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

Example 1 with Operator

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

the class BeautiBase method operatorsAsString.

String operatorsAsString() {
    MCMC mcmc = (MCMC) doc.mcmc.get();
    List<Operator> operators = mcmc.operatorsInput.get();
    return "assertOperatorsEqual" + pluginListAsString(operators);
}

Example 2 with Operator

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

the class OperatorListInputEditor method addPluginItem.

@Override
protected InputEditor addPluginItem(Box itemBox, BEASTInterface beastObject) {
    Operator operator = (Operator) beastObject;
    JTextField entry = new JTextField(" " + getLabel(operator));
    entry.setMinimumSize(new Dimension(200, 16));
    // entry.setMaximumSize(new Dimension(200, 20));
    m_entries.add(entry);
    entry.setBackground(getBackground());
    entry.setBorder(null);
    itemBox.add(Box.createRigidArea(new Dimension(5, 1)));
    itemBox.add(entry);
    entry.setEditable(false);
    // JLabel label = new JLabel(getLabel(operator));
    // label.setBackground(Color.WHITE);
    // m_labels.add(label);
    // m_entries.add(null);
    // itemBox.add(label);
    itemBox.add(Box.createHorizontalGlue());
    JTextField weightEntry = new JTextField();
    weightEntry.setToolTipText(operator.m_pWeight.getHTMLTipText());
    weightEntry.setText(operator.m_pWeight.get() + "");
    weightEntry.getDocument().addDocumentListener(new OperatorDocumentListener(operator, weightEntry));
    Dimension size = new Dimension(50, 25);
    weightEntry.setMinimumSize(size);
    weightEntry.setPreferredSize(size);
    int fontsize = weightEntry.getFont().getSize();
    weightEntry.setMaximumSize(new Dimension(50 * fontsize / 13, 50 * fontsize / 13));
    itemBox.add(weightEntry);
    return this;
}

Example 3 with Operator

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

the class MRCAPriorInputEditor method disableTipSampling.

// remove TipDatesRandomWalker from list of operators
private static void disableTipSampling(BEASTInterface m_beastObject, BeautiDoc doc) {
    // First, find the operator
    TipDatesRandomWalker operator = null;
    MRCAPrior prior = (MRCAPrior) m_beastObject;
    TaxonSet taxonset = prior.taxonsetInput.get();
    // However, if there is an TipDatesRandomWalker with taxonset as input, we want to remove it.
    for (BEASTInterface o : taxonset.getOutputs()) {
        if (o instanceof TipDatesRandomWalker) {
            operator = (TipDatesRandomWalker) o;
        }
    }
    if (operator == null) {
        // should never happen
        return;
    }
    // remove from list of operators
    Object o = doc.mcmc.get().getInput("operator");
    if (o instanceof Input<?>) {
        Input<List<Operator>> operatorInput = (Input<List<Operator>>) o;
        List<Operator> operators = operatorInput.get();
        operators.remove(operator);
    }
}

Example 4 with Operator

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

the class ParameterInputEditor method addComboBox.

@Override
protected void addComboBox(JComponent box, Input<?> input, BEASTInterface beastObject) {
    Box paramBox = Box.createHorizontalBox();
    Parameter.Base<?> parameter = null;
    if (itemNr >= 0) {
        parameter = (Parameter.Base<?>) ((List<?>) input.get()).get(itemNr);
    } else {
        parameter = (Parameter.Base<?>) input.get();
    }
    if (parameter == null) {
        super.addComboBox(box, input, beastObject);
    } else {
        setUpEntry();
        paramBox.add(m_entry);
        if (doc.allowLinking) {
            boolean isLinked = doc.isLinked(m_input);
            if (isLinked || doc.suggestedLinks((BEASTInterface) m_input.get()).size() > 0) {
                JButton linkbutton = new JButton(Utils.getIcon(BeautiPanel.ICONPATH + (isLinked ? "link.png" : "unlink.png")));
                linkbutton.setBorder(BorderFactory.createEmptyBorder());
                linkbutton.setToolTipText("link/unlink this parameter with another compatible parameter");
                linkbutton.addActionListener(e -> {
                    if (doc.isLinked(m_input)) {
                        // unlink
                        try {
                            BEASTInterface candidate = doc.getUnlinkCandidate(m_input, m_beastObject);
                            m_input.setValue(candidate, m_beastObject);
                            doc.deLink(m_input);
                        } catch (RuntimeException e2) {
                            e2.printStackTrace();
                            JOptionPane.showMessageDialog(this, "Could not unlink: " + e2.getMessage());
                        }
                    } else {
                        // create a link
                        List<BEASTInterface> candidates = doc.suggestedLinks((BEASTInterface) m_input.get());
                        JComboBox<BEASTInterface> jcb = new JComboBox<>(candidates.toArray(new BEASTInterface[] {}));
                        JOptionPane.showMessageDialog(null, jcb, "select parameter to link with", JOptionPane.QUESTION_MESSAGE);
                        BEASTInterface candidate = (BEASTInterface) jcb.getSelectedItem();
                        if (candidate != null) {
                            try {
                                m_input.setValue(candidate, m_beastObject);
                                doc.addLink(m_input);
                            } catch (Exception e2) {
                                e2.printStackTrace();
                            }
                        }
                    }
                    refreshPanel();
                });
                paramBox.add(linkbutton);
            }
        }
        paramBox.add(Box.createHorizontalGlue());
        m_isEstimatedBox = new JCheckBox(doc.beautiConfig.getInputLabel(parameter, parameter.isEstimatedInput.getName()));
        m_isEstimatedBox.setName(input.getName() + ".isEstimated");
        if (input.get() != null) {
            m_isEstimatedBox.setSelected(parameter.isEstimatedInput.get());
        }
        m_isEstimatedBox.setToolTipText(parameter.isEstimatedInput.getHTMLTipText());
        boolean isClockRate = false;
        for (Object output : parameter.getOutputs()) {
            if (output instanceof BranchRateModel.Base) {
                isClockRate |= ((BranchRateModel.Base) output).meanRateInput.get() == parameter;
            }
        }
        m_isEstimatedBox.setEnabled(!isClockRate || !getDoc().autoSetClockRate);
        m_isEstimatedBox.addActionListener(e -> {
            try {
                Parameter.Base<?> parameter2 = (Parameter.Base<?>) m_input.get();
                parameter2.isEstimatedInput.setValue(m_isEstimatedBox.isSelected(), parameter2);
                if (isParametricDistributionParameter) {
                    String id = parameter2.getID();
                    if (id.startsWith("RealParameter")) {
                        ParametricDistribution parent = null;
                        for (Object beastObject2 : parameter2.getOutputs()) {
                            if (beastObject2 instanceof ParametricDistribution) {
                                parent = (ParametricDistribution) beastObject2;
                                break;
                            }
                        }
                        Distribution grandparent = null;
                        for (Object beastObject2 : parent.getOutputs()) {
                            if (beastObject2 instanceof Distribution) {
                                grandparent = (Distribution) beastObject2;
                                break;
                            }
                        }
                        id = "parameter.hyper" + parent.getClass().getSimpleName() + "-" + m_input.getName() + "-" + grandparent.getID();
                        doc.pluginmap.remove(parameter2.getID());
                        parameter2.setID(id);
                        doc.addPlugin(parameter2);
                    }
                    PartitionContext context = new PartitionContext(id.substring("parameter.".length()));
                    Log.warning.println(context + " " + id);
                    doc.beautiConfig.hyperPriorTemplate.createSubNet(context, true);
                }
                refreshPanel();
            } catch (Exception ex) {
                Log.err.println("ParameterInputEditor " + ex.getMessage());
            }
        });
        paramBox.add(m_isEstimatedBox);
        // only show the estimate flag if there is an operator that works on this parameter
        m_isEstimatedBox.setVisible(doc.isExpertMode());
        m_isEstimatedBox.setToolTipText("Estimate value of this parameter in the MCMC chain");
        // m_bAddButtons = false;
        if (itemNr < 0) {
            for (Object beastObject2 : ((BEASTInterface) m_input.get()).getOutputs()) {
                if (beastObject2 instanceof ParametricDistribution) {
                    m_isEstimatedBox.setVisible(true);
                    isParametricDistributionParameter = true;
                    break;
                }
            }
            for (Object beastObject2 : ((BEASTInterface) m_input.get()).getOutputs()) {
                if (beastObject2 instanceof Operator) {
                    m_isEstimatedBox.setVisible(true);
                    // m_editPluginButton.setVisible(true);
                    break;
                }
            }
        } else {
            for (Object beastObject2 : ((BEASTInterface) ((List<?>) m_input.get()).get(itemNr)).getOutputs()) {
                if (beastObject2 instanceof Operator) {
                    m_isEstimatedBox.setVisible(true);
                    // m_editPluginButton.setVisible(true);
                    break;
                }
            }
        }
        box.add(paramBox);
    }
}

Example 5 with Operator

use of beast.core.Operator in project MultiTypeTree by tgvaughan.

the class NSR_Test method test.

@Test
public void test() throws Exception {
    System.out.println("NSR test");
    // Fix seed.
    Randomizer.setSeed(42);
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter("0.1 0.1");
    RealParameter popSizes = new RealParameter("7.0 7.0");
    SCMigrationModel migModel = new SCMigrationModel();
    migModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Assemble initial MultiTypeTree
    MultiTypeTree mtTree = new StructuredCoalescentMultiTypeTree();
    mtTree.initByName("typeLabel", "deme", "migrationModel", migModel, "leafTypes", "1 0");
    // Set up state:
    State state = new State();
    state.initByName("stateNode", mtTree);
    // Assemble distribution:
    StructuredCoalescentTreeDensity distribution = new StructuredCoalescentTreeDensity();
    distribution.initByName("migrationModel", migModel, "multiTypeTree", mtTree);
    // Set up operators:
    Operator operatorNSR = new NodeShiftRetype();
    operatorNSR.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel);
    // Set up stat analysis logger:
    MultiTypeTreeStatLogger logger = new MultiTypeTreeStatLogger();
    logger.initByName("multiTypeTree", mtTree, "burninFrac", 0.1, "logEvery", 100);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "1000000", "state", state, "distribution", distribution, "operator", operatorNSR, "logger", logger);
    // Run MCMC:
    mcmc.run();
    System.out.format("height mean = %s\n", logger.getHeightMean());
    System.out.format("height var = %s\n", logger.getHeightVar());
    System.out.format("height ESS = %s\n", logger.getHeightESS());
    // Compare analysis results with truth:
    boolean withinTol = (logger.getHeightESS() > 2000) && (Math.abs(logger.getHeightMean() - 19.0) < 0.5) && (Math.abs(logger.getHeightVar() - 291) < 30);
    Assert.assertTrue(withinTol);
}