Examples with MRCAPrior beast.math.distributions.MRCAPrior used on opensource projects

Example 11 with MRCAPrior

use of beast.math.distributions.MRCAPrior 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 12 with MRCAPrior

use of beast.math.distributions.MRCAPrior 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;
                    }
                }
            }
        }
    }
}

Example 13 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class MRCAPriorInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, final int listItemNr, ExpandOption isExpandOption, boolean addButtons) {
    m_bAddButtons = addButtons;
    m_input = input;
    m_beastObject = beastObject;
    this.itemNr = listItemNr;
    Box itemBox = Box.createHorizontalBox();
    MRCAPrior prior = (MRCAPrior) beastObject;
    String text = prior.getID();
    JButton taxonButton = new JButton(text);
    // taxonButton.setMinimumSize(Base.PREFERRED_SIZE);
    // taxonButton.setPreferredSize(Base.PREFERRED_SIZE);
    itemBox.add(taxonButton);
    taxonButton.addActionListener(e -> {
        List<?> list = (List<?>) m_input.get();
        MRCAPrior prior2 = (MRCAPrior) list.get(itemNr);
        try {
            TaxonSet taxonset = prior2.taxonsetInput.get();
            List<Taxon> originalTaxa = new ArrayList<>();
            originalTaxa.addAll(taxonset.taxonsetInput.get());
            Set<Taxon> candidates = getTaxonCandidates(prior2);
            TaxonSetDialog dlg = new TaxonSetDialog(taxonset, candidates, doc);
            if (dlg.showDialog()) {
                if (dlg.taxonSet.taxonsetInput.get().size() == 0) {
                    JOptionPane.showMessageDialog(doc.beauti, "At least one taxon should be included in the taxon set", "Error specifying taxon set", JOptionPane.ERROR_MESSAGE);
                    taxonset.taxonsetInput.get().addAll(originalTaxa);
                    return;
                }
                prior2.taxonsetInput.setValue(dlg.taxonSet, prior2);
                int i = 1;
                String id = dlg.taxonSet.getID();
                while (doc.pluginmap.containsKey(dlg.taxonSet.getID()) && doc.pluginmap.get(dlg.taxonSet.getID()) != dlg.taxonSet) {
                    dlg.taxonSet.setID(id + i);
                    i++;
                }
                BEASTObjectPanel.addPluginToMap(dlg.taxonSet, doc);
                prior2.setID(dlg.taxonSet.getID() + ".prior");
            }
        } catch (Exception e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
        refreshPanel();
    });
    if (prior.distInput.getType() == null) {
        try {
            prior.distInput.setValue(new OneOnX(), prior);
            prior.distInput.setValue(null, prior);
        } catch (Exception e) {
        // TODO: handle exception
        }
    }
    List<BeautiSubTemplate> availableBEASTObjects = doc.getInputEditorFactory().getAvailableTemplates(prior.distInput, prior, null, doc);
    JComboBox<BeautiSubTemplate> comboBox = new JComboBox<>(availableBEASTObjects.toArray(new BeautiSubTemplate[] {}));
    comboBox.setName(text + ".distr");
    if (prior.distInput.get() != null) {
        String id = prior.distInput.get().getID();
        // id = BeautiDoc.parsePartition(id);
        id = id.substring(0, id.indexOf('.'));
        for (BeautiSubTemplate template : availableBEASTObjects) {
            if (template.classInput.get() != null && template.shortClassName.equals(id)) {
                comboBox.setSelectedItem(template);
            }
        }
    } else {
        comboBox.setSelectedItem(BeautiConfig.NULL_TEMPLATE);
    }
    comboBox.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            @SuppressWarnings("unchecked") JComboBox<BeautiSubTemplate> comboBox = (JComboBox<BeautiSubTemplate>) e.getSource();
            BeautiSubTemplate template = (BeautiSubTemplate) comboBox.getSelectedItem();
            List<?> list = (List<?>) m_input.get();
            MRCAPrior prior = (MRCAPrior) list.get(itemNr);
            // }
            try {
                // BEASTObject beastObject2 =
                template.createSubNet(new PartitionContext(""), prior, prior.distInput, true);
            } catch (Exception e1) {
                e1.printStackTrace();
            }
            refreshPanel();
        }
    });
    itemBox.add(comboBox);
    JCheckBox isMonophyleticdBox = new JCheckBox(doc.beautiConfig.getInputLabel(prior, prior.isMonophyleticInput.getName()));
    isMonophyleticdBox.setName(text + ".isMonophyletic");
    isMonophyleticdBox.setSelected(prior.isMonophyleticInput.get());
    isMonophyleticdBox.setToolTipText(prior.isMonophyleticInput.getHTMLTipText());
    isMonophyleticdBox.addActionListener(new MRCAPriorActionListener(prior));
    itemBox.add(isMonophyleticdBox);
    JButton deleteButton = new SmallButton("-", true);
    deleteButton.setToolTipText("Delete this calibration");
    deleteButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            Log.warning.println("Trying to delete a calibration");
            List<?> list = (List<?>) m_input.get();
            MRCAPrior prior = (MRCAPrior) list.get(itemNr);
            doc.disconnect(prior, "prior", "distribution");
            doc.disconnect(prior, "tracelog", "log");
            if (prior.onlyUseTipsInput.get()) {
                disableTipSampling(m_beastObject, doc);
            }
            doc.unregisterPlugin(prior);
            refreshPanel();
        }
    });
    itemBox.add(Box.createGlue());
    itemBox.add(deleteButton);
    add(itemBox);
}

Example 14 with MRCAPrior

use of beast.math.distributions.MRCAPrior 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 15 with MRCAPrior

use of beast.math.distributions.MRCAPrior in project beast2 by CompEvol.

the class MRCAPriorInputEditor method enableTipSampling.

// add TipDatesRandomWalker (if not present) and add to list of operators
private void enableTipSampling() {
    // First, create/find the operator
    TipDatesRandomWalker operator = null;
    MRCAPrior prior = (MRCAPrior) m_beastObject;
    TaxonSet taxonset = prior.taxonsetInput.get();
    taxonset.initAndValidate();
    // see if an old operator still hangs around -- happens when toggling the TipsOnly checkbox a few times
    for (BEASTInterface o : taxonset.getOutputs()) {
        if (o instanceof TipDatesRandomWalker) {
            operator = (TipDatesRandomWalker) o;
        }
    }
    if (operator == null) {
        operator = new TipDatesRandomWalker();
        operator.initByName("tree", prior.treeInput.get(), "taxonset", taxonset, "windowSize", 1.0, "weight", 1.0);
    }
    operator.setID("tipDatesSampler." + taxonset.getID());
    doc.mcmc.get().setInputValue("operator", operator);
}