHT)) {
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafHeight element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon " + taxonName + " not found for leafHeight element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter newParameter = treeModel.getLeafHeightParameter(node);
                ParameterParser.replaceParameter(cxo, newParameter);
                Taxon taxon = treeModel.getTaxon(index);
                setUncertaintyBounds(newParameter, taxon);
            } else if (cxo.getName().equals(LEAF_HEIGHTS)) {
                // get a set of leaf height parameters out as a compound parameter...
                TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
                Parameter offsetParameter = (Parameter) cxo.getChild(Parameter.class);
                CompoundParameter leafHeights = new CompoundParameter("leafHeights");
                for (Taxon taxon : taxa) {
                    int index = treeModel.getTaxonIndex(taxon);
                    if (index == -1) {
                        throw new XMLParseException("taxon " + taxon.getId() + " not found for leafHeight element in treeModel element");
                    }
                    NodeRef node = treeModel.getExternalNode(index);
                    Parameter newParameter = treeModel.getLeafHeightParameter(node);
                    leafHeights.addParameter(newParameter);
                    setUncertaintyBounds(newParameter, taxon);
                }
                ParameterParser.replaceParameter(cxo, leafHeights);
            } else if (cxo.getName().equals(NODE_HEIGHTS)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeHeights element");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeHeightsParameter(rootNode, internalNodes, leafNodes));
            } else if (cxo.getName().equals(NODE_RATES)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                double[] initialValues = null;
                if (cxo.hasAttribute(INITIAL_VALUE)) {
                    initialValues = cxo.getDoubleArrayAttribute(INITIAL_VALUE);
                }
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeRates element");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeRatesParameter(initialValues, rootNode, internalNodes, leafNodes));
            } else if (cxo.getName().equals(NODE_TRAITS)) {
                parseNodeTraits(cxo, treeModel);
            } else if (cxo.getName().equals(LEAF_TRAIT)) {
                String name = cxo.getAttribute(NAME, "trait");
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafTrait element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon '" + taxonName + "' not found for leafTrait element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter parameter = treeModel.getNodeTraitParameter(node, name);
                if (parameter == null)
                    throw new XMLParseException("trait '" + name + "' not found for leafTrait (taxon, " + taxonName + ") element in treeModel element");
                ParameterParser.replaceParameter(cxo, parameter);
            } else {
                throw new XMLParseException("illegal child element in " + getParserName() + ": " + cxo.getName());
            }
        } else if (xo.getChild(i) instanceof Tree) {
        // do nothing - already handled
        } else {
            throw new XMLParseException("illegal child element in  " + getParserName() + ": " + xo.getChildName(i) + " " + xo.getChild(i));
        }
    }
    // Logger.getLogger("dr.evomodel").info("  initial tree topology = " + TreeUtils.uniqueNewick(treeModel, treeModel.getRoot()));
    Logger.getLogger("dr.evomodel").info("  taxon count = " + treeModel.getExternalNodeCount());
    Logger.getLogger("dr.evomodel").info("  tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
    return treeModel;
}