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

Example 1 with StateNodeInitialiser

use of beast.core.StateNodeInitialiser 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 2 with StateNodeInitialiser

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

the class MultiTypeTree method initAndValidate.

@Override
public void initAndValidate() {
    if (m_initial.get() != null && !(this instanceof StateNodeInitialiser)) {
        if (!(m_initial.get() instanceof MultiTypeTree)) {
            throw new IllegalArgumentException("Attempted to initialise " + "multi-type tree with regular tree object.");
        }
        MultiTypeTree other = (MultiTypeTree) m_initial.get();
        root = other.root.copy();
        nodeCount = other.nodeCount;
        internalNodeCount = other.internalNodeCount;
        leafNodeCount = other.leafNodeCount;
    }
    if (nodeCount < 0) {
        if (m_taxonset.get() != null) {
            // make a caterpillar
            List<String> sTaxa = m_taxonset.get().asStringList();
            Node left = new MultiTypeNode();
            left.labelNr = 0;
            left.height = 0;
            left.setID(sTaxa.get(0));
            for (int i = 1; i < sTaxa.size(); i++) {
                Node right = new MultiTypeNode();
                right.labelNr = i;
                right.height = 0;
                right.setID(sTaxa.get(i));
                Node parent = new MultiTypeNode();
                parent.labelNr = sTaxa.size() + i - 1;
                parent.height = i;
                left.parent = parent;
                parent.setLeft(left);
                right.parent = parent;
                parent.setRight(right);
                left = parent;
            }
            root = left;
            leafNodeCount = sTaxa.size();
            nodeCount = leafNodeCount * 2 - 1;
            internalNodeCount = leafNodeCount - 1;
        } else {
            // make dummy tree with a single root node
            root = new MultiTypeNode();
            root.labelNr = 0;
            root.labelNr = 0;
            root.m_tree = this;
            nodeCount = 1;
            internalNodeCount = 0;
            leafNodeCount = 1;
        }
    }
    if (nodeCount >= 0) {
        initArrays();
    }
    typeLabel = typeLabelInput.get();
    typeSet = typeSetInput.get();
    processTraits(m_traitList.get());
    // Ensure tree is compatible with traits.
    if (hasDateTrait())
        adjustTreeNodeHeights(root);
}

Example 3 with StateNodeInitialiser

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

the class StateNodeInitialiserListInputEditor method customConnector.

public static boolean customConnector(BeautiDoc doc) {
    // scrub Tree initialisers
    // 0. collect state node info
    List<StateNodeInitialiser> inits = ((MCMC) doc.mcmc.get()).initialisersInput.get();
    State state = ((MCMC) doc.mcmc.get()).startStateInput.get();
    List<StateNode> stateNodes = state.stateNodeInput.get();
    List<Tree> trees = new ArrayList<>();
    for (StateNode s : stateNodes) {
        if (s instanceof Tree) {
            trees.add((Tree) s);
        }
    }
    List<List<StateNode>> initStateNodes = new ArrayList<>();
    for (StateNodeInitialiser init : inits) {
        List<StateNode> initStateNodes0 = new ArrayList<>();
        init.getInitialisedStateNodes(initStateNodes0);
        for (int i = initStateNodes0.size() - 1; i >= 0; i--) {
            if (!(initStateNodes0.get(i) instanceof Tree)) {
                initStateNodes0.remove(i);
            }
        }
        initStateNodes.add(initStateNodes0);
    }
    // 1. remove initialisers that have no stateNode in state
    for (int i = inits.size() - 1; i >= 0; i--) {
        boolean found = false;
        for (StateNode stateNode : initStateNodes.get(i)) {
            if (trees.contains(stateNode)) {
                found = true;
                break;
            }
        }
        if (!found) {
            inits.remove(i);
            initStateNodes.remove(i);
        }
    }
    // 2. remove initialisers that share stateNodes
    for (int i = inits.size() - 1; i >= 0; i--) {
        for (int j = i - 1; j >= 0; j--) {
            boolean found = false;
            for (StateNode stateNode : initStateNodes.get(i)) {
                if (initStateNodes.get(j).contains(stateNode)) {
                    found = true;
                    break;
                }
            }
            if (found) {
                inits.remove(i);
                initStateNodes.remove(i);
            }
        }
    }
    // 3. add RandomTree for those trees not having a stateNodeInitialiser
    boolean[] hasInitialiser = new boolean[trees.size()];
    for (int i = inits.size() - 1; i >= 0; i--) {
        for (StateNode stateNode : initStateNodes.get(i)) {
            int k = trees.indexOf(stateNode);
            if (k >= 0) {
                hasInitialiser[k] = true;
                break;
            }
        }
    }
    for (int i = 0; i < hasInitialiser.length; i++) {
        if (!hasInitialiser[i]) {
            for (BeautiSubTemplate tmp : doc.beautiConfig.subTemplates) {
                if (tmp.getID().equals("RandomTree")) {
                    PartitionContext partition = doc.getContextFor(trees.get(i));
                    Object o = tmp.createSubNet(partition, false);
                    inits.add((StateNodeInitialiser) o);
                }
            }
        }
    }
    return true;
}