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

Example 11 with Input

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

the class MRCAPriorInputEditor method createTipsonlyEditor.

public InputEditor createTipsonlyEditor() throws NoSuchMethodException, SecurityException, ClassNotFoundException, InstantiationException, IllegalAccessException, IllegalArgumentException, InvocationTargetException {
    BooleanInputEditor e = new BooleanInputEditor(doc) {

        private static final long serialVersionUID = 1L;

        @Override
        public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption, boolean addButtons) {
            super.init(input, beastObject, itemNr, isExpandOption, addButtons);
            // hack to get to JCheckBox
            Component[] components = getComponents();
            ((JCheckBox) components[0]).addActionListener(e -> {
                JCheckBox src = (JCheckBox) e.getSource();
                if (src.isSelected()) {
                    enableTipSampling();
                } else {
                    disableTipSampling(m_beastObject, doc);
                }
            });
        }
    };
    MRCAPrior prior = (MRCAPrior) m_beastObject;
    Input<?> input = prior.onlyUseTipsInput;
    e.init(input, prior, -1, ExpandOption.FALSE, false);
    return e;
}

Example 12 with Input

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

the class PriorInputEditor 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();
    Prior prior = (Prior) beastObject;
    String text = prior.getParameterName();
    JLabel label = new JLabel(text);
    Font font = label.getFont();
    Dimension size = new Dimension(font.getSize() * 200 / 13, font.getSize() * 25 / 13);
    label.setMinimumSize(size);
    label.setPreferredSize(size);
    itemBox.add(label);
    List<BeautiSubTemplate> availableBEASTObjects = doc.getInputEditorFactory().getAvailableTemplates(prior.distInput, prior, null, doc);
    JComboBox<BeautiSubTemplate> comboBox = new JComboBox<BeautiSubTemplate>(availableBEASTObjects.toArray(new BeautiSubTemplate[] {}));
    comboBox.setName(text + ".distr");
    String id = prior.distInput.get().getID();
    // Log.warning.println("id=" + id);
    id = id.substring(0, id.indexOf('.'));
    for (BeautiSubTemplate template : availableBEASTObjects) {
        if (template.classInput.get() != null && template.shortClassName.equals(id)) {
            comboBox.setSelectedItem(template);
        }
    }
    comboBox.addActionListener(e -> {
        @SuppressWarnings("unchecked") JComboBox<BeautiSubTemplate> comboBox1 = (JComboBox<BeautiSubTemplate>) e.getSource();
        List<?> list = (List<?>) m_input.get();
        BeautiSubTemplate template = (BeautiSubTemplate) comboBox1.getSelectedItem();
        // String id = ((BEASTObject) list.get(item)).getID();
        // String partition = BeautiDoc.parsePartition(id);
        PartitionContext context = doc.getContextFor((BEASTInterface) list.get(itemNr));
        Prior prior1 = (Prior) list.get(itemNr);
        try {
            template.createSubNet(context, prior1, prior1.distInput, true);
        } catch (Exception e1) {
            e1.printStackTrace();
        }
        sync();
        refreshPanel();
    });
    JPanel panel = new JPanel();
    panel.add(comboBox);
    panel.setMaximumSize(size);
    itemBox.add(panel);
    if (prior.m_x.get() instanceof RealParameter) {
        // add range button for real parameters
        RealParameter p = (RealParameter) prior.m_x.get();
        JButton rangeButton = new JButton(paramToString(p));
        rangeButton.addActionListener(e -> {
            JButton rangeButton1 = (JButton) e.getSource();
            List<?> list = (List<?>) m_input.get();
            Prior prior1 = (Prior) list.get(itemNr);
            RealParameter p1 = (RealParameter) prior1.m_x.get();
            BEASTObjectDialog dlg = new BEASTObjectDialog(p1, RealParameter.class, doc);
            if (dlg.showDialog()) {
                dlg.accept(p1, doc);
                rangeButton1.setText(paramToString(p1));
                refreshPanel();
            }
        });
        itemBox.add(Box.createHorizontalStrut(10));
        itemBox.add(rangeButton);
    } else if (prior.m_x.get() instanceof IntegerParameter) {
        // add range button for real parameters
        IntegerParameter p = (IntegerParameter) prior.m_x.get();
        JButton rangeButton = new JButton(paramToString(p));
        rangeButton.addActionListener(e -> {
            JButton rangeButton1 = (JButton) e.getSource();
            List<?> list = (List<?>) m_input.get();
            Prior prior1 = (Prior) list.get(itemNr);
            IntegerParameter p1 = (IntegerParameter) prior1.m_x.get();
            BEASTObjectDialog dlg = new BEASTObjectDialog(p1, IntegerParameter.class, doc);
            if (dlg.showDialog()) {
                dlg.accept(p1, doc);
                rangeButton1.setText(paramToString(p1));
                refreshPanel();
            }
        });
        itemBox.add(Box.createHorizontalStrut(10));
        itemBox.add(rangeButton);
    }
    int fontsize = comboBox.getFont().getSize();
    comboBox.setMaximumSize(new Dimension(1024 * fontsize / 13, 24 * fontsize / 13));
    String tipText = getDoc().tipTextMap.get(beastObject.getID());
    // System.out.println(beastObject.getID());
    if (tipText != null) {
        JLabel tipTextLabel = new JLabel(" " + tipText);
        itemBox.add(tipTextLabel);
    }
    itemBox.add(Box.createGlue());
    add(itemBox);
}

Example 13 with Input

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

the class BeautiAlignmentProvider method replaceItem.

@SuppressWarnings({ "rawtypes", "unchecked" })
private void replaceItem(BeautiDoc doc, BEASTInterface oldData, BEASTInterface newData) {
    doc.pluginmap.remove(newData.getID());
    Set<BEASTInterface> outputs = new LinkedHashSet<>();
    outputs.addAll(oldData.getOutputs());
    for (BEASTInterface o : outputs) {
        for (Input i : o.listInputs()) {
            if (i.get() == oldData) {
                i.setValue(newData, o);
            } else if (i.get() != null && i.get() instanceof List) {
                List list = (List) i.get();
                int index = list.indexOf(oldData);
                if (index >= 0) {
                    list.set(index, newData);
                    newData.getOutputs().add(o);
                }
            }
        }
    }
}

Example 14 with Input

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

the class BeautiPanel method cloneFrom.

/**
 * Clones partition identified by sourceID to targetID and type (Site/Clock/Tree model)
 * as stored in config.
 * @param sourceID
 * @param targetID
 */
public void cloneFrom(String sourceID, String targetID) {
    if (sourceID.equals(targetID)) {
        return;
    }
    String type = config.hasPartitionsInput.get().toString();
    java.util.List<BEASTInterface> list = doc.getPartitions(type);
    int source = -1, target = -1;
    for (int i = 0; i < list.size(); i++) {
        BEASTInterface partition = list.get(i);
        if (type.equals("SiteModel")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).siteModelInput.get();
        } else if (type.equals("ClockModel")) {
            partition = ((GenericTreeLikelihood) partition).branchRateModelInput.get();
        } else if (type.equals("Tree")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).treeInput.get();
        }
        String partitionID = partition.getID();
        partitionID = partitionID.substring(partitionID.lastIndexOf('.') + 1);
        if (partitionID.length() > 1 && partitionID.charAt(1) == ':') {
            partitionID = partitionID.substring(2);
        }
        if (partitionID.equals(sourceID)) {
            source = i;
        }
        if (partitionID.equals(targetID)) {
            target = i;
        }
    }
    if (target == -1) {
        throw new RuntimeException("Programmer error: sourceID and targetID should be in list");
    }
    CompoundDistribution likelihoods = (CompoundDistribution) doc.pluginmap.get("likelihood");
    GenericTreeLikelihood likelihoodSource = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(source);
    GenericTreeLikelihood likelihood = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(target);
    PartitionContext oldContext = doc.getContextFor(likelihoodSource);
    PartitionContext newContext = doc.getContextFor(likelihood);
    // this ensures the config.sync does not set any input value
    config._input.setValue(null, config);
    if (type.equals("SiteModel")) {
        SiteModelInterface siteModelSource = likelihoodSource.siteModelInput.get();
        SiteModelInterface siteModel = null;
        try {
            siteModel = (SiteModel.Base) BeautiDoc.deepCopyPlugin((BEASTInterface) siteModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (RuntimeException e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        likelihood.siteModelInput.setValue(siteModel, likelihood);
        return;
    } else if (type.equals("ClockModel")) {
        BranchRateModel clockModelSource = likelihoodSource.branchRateModelInput.get();
        BranchRateModel clockModel = null;
        try {
            clockModel = (BranchRateModel) BeautiDoc.deepCopyPlugin((BEASTInterface) clockModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // make sure that *if* the clock model has a tree as input, it is
        // the same as for the likelihood
        TreeInterface tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (TreeInterface) input.get();
                }
            }
        } catch (IllegalArgumentException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        if (tree != null && tree != likelihood.treeInput.get()) {
            // likelihood.treeInput.setValue(tree, likelihood);
            JOptionPane.showMessageDialog(null, "Cannot clone clock model with different trees");
            return;
        }
        likelihood.branchRateModelInput.setValue(clockModel, likelihood);
        return;
    } else if (type.equals("Tree")) {
        TreeInterface tree = null;
        TreeInterface treeSource = likelihoodSource.treeInput.get();
        try {
            tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) treeSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // sanity check: make sure taxon sets are compatible
        Taxon.assertSameTaxa(tree.getID(), tree.getTaxonset().getTaxaNames(), likelihood.dataInput.get().getID(), likelihood.dataInput.get().getTaxaNames());
        likelihood.treeInput.setValue(tree, likelihood);
        return;
    } else {
        throw new RuntimeException("Programmer error calling cloneFrom: Should only clone Site/Clock/Tree model");
    }
}

Example 15 with Input

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

the class DocMaker method getHTML.

// createBEASTObjectPage
public String getHTML(String beastObjectName, boolean useExternalStyleSheet) throws InstantiationException, IllegalAccessException, ClassNotFoundException {
    StringBuffer buf = new StringBuffer();
    buf.append("<html>\n<head>\n<title>BEAST " + version.getVersionString() + " Documentation: " + beastObjectName + "</title>\n");
    if (useExternalStyleSheet) {
        buf.append("<link rel='StyleSheet' href='/tmp/styles.css' type='text/css'>\n");
    } else {
        buf.append("<style type='text/css'>\n");
        buf.append(getCSS());
        buf.append("</style>\n");
    }
    buf.append("</head>\n");
    buf.append("<body>\n");
    buf.append("<h1>BEAST " + version.getVersionString() + " Documentation: " + beastObjectName + "</h1>\n");
    BEASTObject beastObject = (BEASTObject) Class.forName(beastObjectName).newInstance();
    // show all implementation of this plug-in
    String[] implementations = m_isa.get(beastObjectName);
    if (implementations == null) {
        // this class is not documented, perhaps outside ClassDiscover path?
        buf.append("No documentation available for " + beastObjectName + ". Perhaps it is not in the ClassDiscovery path\n");
        buf.append("</body>\n");
        buf.append("</html>\n");
        return buf.toString();
    }
    if (implementations.length > 0) {
        buf.append("<table border='1px'>\n");
        buf.append("<thead><tr><td>implemented by the following</td></tr></thead>\n");
        for (String imp : implementations) {
            buf.append("<tr><td><a href='" + imp + ".html'>" + imp + "</a></td></tr>\n");
        }
        buf.append("</table>\n");
    }
    // show descriptions of all plug-ins implemented by this plug in...
    buf.append("<p>" + m_descriptions.get(beastObjectName) + "</p>\n");
    // show citation (if any)
    for (Citation citation : beastObject.getCitationList()) {
        buf.append("<h2>Reference:</h2><p>" + citation.value() + "</p>\n");
        if (citation.DOI().length() > 0) {
            buf.append("<p><a href=\"http://dx.doi.org/" + citation.DOI() + "\">doi:" + citation.DOI() + "</a></p>\n");
        }
    }
    // show if this is Loggable
    if (m_sLoggables.contains(beastObjectName)) {
        buf.append("<p>Logable:");
        buf.append(" yes, this can be used in a log.");
        buf.append("</p>\n");
    // } else {
    // buf.append(" no, this cannot be used in a log.");
    }
    // show short list its inputs
    buf.append("<h2>Inputs:</h2>\n");
    buf.append("<p>");
    List<Input<?>> inputs = beastObject.listInputs();
    for (Input<?> input : inputs) {
        buf.append("<a href='#" + input.getName() + "'>" + input.getName() + "</a>, ");
    }
    buf.delete(buf.length() - 3, buf.length() - 1);
    buf.append("</p>\n");
    // list its inputs
    if (inputs.size() == 0) {
        buf.append("&lt;none&gt;");
    }
    for (Input<?> input : inputs) {
        buf.append("<p>&nbsp</p>");
        buf.append("<table id='" + input.getName() + "' border='1px' width='90%'>\n");
        buf.append("<caption>" + input.getName() + "</caption>\n");
        buf.append("<thead><tr bgcolor='#AAAAAA'><td>type: " + getType(beastObject, input.getName()) + "</td></tr></thead>\n");
        buf.append("<tr><td>" + input.getTipText() + "</td></tr>\n");
        buf.append("<tr><td>\n");
        switch(input.getRule()) {
            case OPTIONAL:
                buf.append("Optional input");
                if (input.defaultValue != null) {
                    if (input.defaultValue instanceof Integer || input.defaultValue instanceof Double || input.defaultValue instanceof Boolean || input.defaultValue instanceof String) {
                        buf.append(". Default: " + input.defaultValue.toString());
                    }
                }
                break;
            case REQUIRED:
                buf.append("Required input");
                break;
            case XOR:
                buf.append("Either this, or " + input.getOther().getName() + " needs to be specified");
                break;
            case FORBIDDEN:
                buf.append("Forbidden: must not be specified");
                break;
        }
        buf.append("</td></tr>\n");
        buf.append("</table>\n");
    }
    buf.append("</body>\n");
    buf.append("</html>\n");
    return buf.toString();
}