Examples with MRCAPrior beast.math.distributions.MRCAPrior used on opensource projects

Example 6 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class YuleModel method validateInputs.

@Override
public void validateInputs() {
    if (conditionalOnRootInput.get()) {
        // make sure there is an MRCAPrior on the root
        TreeInterface tree = treeInput.get();
        int n = tree.getTaxonset().getTaxonCount();
        boolean found = false;
        for (BEASTInterface o : ((BEASTInterface) tree).getOutputs()) {
            if (o instanceof MRCAPrior) {
                MRCAPrior prior = (MRCAPrior) o;
                int n2 = prior.taxonsetInput.get().taxonsetInput.get().size();
                if (n2 == n) {
                    found = true;
                }
            }
        }
        if (!found) {
            Log.warning("WARNING: There must be an MRCAPrior on the root when conditionalOnRoot=true, but could not find any");
        }
    }
    super.validateInputs();
}

Example 7 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class BeautiAlignmentProvider method getAlignments.

/**
 * return new alignment given files
 * @param doc
 * @param files
 * @return
 */
public List<BEASTInterface> getAlignments(BeautiDoc doc, File[] files) {
    if (files == null) {
        // merge "+ button" and "drag drop" function
        return getAlignments(doc);
    }
    if (importers == null) {
        initImporters();
    }
    List<BEASTInterface> selectedBEASTObjects = new ArrayList<>();
    List<MRCAPrior> calibrations = new ArrayList<>();
    for (File file : files) {
        // create list of importers that can handle the file
        List<AlignmentImporter> availableImporters = new ArrayList<>();
        for (AlignmentImporter importer : importers) {
            if (importer.canHandleFile(file)) {
                availableImporters.add(importer);
            }
        }
        if (availableImporters.size() > 0) {
            AlignmentImporter importer = availableImporters.get(0);
            if (availableImporters.size() > 1) {
                // let user choose an importer
                List<String> descriptions = new ArrayList<>();
                for (AlignmentImporter i : availableImporters) {
                    descriptions.add(((BEASTInterface) i).getDescription());
                }
                String option = (String) JOptionPane.showInputDialog(null, "Which importer is appropriate", "Option", JOptionPane.WARNING_MESSAGE, null, descriptions.toArray(), descriptions.get(0));
                if (option == null) {
                    return selectedBEASTObjects;
                }
                int i = descriptions.indexOf(option);
                importer = availableImporters.get(i);
            }
            // get a fresh instance
            // try {
            // importer = importer.getClass().newInstance();
            // } catch (InstantiationException | IllegalAccessException e) {
            // // TODO Auto-generated catch block
            // e.printStackTrace();
            // }
            List<BEASTInterface> list = importer.loadFile(file);
            selectedBEASTObjects.addAll(list);
        } else {
            JOptionPane.showMessageDialog(null, "Unsupported sequence file.", "Error", JOptionPane.ERROR_MESSAGE);
        }
    }
    addAlignments(doc, selectedBEASTObjects);
    if (calibrations != null) {
        selectedBEASTObjects.addAll(calibrations);
    }
    // doc.addMRCAPriors(calibrations);
    return selectedBEASTObjects;
}

Example 8 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class MRCAPriorTest method testMRCATimePrior.

@Test
public void testMRCATimePrior() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035," + "(gorilla:0.024003,(orangutan:0.010772,siamang:0.010772):0.013231):0.012035);", "IsLabelledNewick", true);
    Taxon human = new Taxon();
    human.setID("human");
    Taxon bonobo = new Taxon();
    bonobo.setID("bonobo");
    Taxon chimp = new Taxon();
    chimp.setID("chimp");
    Taxon gorilla = new Taxon();
    gorilla.setID("gorilla");
    Taxon orangutan = new Taxon();
    orangutan.setID("orangutan");
    Taxon siamang = new Taxon();
    siamang.setID("siamang");
    MRCAPrior prior = new MRCAPrior();
    TaxonSet set = new TaxonSet();
    set.initByName("taxon", human, "taxon", bonobo, "taxon", chimp);
    Exponential exp = new Exponential();
    /* get distribution for set (human, bonobo, chimp) */
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true, "distr", exp);
    double logP = prior.calculateLogP();
    assertEquals(-0.024003, logP, BEASTTestCase.PRECISION);
    /* get distribution for set (human, chimp), do not require the set to by monophyletic */
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", chimp);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", false);
    logP = prior.calculateLogP();
    assertEquals(-0.024003, logP, BEASTTestCase.PRECISION);
    /* get distribution for set (human, chimp), DO require the set to by monophyletic */
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(Double.NEGATIVE_INFINITY, logP, 0);
    /* get distribution for set (human, gorilla) = root, not monophyletic */
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", gorilla);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", false);
    logP = prior.calculateLogP();
    assertEquals(-0.024003 - 0.012035, logP, BEASTTestCase.PRECISION);
}

Example 9 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class MRCAPriorTest method testSingleMonophyleticConstraint.

@Test
public void testSingleMonophyleticConstraint() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035," + "(gorilla:0.024003,(orangutan:0.010772,siamang:0.010772):0.013231):0.012035);", "IsLabelledNewick", true);
    Taxon human = new Taxon();
    human.setID("human");
    Taxon bonobo = new Taxon();
    bonobo.setID("bonobo");
    Taxon chimp = new Taxon();
    chimp.setID("chimp");
    Taxon gorilla = new Taxon();
    gorilla.setID("gorilla");
    Taxon orangutan = new Taxon();
    orangutan.setID("orangutan");
    Taxon siamang = new Taxon();
    siamang.setID("siamang");
    MRCAPrior prior = new MRCAPrior();
    /* check (human, bonobo, chimp) is monophyletic **/
    TaxonSet set = new TaxonSet();
    set.initByName("taxon", human, "taxon", bonobo, "taxon", chimp);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    double logP = prior.calculateLogP();
    assertEquals(logP, 0, 0);
    /* check (gorilla, siamang) is NOT monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", gorilla, "taxon", siamang);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, Double.NEGATIVE_INFINITY, 0);
    /* check (gorilla, orangutan, siamang) is monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", gorilla, "taxon", orangutan, "taxon", siamang);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, 0, 0);
    /* check (human, gorilla) is NOT monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", gorilla);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, Double.NEGATIVE_INFINITY, 0);
    set.setID("test");
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream ps = new PrintStream(baos);
    prior.init(ps);
    String log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
    assertEquals(log, "mrcatime(test)\t");
    baos = new ByteArrayOutputStream();
    ps = new PrintStream(baos);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true, "useOriginate", true);
    prior.init(ps);
    log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
    assertEquals(log, "mrcatime(test.originate)\t");
}

Example 10 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class PriorListInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption, boolean addButtons) {
    List<?> list = (List<?>) input.get();
    Collections.sort(list, (Object o1, Object o2) -> {
        if (o1 instanceof BEASTInterface && o2 instanceof BEASTInterface) {
            String d1 = ((BEASTInterface) o1).getID();
            String id2 = ((BEASTInterface) o2).getID();
            // first the tree priors
            if (o1 instanceof TreeDistribution) {
                if (o2 instanceof TreeDistribution) {
                    TreeInterface tree1 = ((TreeDistribution) o1).treeInput.get();
                    if (tree1 == null) {
                        tree1 = ((TreeDistribution) o1).treeIntervalsInput.get().treeInput.get();
                    }
                    TreeInterface tree2 = ((TreeDistribution) o2).treeInput.get();
                    if (tree2 == null) {
                        tree2 = ((TreeDistribution) o2).treeIntervalsInput.get().treeInput.get();
                    }
                    return d1.compareTo(id2);
                } else {
                    return -1;
                }
            } else if (o1 instanceof MRCAPrior) {
                // last MRCA priors
                if (o2 instanceof MRCAPrior) {
                    return d1.compareTo(id2);
                } else {
                    return 1;
                }
            } else {
                if (o2 instanceof TreeDistribution) {
                    return 1;
                }
                if (o2 instanceof MRCAPrior) {
                    return -1;
                }
                if (o1 instanceof Prior) {
                    d1 = ((Prior) o1).getParameterName();
                }
                if (o2 instanceof Prior) {
                    id2 = ((Prior) o2).getParameterName();
                }
                return d1.compareTo(id2);
            }
        }
        return 0;
    });
    rangeButtons = new ArrayList<>();
    taxonButtons = new ArrayList<>();
    // m_buttonStatus = ButtonStatus.NONE;
    super.init(input, beastObject, itemNr, isExpandOption, addButtons);
    if (beastObject instanceof BeautiPanelConfig) {
        BeautiPanelConfig config = (BeautiPanelConfig) beastObject;
        if (config.parentBEASTObjects != null && config.parentBEASTObjects.size() > 0 && config.parentBEASTObjects.get(0).getID().equals("speciescoalescent")) {
            m_buttonStatus = ButtonStatus.NONE;
        }
    }
    if (m_buttonStatus == ButtonStatus.ALL || m_buttonStatus == ButtonStatus.ADD_ONLY) {
        addButton = new SmallButton("+ Add Prior", true);
        addButton.setName("addItem");
        addButton.setToolTipText("Add new prior (like an MRCA-prior) to the list of priors");
        addButton.addActionListener(e -> {
            addItem();
        });
        buttonBox.add(addButton);
        buttonBox.add(Box.createHorizontalGlue());
    }
}