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

Example 41 with BEASTInterface

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

the class BEASTObjectPanel method getOutputs.

/* calculate outputs for each beastObject
      * and put them as ArrayLists in a Map
      * so they can be retrieved indexed by beastObject like this:
      * ArrayList<BEASTObject> output = outputs.get(beastObject)*/
static HashMap<BEASTInterface, List<BEASTInterface>> getOutputs(Collection<BEASTInterface> beastObjects) {
    HashMap<BEASTInterface, List<BEASTInterface>> outputs = new HashMap<>();
    for (BEASTInterface beastObject : beastObjects) {
        outputs.put(beastObject, new ArrayList<>());
    }
    for (BEASTInterface beastObject : beastObjects) {
        try {
            for (Input<?> input2 : beastObject.listInputs()) {
                Object o = input2.get();
                if (o != null && o instanceof BEASTInterface) {
                    List<BEASTInterface> list = outputs.get(o);
                    // if (list == null) {
                    // int h = 3;
                    // h++;
                    // } else {
                    list.add(beastObject);
                // }
                }
                if (o != null && o instanceof List<?>) {
                    for (Object o2 : (List<?>) o) {
                        if (o2 != null && o2 instanceof BEASTInterface) {
                            List<BEASTInterface> list = outputs.get(o2);
                            if (list != null) {
                                list.add(beastObject);
                            }
                        }
                    }
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    return outputs;
}

Example 42 with BEASTInterface

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

the class BEASTObjectPanel method main.

/**
 * rudimentary test *
 */
public static void main(String[] args) {
    init();
    BEASTObjectPanel pluginPanel = null;
    try {
        if (args.length == 0) {
            pluginPanel = new BEASTObjectPanel(new MCMC(), Runnable.class, 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);
            pluginPanel = new BEASTObjectPanel(beastObject, beastObject.getClass(), null);
        } else if (args.length == 1) {
            pluginPanel = new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[0]), null);
        } else if (args.length == 2) {
            pluginPanel = new BEASTObjectPanel((BEASTInterface) Class.forName(args[0]).newInstance(), Class.forName(args[1]), null);
        } else {
            throw new IllegalArgumentException("Incorrect number of arguments");
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("Usage: " + BEASTObjectPanel.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);
    }
    pluginPanel.setVisible(true);
    if (pluginPanel.m_bOK) {
        BEASTInterface beastObject = pluginPanel.m_beastObject;
        String xml = new XMLProducer().modelToXML(beastObject);
        System.out.println(xml);
    }
}

Example 43 with BEASTInterface

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

the class Document method setPluginID.

void setPluginID(BEASTObjectShape shape) {
    if (shape.m_beastObject.getID() != null && shape.m_beastObject.getID().length() > 0) {
        return;
    }
    BEASTInterface beastObject = shape.m_beastObject;
    String base = beastObject.getClass().getName().replaceAll(".*\\.", "");
    int _id = 0;
    while (containsID(base + _id, m_objects, null)) {
        _id++;
    }
    beastObject.setID(base + _id);
}

Example 44 with BEASTInterface

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

the class Document method process.

void process(BEASTObjectShape shape, int depth) throws IllegalArgumentException, IllegalAccessException, InstantiationException, ClassNotFoundException {
    BEASTInterface beastObject = shape.m_beastObject;
    List<Input<?>> inputs = beastObject.listInputs();
    for (Input<?> input_ : inputs) {
        Object o = input_.get();
        if (o != null) {
            if (o instanceof List<?>) {
                for (Object o2 : (List<?>) o) {
                    addInput(shape, o2, depth + 1, input_.getName());
                }
            } else if (o instanceof BEASTInterface) {
                addInput(shape, o, depth + 1, input_.getName());
            // } else {
            // it is a primitive type
            }
        }
    }
}

Example 45 with BEASTInterface

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

the class Document method init.

public void init(BEASTInterface plugin0) {
    try {
        if (plugin0 instanceof BEASTObjectSet) {
            List<BEASTInterface> set = ((BEASTObjectSet) plugin0).m_plugins.get();
            if (set == null) {
                return;
            }
            for (BEASTInterface beastObject : set) {
                BEASTObjectShape shape = new BEASTObjectShape(beastObject, this);
                shape.m_beastObject = beastObject;
                setPluginID(shape);
                m_objects.add(shape);
                process(shape, 1);
                shape.m_x = DX;
                shape.m_w = 100;
                Random random = new Random();
                shape.m_y = random.nextInt(800);
                shape.m_h = 50;
            }
        } else {
            BEASTObjectShape shape = new BEASTObjectShape(plugin0, this);
            shape.m_beastObject = plugin0;
            setPluginID(shape);
            m_objects.add(shape);
            process(shape, 1);
            shape.m_x = DX;
            shape.m_w = 100;
            Random random = new Random();
            shape.m_y = random.nextInt(800);
            shape.m_h = 50;
        }
    } catch (Exception e) {
        e.printStackTrace();
    // TODO: handle exception
    }
    // clear undo stack after all items have been
    // added since the stack is affected by parsing...
    clearUndoStack();
    recalcArrows();
    layout();
    adjustArrows();
}