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

Example 46 with BEASTInterface

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

the class OperatorListInputEditor method getLabel.

String getLabel(Operator operator) {
    String name = operator.getClass().getName();
    name = name.substring(name.lastIndexOf('.') + 1);
    name = name.replaceAll("Operator", "");
    if (name.matches(".*[A-Z].*")) {
        name = name.replaceAll("(.)([A-Z])", "$1 $2");
    }
    name += ": ";
    try {
        for (BEASTInterface beastObject2 : operator.listActiveBEASTObjects()) {
            if (beastObject2 instanceof StateNode && ((StateNode) beastObject2).isEstimatedInput.get()) {
                name += beastObject2.getID() + " ";
            }
            // issue https://github.com/CompEvol/beast2/issues/661
            if (name.length() > 100) {
                name += "... ";
                break;
            }
        }
    } catch (Exception e) {
    // ignore
    }
    String tipText = getDoc().tipTextMap.get(operator.getID());
    if (tipText != null) {
        name += " " + tipText;
    }
    return name;
}

Example 47 with BEASTInterface

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

the class PriorListInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption, boolean addButtons) {
    List<?> list = (List<?>) input.get();
    Collections.sort(list, (Object o1, Object o2) -> {
        if (o1 instanceof BEASTInterface && o2 instanceof BEASTInterface) {
            String d1 = ((BEASTInterface) o1).getID();
            String id2 = ((BEASTInterface) o2).getID();
            // first the tree priors
            if (o1 instanceof TreeDistribution) {
                if (o2 instanceof TreeDistribution) {
                    TreeInterface tree1 = ((TreeDistribution) o1).treeInput.get();
                    if (tree1 == null) {
                        tree1 = ((TreeDistribution) o1).treeIntervalsInput.get().treeInput.get();
                    }
                    TreeInterface tree2 = ((TreeDistribution) o2).treeInput.get();
                    if (tree2 == null) {
                        tree2 = ((TreeDistribution) o2).treeIntervalsInput.get().treeInput.get();
                    }
                    return d1.compareTo(id2);
                } else {
                    return -1;
                }
            } else if (o1 instanceof MRCAPrior) {
                // last MRCA priors
                if (o2 instanceof MRCAPrior) {
                    return d1.compareTo(id2);
                } else {
                    return 1;
                }
            } else {
                if (o2 instanceof TreeDistribution) {
                    return 1;
                }
                if (o2 instanceof MRCAPrior) {
                    return -1;
                }
                if (o1 instanceof Prior) {
                    d1 = ((Prior) o1).getParameterName();
                }
                if (o2 instanceof Prior) {
                    id2 = ((Prior) o2).getParameterName();
                }
                return d1.compareTo(id2);
            }
        }
        return 0;
    });
    rangeButtons = new ArrayList<>();
    taxonButtons = new ArrayList<>();
    // m_buttonStatus = ButtonStatus.NONE;
    super.init(input, beastObject, itemNr, isExpandOption, addButtons);
    if (beastObject instanceof BeautiPanelConfig) {
        BeautiPanelConfig config = (BeautiPanelConfig) beastObject;
        if (config.parentBEASTObjects != null && config.parentBEASTObjects.size() > 0 && config.parentBEASTObjects.get(0).getID().equals("speciescoalescent")) {
            m_buttonStatus = ButtonStatus.NONE;
        }
    }
    if (m_buttonStatus == ButtonStatus.ALL || m_buttonStatus == ButtonStatus.ADD_ONLY) {
        addButton = new SmallButton("+ Add Prior", true);
        addButton.setName("addItem");
        addButton.setToolTipText("Add new prior (like an MRCA-prior) to the list of priors");
        addButton.addActionListener(e -> {
            addItem();
        });
        buttonBox.add(addButton);
        buttonBox.add(Box.createHorizontalGlue());
    }
}

Example 48 with BEASTInterface

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

the class StateNodeInitialiserListInputEditor method addPluginItem.

@Override
protected InputEditor addPluginItem(Box itemBox, BEASTInterface beastObject) {
    final StateNodeInitialiser currentInitialiser = (StateNodeInitialiser) beastObject;
    Input initialInput = beastObject.getInput("initial");
    List<BeautiSubTemplate> sAvailablePlugins = doc.getInputEditorFactory().getAvailableTemplates(initialInput, (BEASTInterface) beastObject, null, doc);
    JComboBox<?> comboBox = null;
    if (sAvailablePlugins.size() > 0) {
        sAvailablePlugins.remove(sAvailablePlugins.size() - 1);
        comboBox = new JComboBox<>(sAvailablePlugins.toArray());
        String sID = beastObject.getID();
        try {
            sID = sID.substring(0, sID.indexOf('.'));
        } catch (Exception e) {
            throw new RuntimeException("Improperly formatted ID: " + sID);
        }
        for (BeautiSubTemplate template : sAvailablePlugins) {
            if (template.matchesName(sID)) {
                comboBox.setSelectedItem(template);
            }
        }
        comboBox.setName("Initialiser");
        comboBox.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent e) {
                SwingUtilities.invokeLater(new Runnable() {

                    @Override
                    public void run() {
                        JComboBox<?> currentComboBox = (JComboBox<?>) e.getSource();
                        BeautiSubTemplate template = (BeautiSubTemplate) currentComboBox.getSelectedItem();
                        PartitionContext partitionContext;
                        partitionContext = doc.getContextFor(beastObject);
                        try {
                            Object o = template.createSubNet(partitionContext, true);
                            StateNodeInitialiser newInitialiser = (StateNodeInitialiser) o;
                            List<StateNodeInitialiser> inits = (List<StateNodeInitialiser>) m_input.get();
                            int i = inits.indexOf(currentInitialiser);
                            inits.set(i, newInitialiser);
                            System.out.println(inits.size());
                        } catch (Exception ex) {
                            ex.printStackTrace();
                        }
                        sync();
                        refreshPanel();
                    }
                });
            }
        });
    }
    String name = beastObject.getID();
    Object o = beastObject.getInput("initial").get();
    if (o instanceof BEASTInterface) {
        name = ((BEASTInterface) o).getID();
    }
    if (name == null || name.length() == 0) {
        name = beastObject.getClass().getName();
        name = name.substring(name.lastIndexOf('.') + 1);
    }
    JLabel label = new JLabel("Initial " + name + ":");
    itemBox.add(Box.createRigidArea(new Dimension(5, 1)));
    itemBox.add(label);
    if (comboBox != null) {
        itemBox.add(comboBox);
    }
    itemBox.add(Box.createHorizontalGlue());
    return this;
}

Example 49 with BEASTInterface

use of beast.core.BEASTInterface 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 50 with BEASTInterface

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

the class MRCAPriorInputEditor method customConnector.

public static void customConnector(BeautiDoc doc) {
    Object o0 = doc.pluginmap.get("prior");
    if (o0 != null && o0 instanceof CompoundDistribution) {
        CompoundDistribution p = (CompoundDistribution) o0;
        for (Distribution p0 : p.pDistributions.get()) {
            if (p0 instanceof MRCAPrior) {
                MRCAPrior prior = (MRCAPrior) p0;
                if (prior.treeInput.get() != null) {
                    boolean isInState = false;
                    for (BEASTInterface o : prior.treeInput.get().getOutputs()) {
                        if (o instanceof State) {
                            isInState = true;
                            break;
                        }
                    }
                    if (!isInState) {
                        doc.disconnect(prior, "prior", "distribution");
                        doc.disconnect(prior, "tracelog", "log");
                        if (prior.onlyUseTipsInput.get()) {
                            disableTipSampling(prior, doc);
                        }
                        doc.unregisterPlugin(prior);
                        return;
                    }
                }
            }
        }
    }
}