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

Example 91 with BEASTInterface

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

the class Document method calcPluginSet.

// toXML
/**
 * collect all objects and put all top-level beastObjects in a PluginSet
 */
BEASTObjectSet calcPluginSet() {
    // collect all plug-ins
    Collection<BEASTInterface> beastObjects = getPlugins();
    // calc outputs
    HashMap<BEASTInterface, List<BEASTInterface>> outputs = BEASTObjectPanel.getOutputs(beastObjects);
    // put all beastObjects with no ouputs in the PluginSet
    BEASTObjectSet pluginSet = new BEASTObjectSet();
    for (BEASTInterface beastObject : outputs.keySet()) {
        if (outputs.get(beastObject).size() == 0) {
            try {
                pluginSet.setInputValue("beastObject", beastObject);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    return pluginSet;
}

Example 92 with BEASTInterface

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

the class Document method checkForOtherPluginShapes.

// addNewShape
void checkForOtherPluginShapes(List<Integer> objects, BEASTObjectShape shape) {
    // check whether we need to create any input beastObjects
    try {
        List<Input<?>> inputs = shape.m_beastObject.listInputs();
        for (Input<?> input : inputs) {
            if (input.get() instanceof BEASTInterface) {
                BEASTInterface beastObject = (BEASTInterface) input.get();
                BEASTObjectShape beastObjectShape = new BEASTObjectShape(beastObject, this);
                beastObjectShape.m_x = Math.max(shape.m_x - DX, 0);
                beastObjectShape.m_y = shape.m_y;
                beastObjectShape.m_w = 100;
                beastObjectShape.m_h = 80;
                setPluginID(beastObjectShape);
                m_objects.add(beastObjectShape);
                objects.add(m_objects.size() - 1);
                Arrow arrow = new Arrow(beastObjectShape, shape, input.getName());
                m_objects.add(arrow);
                objects.add(m_objects.size() - 1);
                // recurse
                checkForOtherPluginShapes(objects, beastObjectShape);
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 93 with BEASTInterface

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

the class Document method reinit.

void reinit() {
    String xml = toXML();
    m_objects.clear();
    try {
        XMLParser parser = new XMLParser();
        BEASTInterface plugin0 = parser.parseBareFragment(xml, false);
        init(plugin0);
    } catch (Exception e) {
        e.printStackTrace();
    // TODO: handle exception
    }
}

Example 94 with BEASTInterface

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

the class Document method isValidModel.

int isValidModel() {
    BEASTObjectSet pluginSet = calcPluginSet();
    if (pluginSet.m_plugins.get().size() == 0) {
        return STATUS_EMPTY_MODEL;
    }
    if (pluginSet.m_plugins.get().size() > 1) {
        return STATUS_ORPHANS_IN_MODEL;
    }
    boolean hasRunable = false;
    for (BEASTInterface beastObject : pluginSet.m_plugins.get()) {
        if (beastObject instanceof Runnable) {
            hasRunable = true;
        }
    }
    if (!hasRunable) {
        return STATUS_NOT_RUNNABLE;
    }
    return STATUS_OK;
}

Example 95 with BEASTInterface

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

the class Document method loadFile.

public void loadFile(String fileName) {
    m_objects.clear();
    XMLParser parser = new XMLParser();
    try {
        // fileName;
        StringBuilder xml = new StringBuilder();
        String NL = System.getProperty("line.separator");
        Scanner scanner = new Scanner(new File(fileName));
        try {
            while (scanner.hasNextLine()) {
                xml.append(scanner.nextLine() + NL);
            }
        } finally {
            scanner.close();
        }
        BEASTInterface plugin0 = parser.parseBareFragment(xml.toString(), false);
        init(plugin0);
    } catch (Exception e) {
        e.printStackTrace();
    // TODO: handle exception
    }
}