Examples with BEASTInterface beast.core.BEASTInterface used on opensource projects

Example 36 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class ThreadedTreeLikelihood method duplicate.

/**
 * create new instance of src object, connecting all inputs from src object
 * Note if input is a SubstModel, it is duplicated as well.
 * @param src object to be copied
 * @param i index used to extend ID with.
 * @return copy of src object
 */
private Object duplicate(BEASTInterface src, int i) {
    if (src == null) {
        return null;
    }
    BEASTInterface copy;
    try {
        copy = src.getClass().newInstance();
        copy.setID(src.getID() + "_" + i);
    } catch (InstantiationException | IllegalAccessException e) {
        e.printStackTrace();
        throw new RuntimeException("Programmer error: every object in the model should have a default constructor that is publicly accessible: " + src.getClass().getName());
    }
    for (Input<?> input : src.listInputs()) {
        if (input.get() != null) {
            if (input.get() instanceof List) {
                // ((List)copy.getInput(input.getName())).clear();
                for (Object o : (List<?>) input.get()) {
                    if (o instanceof BEASTInterface) {
                        // make sure it is not already in the list
                        copy.setInputValue(input.getName(), o);
                    }
                }
            } else if (input.get() instanceof SubstitutionModel) {
                // duplicate subst models
                BEASTInterface substModel = (BEASTInterface) duplicate((BEASTInterface) input.get(), i);
                copy.setInputValue(input.getName(), substModel);
            } else {
                // it is some other value
                copy.setInputValue(input.getName(), input.get());
            }
        }
    }
    copy.initAndValidate();
    return copy;
}

Example 37 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class XMLProducerTest method test_ThatNexusExamplesProduces.

// @Test
// public void test_ThatXmlExamplesProduces() {
// System.setProperty("java.only", "true");
// String dir = System.getProperty("user.dir") + "/examples";
// //String dir = "/tmp";
// List<String> exceptions = new ArrayList<String>();
// exceptions.add("testExponentialGrowth.xml");
// test_ThatXmlExamplesProduces(dir, exceptions);
// }
@Test
public void test_ThatNexusExamplesProduces() {
    try {
        String dirName = System.getProperty("user.dir") + "/examples/nexus";
        System.out.println("Test Nexus Examples in " + dirName);
        File exampleDir = new File(dirName);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".nex") || name.endsWith(".nxs");
            }
        });
        List<String> failedFiles = new ArrayList<>();
        for (String fileName : exampleFiles) {
            System.out.println("Processing " + fileName);
            NexusParser parser = new NexusParser();
            try {
                parser.parseFile(new File(dirName + "/" + fileName));
            } catch (Exception e) {
                System.out.println("ExampleNexusParsing::Failed for " + fileName + ": " + e.getMessage());
                failedFiles.add(fileName);
            }
            XMLProducer producer = new XMLProducer();
            BEASTInterface o = parser.m_alignment;
            if (o != null) {
                String xml = producer.toXML(o);
                // FileWriter outfile = new FileWriter(new File("/tmp/XMLProducerTest.xml"));
                // outfile.write(xml);
                // outfile.close();
                XMLParser parser2 = new XMLParser();
                try {
                    BEASTInterface o2 = parser2.parseFragment(xml, false);
                    System.out.println(o2);
                } catch (Exception e) {
                    System.out.println("test_ThatNexusExamplesProduces::Failed for " + fileName + ": " + e.getMessage());
                    failedFiles.add(fileName);
                }
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\test_ThatNexusExamplesProduces::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\test_ThatNexusExamplesProduces::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 38 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class BEASTObjectDialog method main.

/**
 * rudimentary test *
 */
public static void main(String[] args) {
    BEASTObjectDialog dlg = null;
    try {
        if (args.length == 0) {
            dlg = new BEASTObjectDialog(new BEASTObjectPanel(new MCMC(), Runnable.class, null), null);
        } else if (args[0].equals("-x")) {
            StringBuilder text = new StringBuilder();
            String NL = System.getProperty("line.separator");
            Scanner scanner = new Scanner(new File(args[1]));
            try {
                while (scanner.hasNextLine()) {
                    text.append(scanner.nextLine() + NL);
                }
            } finally {
                scanner.close();
            }
            BEASTInterface beastObject = new beast.util.XMLParser().parseBareFragment(text.toString(), false);
            dlg = new BEASTObjectDialog(new BEASTObjectPanel(beastObject, beastObject.getClass(), null), null);
        } else if (args.length == 1) {
            dlg = new BEASTObjectDialog(new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[0]), null), null);
        } else if (args.length == 2) {
            dlg = new BEASTObjectDialog(new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[1]), null), null);
        } else {
            throw new IllegalArgumentException("Incorrect number of arguments");
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("Usage: " + BEASTObjectDialog.class.getName() + " [-x file ] [class [type]]\n" + "where [class] (optional, default MCMC) is a BEASTObject to edit\n" + "and [type] (optional only if class is specified, default Runnable) the type of the BEASTObject.\n" + "for example\n" + "");
        System.exit(1);
    }
    dlg.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
    if (dlg.showDialog()) {
        BEASTInterface beastObject = dlg.m_panel.m_beastObject;
        String xml = new XMLProducer().modelToXML(beastObject);
        System.out.println(xml);
    }
}

Example 39 with BEASTInterface

use of beast.core.BEASTInterface 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 40 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class BEASTObjectInputEditor method addComboBox.

// expandedInit
/**
 * add combobox with BEASTObjects to choose from
 * On choosing a new value, create beastObject (if is not already an object)
 * Furthermore, if expanded, update expanded inputs
 */
protected void addComboBox(JComponent box, Input<?> input, BEASTInterface beastObject0) {
    if (itemNr >= 0) {
        box.add(new JLabel(beastObject0.getID()));
        box.add(Box.createGlue());
        return;
    }
    List<BeautiSubTemplate> availableTemplates = doc.getInputEditorFactory().getAvailableTemplates(m_input, m_beastObject, null, doc);
    if (availableTemplates.size() > 0) {
        // if (m_input.getRule() != Validate.REQUIRED || beastObject == null) {
        // availableBEASTObjects.add(NO_VALUE);
        // }
        // for (int i = 0; i < availableBEASTObjects.size(); i++) {
        // String beastObjectName = availableBEASTObjects.get(i);
        // if (beastObjectName.startsWith("new ")) {
        // beastObjectName = beastObjectName.substring(beastObjectName.lastIndexOf('.'));
        // availableBEASTObjects.set(i, beastObjectName);
        // }
        // 
        // }
        m_selectBEASTObjectBox = new JComboBox<>(availableTemplates.toArray());
        m_selectBEASTObjectBox.setName(input.getName());
        Object o = input.get();
        if (itemNr >= 0) {
            o = ((List<?>) o).get(itemNr);
        }
        String id2;
        if (o == null) {
            id2 = beastObject0.getID();
        } else {
            id2 = ((BEASTInterface) o).getID();
        }
        if (id2.indexOf('.') >= 0) {
            id2 = id2.substring(0, id2.indexOf('.'));
        }
        for (BeautiSubTemplate template : availableTemplates) {
            if (template.matchesName(id2)) {
                m_selectBEASTObjectBox.setSelectedItem(template);
            }
        }
        m_selectBEASTObjectBox.addActionListener(e -> {
            // SwingUtilities.invokeLater(new Runnable() {
            // 
            // @Override
            // public void run() {
            // get a handle of the selected beastObject
            BeautiSubTemplate selected = (BeautiSubTemplate) m_selectBEASTObjectBox.getSelectedItem();
            BEASTInterface beastObject = (BEASTInterface) m_input.get();
            String id = beastObject.getID();
            String partition = id.indexOf('.') >= 0 ? id.substring(id.indexOf('.') + 1) : "";
            if (partition.indexOf(':') >= 0) {
                partition = id.substring(id.indexOf(':') + 1);
            }
            if (selected.equals(NO_VALUE)) {
                beastObject = null;
            // } else if (PluginPanel.g_plugins.containsKey(newID)) {
            // beastObject = PluginPanel.g_plugins.get(newID);
            } else {
                try {
                    beastObject = selected.createSubNet(doc.getContextFor(beastObject), m_beastObject, m_input, true);
                // PluginPanel.addPluginToMap(beastObject);
                // tricky: try to connect up new inputs with old inputs of existing name
                // beastObject oldPlugin = (beastObject) m_input.get();
                // for (Input<?> oldInput: oldPlugin.listInputs()) {
                // String name = oldInput.getName();
                // try {
                // Input<?> newInput = beastObject.getInput(name);
                // if (newInput.get() instanceof List) {
                // List<?> values = (List<?>) oldInput.get();
                // for (Object value: values) {
                // newInput.setValue(value, beastObject);
                // }
                // } else {
                // newInput.setValue(oldInput.get(), beastObject);
                // }
                // } catch (Exception ex) {
                // // ignore
                // }
                // }
                } catch (Exception ex) {
                    JOptionPane.showMessageDialog(null, "Could not select beastObject: " + ex.getClass().getName() + " " + ex.getMessage());
                }
            }
            try {
                if (beastObject == null) {
                    m_selectBEASTObjectBox.setSelectedItem(NO_VALUE);
                    // is this input expanded?
                    if (m_expansionBox != null) {
                        // remove items from Expansion Box, if any
                        for (int i = 1; i < m_expansionBox.getComponentCount(); i++) {
                            m_expansionBox.remove(i);
                        }
                    } else {
                        // not expanded
                        if (m_bAddButtons && m_editBEASTObjectButton != null) {
                            m_editBEASTObjectButton.setEnabled(false);
                        }
                    }
                } else {
                    if (!m_input.canSetValue(beastObject, m_beastObject)) {
                        throw new IllegalArgumentException("Cannot set input to this value");
                    }
                    // // get handle on ID of the beastObject, and add to combobox if necessary
                    // String id = beastObject.getID();
                    // // TODO RRB: have to remove ID first, then add it
                    // // The addition is necessary to make the items in the expansionBox scale and show up
                    // // Is there another way?
                    // m_selectPluginBox.removeItem(id);
                    // m_selectPluginBox.addItem(id);
                    // m_selectPluginBox.setSelectedItem(id);
                    id = beastObject.getID();
                    if (id.indexOf('.') != -1) {
                        id = id.substring(0, id.indexOf('.'));
                    }
                    for (int i = 0; i < m_selectBEASTObjectBox.getItemCount(); i++) {
                        BeautiSubTemplate template = (BeautiSubTemplate) m_selectBEASTObjectBox.getItemAt(i);
                        if (template.getMainID().replaceAll(".\\$\\(n\\)", "").equals(id) || template.getMainID().replaceAll(".s:\\$\\(n\\)", "").equals(id) || template.getMainID().replaceAll(".c:\\$\\(n\\)", "").equals(id) || template.getMainID().replaceAll(".t:\\$\\(n\\)", "").equals(id)) {
                            m_selectBEASTObjectBox.setSelectedItem(template);
                        }
                    }
                }
                setValue(beastObject);
                if (m_expansionBox != null) {
                    // remove items from Expansion Box
                    for (int i = 1; i < m_expansionBox.getComponentCount(); ) {
                        m_expansionBox.remove(i);
                    }
                    // add new items to Expansion Box
                    if (beastObject != null) {
                        doc.getInputEditorFactory().addInputs(m_expansionBox, beastObject, _this, _this, doc);
                    }
                } else {
                    // it is not expanded, enable the edit button
                    if (m_bAddButtons && m_editBEASTObjectButton != null) {
                        m_editBEASTObjectButton.setEnabled(true);
                    }
                    validateInput();
                }
                sync();
                refreshPanel();
            } catch (Exception ex) {
                id = ((BEASTInterface) m_input.get()).getID();
                m_selectBEASTObjectBox.setSelectedItem(id);
                ex.printStackTrace();
                JOptionPane.showMessageDialog(null, "Could not change beastObject: " + ex.getClass().getName() + " " + ex.getMessage());
            }
        });
        m_selectBEASTObjectBox.setToolTipText(input.getHTMLTipText());
        int fontsize = m_selectBEASTObjectBox.getFont().getSize();
        m_selectBEASTObjectBox.setMaximumSize(new Dimension(1024, 200 * fontsize / 13));
        box.add(m_selectBEASTObjectBox);
    }
}