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

Example 56 with BEASTInterface

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

the class ModelBuilder method setDrawingFlag.

public void setDrawingFlag() {
    for (int i = 0; i < m_doc.m_objects.size(); i++) {
        Shape shape = m_doc.m_objects.get(i);
        shape.m_bNeedsDrawing = false;
        if (shape.m_bNeedsDrawing) {
            shape.m_bNeedsDrawing = true;
        }
        if (shape instanceof BEASTObjectShape) {
            BEASTInterface beastObject = ((BEASTObjectShape) shape).m_beastObject;
            if (needsDrawing(beastObject)) {
                shape.m_bNeedsDrawing = true;
            }
        } else if (shape instanceof InputShape) {
            BEASTObjectShape beastObjectShape = ((InputShape) shape).m_beastObjectShape;
            if (beastObjectShape != null) {
                if (needsDrawing(beastObjectShape.m_beastObject)) {
                    shape.m_bNeedsDrawing = true;
                }
            } else {
                shape.m_bNeedsDrawing = true;
            }
        } else if (shape instanceof Arrow) {
            Shape tail = ((Arrow) shape).m_tailShape;
            boolean needsDrawing = true;
            if (tail instanceof BEASTObjectShape) {
                needsDrawing = needsDrawing(((BEASTObjectShape) tail).m_beastObject);
            }
            if (needsDrawing) {
                Shape head = ((Arrow) shape).m_headShape;
                if (head instanceof InputShape) {
                    BEASTObjectShape beastObjectShape = ((InputShape) head).m_beastObjectShape;
                    if (beastObjectShape != null) {
                        needsDrawing = needsDrawing(beastObjectShape.m_beastObject);
                    }
                }
                if (needsDrawing) {
                    shape.m_bNeedsDrawing = true;
                }
            }
        } else {
            shape.m_bNeedsDrawing = true;
        }
    }
}

Example 57 with BEASTInterface

use of beast.core.BEASTInterface 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 58 with BEASTInterface

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

the class IntegerListInputEditor method setValue.

@Override
@SuppressWarnings({ "unchecked", "rawtypes" })
protected void setValue(Object o) {
    if (itemNr < 0) {
        m_input.setValue(o, m_beastObject);
    } else {
        // set value of an item in a list
        List list = (List) m_input.get();
        Object other = list.get(itemNr);
        if (other != o) {
            if (other instanceof BEASTInterface) {
                BEASTInterface.getOutputs(other).remove(m_beastObject);
            }
            list.set(itemNr, o);
            if (o instanceof BEASTInterface) {
                BEASTInterface.getOutputs(o).add(m_beastObject);
            }
        }
    }
}

Example 59 with BEASTInterface

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

the class InitMigrationModelConnector method customConnector.

public static boolean customConnector(BeautiDoc doc) {
    for (BEASTInterface p : doc.getPartitions("Tree")) {
        TreeLikelihood treeLikelihood = (TreeLikelihood) p;
        StructuredCoalescentMultiTypeTree tree = (StructuredCoalescentMultiTypeTree) treeLikelihood.treeInput.get();
        String pID = BeautiDoc.parsePartition(tree.getID());
        SCMigrationModel migModel = (SCMigrationModel) doc.pluginmap.get("migModel.t:" + pID);
        SCMigrationModel migModelInit = (SCMigrationModel) doc.pluginmap.get("migModelInit.t:" + pID);
        String rateMatrixStr = getParameterString((RealParameter) migModel.rateMatrixInput.get());
        String popSizesStr = getParameterString((RealParameter) migModel.popSizesInput.get());
        // Ensure model has appropriate number of demes
        int uniqueTraitCount = uniqueTraitsInData(tree).size();
        StringBuilder rateMatrixStrBuilder = new StringBuilder();
        StringBuilder popSizesStrBuilder = new StringBuilder();
        migModel.getTypeSet().initAndValidate();
        if (migModel.popSizesInput.get().getDimension() != migModel.getNTypes()) {
            for (int i = 0; i < migModel.getNTypes(); i++) {
                popSizesStrBuilder.append(" 1.0");
                for (int j = 0; j < migModel.getNTypes(); j++) {
                    if (j == i)
                        continue;
                    rateMatrixStrBuilder.append(" 1.0");
                }
            }
            popSizesStr = popSizesStrBuilder.toString();
            rateMatrixStr = rateMatrixStrBuilder.toString();
            ((RealParameter) migModel.popSizesInput.get()).setDimension(migModel.getNTypes());
            ((RealParameter) migModel.popSizesInput.get()).valuesInput.setValue(popSizesStr, (RealParameter) migModel.popSizesInput.get());
            ((RealParameter) migModel.rateMatrixInput.get()).setDimension(migModel.getNTypes() * (migModel.getNTypes() - 1));
            ((RealParameter) migModel.rateMatrixInput.get()).valuesInput.setValue(rateMatrixStr, (RealParameter) migModel.rateMatrixInput.get());
            ((RealParameter) migModel.popSizesInput.get()).initAndValidate();
            ((RealParameter) migModel.rateMatrixInput.get()).initAndValidate();
            migModel.initAndValidate();
        }
        ((RealParameter) migModelInit.popSizesInput.get()).setDimension(migModel.getNTypes());
        ((RealParameter) migModelInit.popSizesInput.get()).valuesInput.setValue(popSizesStr, (RealParameter) migModelInit.popSizesInput.get());
        ((RealParameter) migModelInit.rateMatrixInput.get()).setDimension(migModel.getNTypes() * (migModel.getNTypes() - 1));
        ((RealParameter) migModelInit.rateMatrixInput.get()).valuesInput.setValue(rateMatrixStr, (RealParameter) migModelInit.rateMatrixInput.get());
        try {
            ((RealParameter) migModelInit.popSizesInput.get()).initAndValidate();
            ((RealParameter) migModelInit.rateMatrixInput.get()).initAndValidate();
            migModelInit.initAndValidate();
        } catch (Exception ex) {
            System.err.println("Error configuring initial migration model.");
        }
    }
    return false;
}

Example 60 with BEASTInterface

use of beast.core.BEASTInterface in project bacter by tgvaughan.

the class CustomConnectors method applyRestrictions.

public static void applyRestrictions(BeautiDoc doc) {
    for (BEASTInterface p : doc.getPartitions("Tree")) {
        ACGLikelihood acgLikelihood = (ACGLikelihood) p;
        SimulatedACG acg = (SimulatedACG) ((ACGLikelihood) p).treeInput.get();
        ACGCoalescent coalescent = null;
        for (BEASTInterface output : acg.getOutputs()) {
            if (output instanceof ACGCoalescent) {
                coalescent = (ACGCoalescent) output;
                break;
            }
        }
        if (coalescent == null)
            continue;
        acg.setWholeLocusMode(coalescent.wholeLocusConversionsInput.get());
    }
}