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

Example 36 with Taxon

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

the class StatisticsPanel method createStatistic.

public TreeSummaryStatistic createStatistic(TreeSummaryStatistic.Factory factory) {
    if (!factory.allowsTaxonList() && !factory.allowsDouble() && !factory.allowsInteger() && !factory.allowsString()) {
        return factory.createStatistic();
    }
    OptionsPanel optionPanel = new OptionsPanel();
    optionPanel.addSpanningComponent(new JLabel(factory.getSummaryStatisticDescription()));
    final JRadioButton wholeTreeRadio = new JRadioButton("For the whole tree", false);
    final JRadioButton taxonSetRadio = new JRadioButton("Using a given taxon set", false);
    final JComboBox taxonSetCombo = new JComboBox();
    final JTextField valueField;
    if (factory.allowsTaxonList()) {
        for (Object taxonSet : treeStatData.taxonSets) {
            taxonSetCombo.addItem(taxonSet);
        }
        ButtonGroup group = new ButtonGroup();
        ItemListener listener = new ItemListener() {

            public void itemStateChanged(ItemEvent e) {
                taxonSetCombo.setEnabled(taxonSetRadio.isSelected());
            }
        };
        if (factory.allowsWholeTree()) {
            group.add(wholeTreeRadio);
            wholeTreeRadio.addItemListener(listener);
            optionPanel.addSpanningComponent(wholeTreeRadio);
            optionPanel.addSeparator();
        }
        if (factory.allowsTaxonList()) {
            group.add(taxonSetRadio);
            taxonSetRadio.addItemListener(listener);
            optionPanel.addSpanningComponent(taxonSetRadio);
            optionPanel.addComponentWithLabel("Taxon Set: ", taxonSetCombo);
            optionPanel.addSeparator();
        }
        if (factory.allowsTaxonList()) {
            taxonSetRadio.setSelected(true);
        }
        if (factory.allowsWholeTree()) {
            wholeTreeRadio.setSelected(true);
        }
    }
    if (factory.allowsDouble() || factory.allowsInteger() || factory.allowsString()) {
        if (factory.allowsDouble()) {
            valueField = new RealNumberField();
            valueField.setColumns(12);
            optionPanel.addComponentWithLabel(factory.getValueName(), valueField);
        } else if (factory.allowsInteger()) {
            valueField = new WholeNumberField();
            valueField.setColumns(12);
            optionPanel.addComponentWithLabel(factory.getValueName(), valueField);
        } else {
            // allowsString
            valueField = new JTextField();
            valueField.setColumns(24);
            optionPanel.addComponentWithLabel(factory.getValueName(), valueField);
        }
    } else {
        valueField = null;
    }
    JOptionPane optionPane = new JOptionPane(optionPanel, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null);
    optionPane.setBorder(new EmptyBorder(12, 12, 12, 12));
    JDialog dialog = optionPane.createDialog(frame, factory.getSummaryStatisticName());
    //		dialog.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
    dialog.pack();
    dialog.setVisible(true);
    if (optionPane.getValue() == null) {
        return null;
    }
    int result = (Integer) optionPane.getValue();
    if (result == -1 || result == JOptionPane.CANCEL_OPTION) {
        return null;
    }
    TreeSummaryStatistic statistic = factory.createStatistic();
    if (wholeTreeRadio.isSelected()) {
        statistic = factory.createStatistic();
    } else if (taxonSetRadio.isSelected()) {
        TreeStatData.TaxonSet t = (TreeStatData.TaxonSet) taxonSetCombo.getSelectedItem();
        Taxa taxa = new Taxa();
        taxa.setId(t.name);
        //Iterator iter = t.taxa.iterator();
        for (Object aTaxa : t.taxa) {
            String id = (String) aTaxa;
            Taxon taxon = new Taxon(id);
            taxa.addTaxon(taxon);
        }
        statistic.setTaxonList(taxa);
    } else {
        return null;
    }
    if (factory.allowsDouble()) {
        assert valueField instanceof RealNumberField;
        Double value = ((RealNumberField) valueField).getValue();
        statistic.setDouble(value);
    } else if (factory.allowsInteger()) {
        assert valueField instanceof WholeNumberField;
        Integer value = ((WholeNumberField) valueField).getValue();
        statistic.setInteger(value);
    } else if (factory.allowsString()) {
        String value = valueField.getText();
        statistic.setString(value);
    }
    return statistic;
}

Example 37 with Taxon

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

the class BetaTreeDiversityStatistic method main.

public static void main(String[] arg) throws IOException, Importer.ImportException {
    Tree tree = (new NewickImporter("((A:1,B:1):1,(C:1, D:1):1);")).importNextTree();
    BetaTreeDiversityStatistic statistic = (BetaTreeDiversityStatistic) BetaTreeDiversityStatistic.FACTORY.createStatistic();
    Taxa taxa = new Taxa();
    taxa.addTaxon(new Taxon("A"));
    taxa.addTaxon(new Taxon("C"));
    statistic.setTaxonList(taxa);
    System.out.println(statistic.getSummaryStatistic(tree)[0]);
}

Example 38 with Taxon

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

the class SpeciesTreeModel method compatibleUninformedSpeciesTree.

private SimpleTree compatibleUninformedSpeciesTree(Tree startTree) {
    double rootHeight = Double.MAX_VALUE;
    for (SpeciesBindings.GeneTreeInfo t : species.getGeneTrees()) {
        rootHeight = Math.min(rootHeight, t.getCoalInfo()[0].ctime);
    }
    final SpeciesBindings.SPinfo[] spp = species.species;
    if (startTree != null) {
        if (startTree.getExternalNodeCount() != spp.length) {
            throw new Error("Start tree error - different number of tips");
        }
        final FlexibleTree tree = new FlexibleTree(startTree, true);
        tree.resolveTree();
        final double treeHeight = tree.getRootHeight();
        if (treeHeight <= 0) {
            tree.setRootHeight(1.0);
            MutableTree.Utils.correctHeightsForTips(tree);
            SimpleTree.Utils.scaleNodeHeights(tree, rootHeight / tree.getRootHeight());
        }
        SimpleTree sTree = new SimpleTree(tree);
        for (int ns = 0; ns < spp.length; ns++) {
            SpeciesBindings.SPinfo sp = spp[ns];
            final int i = sTree.getTaxonIndex(sp.name);
            if (i < 0) {
                throw new Error(sp.name + " is not present in the start tree");
            }
            final SimpleNode node = sTree.getExternalNode(i);
            node.setAttribute(spIndexAttrName, ns);
            // set for possible pops
            tree.setNodeAttribute(tree.getNode(tree.getTaxonIndex(sp.name)), spIndexAttrName, ns);
        }
        if (treeHeight > 0) {
            sTree.setAttribute("check", new Double(rootHeight));
        }
        {
            //assert ! constantPopulation; // not implemented yet
            int[] pos = { 0 };
            setInitialSplitPopulations(tree, tree.getRoot(), pos);
        }
        return sTree;
    }
    final double delta = rootHeight / (spp.length + 1);
    double cTime = delta;
    List<SimpleNode> subs = new ArrayList<SimpleNode>(spp.length);
    for (int ns = 0; ns < spp.length; ns++) {
        SpeciesBindings.SPinfo sp = spp[ns];
        final SimpleNode node = new SimpleNode();
        node.setTaxon(new Taxon(sp.name));
        subs.add(node);
        node.setAttribute(spIndexAttrName, ns);
    }
    while (subs.size() > 1) {
        final SimpleNode node = new SimpleNode();
        int i = 0, j = 1;
        node.addChild(subs.get(i));
        node.addChild(subs.get(j));
        node.setHeight(cTime);
        cTime += delta;
        subs.set(j, node);
        subs.remove(i);
    }
    return new SimpleTree(subs.get(0));
}

Example 39 with Taxon

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

the class TraitGibbsOperator method doOperation.

public double doOperation() {
    NodeRef node = null;
    final NodeRef root = treeModel.getRoot();
    while (node == null) {
        if (onlyInternalNodes)
            node = treeModel.getInternalNode(MathUtils.nextInt(treeModel.getInternalNodeCount()));
        else {
            node = treeModel.getNode(MathUtils.nextInt(treeModel.getNodeCount()));
            if (onlyTipsWithPriors && // Is a tip
            (treeModel.getChildCount(node) == 0) && !nodeGeoSpatialPriorExists(node)) {
                // Does not have a prior
                node = null;
            }
        }
        if (!sampleRoot && node == root)
            node = null;
    }
    // select any internal (or internal/external) node
    final double[] initialValue = treeModel.getMultivariateNodeTrait(node, traitName);
    MeanPrecision mp;
    if (node != root)
        mp = operateNotRoot(node);
    else
        mp = operateRoot(node);
    final Taxon taxon = treeModel.getNodeTaxon(node);
    //        final boolean nodePriorExists = nodeGeoSpatialPrior != null && nodeGeoSpatialPrior.containsKey(taxon);
    final boolean nodePriorExists = nodeGeoSpatialPriorExists(node);
    //        if (!onlyInternalNodes) {
    //            final boolean isTip = (treeModel.getChildCount(node) == 0);
    //            if (!nodePriorExists && isTip)
    //                System.err.println("Warning: sampling taxon '"+treeModel.getNodeTaxon(node).getId()
    //                        +"' tip trait without a prior!!!");
    //        }
    int count = 0;
    final boolean parameterPriorExists = parameterPrior != null;
    double[] draw;
    do {
        do {
            if (count > maxTries) {
                // TODO Add to MTT interface
                treeModel.setMultivariateTrait(node, traitName, initialValue);
                throw new RuntimeException("Truncated Gibbs is stuck!");
            }
            draw = MultivariateNormalDistribution.nextMultivariateNormalPrecision(mp.mean, mp.precision);
            count++;
        } while (// There is a prior for this node
        nodePriorExists && // And draw is invalid under prior
        (nodeGeoSpatialPrior.get(taxon)).logPdf(draw) == Double.NEGATIVE_INFINITY);
        // TODO Currently only works for flat/truncated priors, make work for MVN
        treeModel.setMultivariateTrait(node, traitName, draw);
    } while (parameterPriorExists && (parameterPrior.getLogLikelihood() == Double.NEGATIVE_INFINITY));
    return 0;
}

Example 40 with Taxon

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

the class TransmissionHistoryModel method createTreeColouring.

private Taxon createTreeColouring(Tree tree, NodeRef node, DefaultTreeColouring treeColouring) {
    Taxon parentHost = null;
    Taxon childHost;
    if (tree.isExternal(node)) {
        childHost = (Taxon) tree.getNodeTaxon(node).getAttribute("host");
        if (childHost == null) {
            throw new RuntimeException("One or more of the viruses tree's taxa are missing the 'host' attribute");
        }
    } else {
        Taxon h1 = createTreeColouring(tree, tree.getChild(node, 0), treeColouring);
        Taxon h2 = createTreeColouring(tree, tree.getChild(node, 1), treeColouring);
        if (h1 != h2) {
            throw new RuntimeException("Two children have different hosts at coalescent event");
        }
        childHost = h1;
    }
    NodeRef parent = tree.getParent(node);
    if (parent != null) {
        double height0 = tree.getNodeHeight(node);
        double height1 = tree.getNodeHeight(parent);
        TransmissionEvent event = getTransmissionEventToHost(childHost);
        DefaultBranchColouring branchColouring;
        if (event != null && event.getTransmissionTime() < height1) {
            if (event.getTransmissionTime() < height0) {
                throw new RuntimeException("Transmission event is before the node");
            }
            List<Taxon> hosts = new ArrayList<Taxon>();
            List<Double> times = new ArrayList<Double>();
            parentHost = childHost;
            while (event != null && event.getTransmissionTime() < height1) {
                hosts.add(parentHost);
                times.add(event.getTransmissionTime());
                parentHost = event.donor;
                event = getTransmissionEventToHost(parentHost);
            }
            int host1 = getHostIndex(childHost);
            int host2 = getHostIndex(parentHost);
            branchColouring = new DefaultBranchColouring(host2, host1);
            for (int i = hosts.size() - 1; i >= 0; i--) {
                int host = getHostIndex(hosts.get(i));
                double time = times.get(i);
                branchColouring.addEvent(host, time);
            }
        } else {
            int host = getHostIndex(childHost);
            branchColouring = new DefaultBranchColouring(host, host);
            parentHost = childHost;
        }
        treeColouring.setBranchColouring(node, branchColouring);
    }
    return parentHost;
}