Examples with TreeDistribution beast.evolution.tree.TreeDistribution used on opensource projects

Example 1 with TreeDistribution

use of beast.evolution.tree.TreeDistribution in project beast2 by CompEvol.

the class TreeDistributionInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, int listItemNr, ExpandOption isExpandOption, boolean addButtons) {
    m_bAddButtons = addButtons;
    m_input = input;
    m_beastObject = beastObject;
    this.itemNr = listItemNr;
    Box itemBox = Box.createHorizontalBox();
    TreeDistribution distr = (TreeDistribution) beastObject;
    String text = "";
    if (distr.treeInput.get() != null) {
        text += distr.treeInput.get().getID();
    } else {
        text += distr.treeIntervalsInput.get().treeInput.get().getID();
    }
    JLabel label = new JLabel(text);
    Font font = label.getFont();
    Dimension size = new Dimension(font.getSize() * 200 / 12, font.getSize() * 2);
    label.setMinimumSize(size);
    label.setPreferredSize(size);
    itemBox.add(label);
    // List<String> availableBEASTObjects =
    // PluginPanel.getAvailablePlugins(m_input, m_beastObject, null);
    List<BeautiSubTemplate> availableBEASTObjects = doc.getInputEditorFactory().getAvailableTemplates(m_input, m_beastObject, null, doc);
    // make sure we are dealing with a TreeDistribution
    for (int i = availableBEASTObjects.size() - 1; i >= 0; i--) {
        BeautiSubTemplate t = availableBEASTObjects.get(i);
        Class<?> c = t._class;
        if (!(TreeDistribution.class.isAssignableFrom(c))) {
            availableBEASTObjects.remove(i);
        }
    }
    JComboBox<BeautiSubTemplate> comboBox = new JComboBox<>(availableBEASTObjects.toArray(new BeautiSubTemplate[] {}));
    comboBox.setName("TreeDistribution");
    for (int i = availableBEASTObjects.size() - 1; i >= 0; i--) {
        if (!TreeDistribution.class.isAssignableFrom(availableBEASTObjects.get(i)._class)) {
            availableBEASTObjects.remove(i);
        }
    }
    String id = distr.getID();
    try {
        // id = BeautiDoc.parsePartition(id);
        id = id.substring(0, id.indexOf('.'));
    } catch (Exception e) {
        throw new RuntimeException("Improperly formatted ID: " + distr.getID());
    }
    for (BeautiSubTemplate template : availableBEASTObjects) {
        if (template.matchesName(id)) {
            // getMainID().replaceAll(".\\$\\(n\\)",
            // "").equals(id)) {
            comboBox.setSelectedItem(template);
        }
    }
    comboBox.addActionListener(e -> {
        m_e = e;
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                @SuppressWarnings("unchecked") JComboBox<BeautiSubTemplate> currentComboBox = (JComboBox<BeautiSubTemplate>) m_e.getSource();
                @SuppressWarnings("unchecked") List<BEASTInterface> list = (List<BEASTInterface>) m_input.get();
                BeautiSubTemplate template = (BeautiSubTemplate) currentComboBox.getSelectedItem();
                PartitionContext partitionContext = doc.getContextFor(list.get(itemNr));
                try {
                    template.createSubNet(partitionContext, list, itemNr, true);
                } catch (Exception ex) {
                    ex.printStackTrace();
                }
                sync();
                refreshPanel();
            }
        });
    });
    itemBox.add(comboBox);
    itemBox.add(Box.createGlue());
    m_validateLabel = new SmallLabel("x", new Color(200, 0, 0));
    m_validateLabel.setVisible(false);
    validateInput();
    itemBox.add(m_validateLabel);
    add(itemBox);
}

Example 2 with TreeDistribution

use of beast.evolution.tree.TreeDistribution 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());
    }
}

Example 3 with TreeDistribution

use of beast.evolution.tree.TreeDistribution in project beast2 by CompEvol.

the class TreeDistributionInputEditor method validateInput.

@Override
public void validateInput() {
    TreeDistribution distr = (TreeDistribution) m_beastObject;
    // TODO: robustify for the case the tree is not a simple binary tree
    Tree tree = (Tree) distr.treeInput.get();
    if (tree == null) {
        tree = distr.treeIntervalsInput.get().treeInput.get();
    }
    if (tree.hasDateTrait()) {
        if (!distr.canHandleTipDates()) {
            m_validateLabel.setToolTipText("This tree prior cannot handle dated tips. Choose another tree prior.");
            m_validateLabel.m_circleColor = Color.red;
            m_validateLabel.setVisible(true);
            return;
        }
    }
    super.validateInput();
}