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

Example 6 with StateNode

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

the class CompoundValuable method recompute.

/**
 * collect values of the compounds into an array *
 */
private void recompute() {
    int k = 0;
    for (BEASTObject beastObject : m_values.get()) {
        Function valuable = (Function) beastObject;
        if (beastObject instanceof StateNode) {
            valuable = ((StateNode) beastObject).getCurrent();
        }
        int dimension = valuable.getDimension();
        for (int i = 0; i < dimension; i++) {
            m_fValues[k++] = valuable.getArrayValue(i);
        }
    }
    m_bRecompute = false;
}

Example 7 with StateNode

use of beast.core.StateNode 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 8 with StateNode

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

the class BeautiBase method stateAsString.

String stateAsString() {
    State state = (State) doc.pluginmap.get("state");
    List<StateNode> stateNodes = state.stateNodeInput.get();
    return "assertStateEquals" + pluginListAsString(stateNodes);
}

Example 9 with StateNode

use of beast.core.StateNode 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;
}

Example 10 with StateNode

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

the class UpDownOperator method proposal.

/**
 * override this for proposals,
 *
 * @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal
 *         should not be accepted
 */
@Override
public final double proposal() {
    final double scale = (scaleFactor + (Randomizer.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
    int goingUp = 0, goingDown = 0;
    if (elementWiseInput.get()) {
        int size = 0;
        for (StateNode up : upInput.get()) {
            if (size == 0)
                size = up.getDimension();
            if (size > 0 && up.getDimension() != size) {
                throw new RuntimeException("elementWise=true but parameters of differing lengths!");
            }
            goingUp += 1;
        }
        for (StateNode down : downInput.get()) {
            if (size == 0)
                size = down.getDimension();
            if (size > 0 && down.getDimension() != size) {
                throw new RuntimeException("elementWise=true but parameters of differing lengths!");
            }
            goingDown += 1;
        }
        int index = Randomizer.nextInt(size);
        for (StateNode up : upInput.get()) {
            if (up instanceof RealParameter) {
                RealParameter p = (RealParameter) up;
                p.setValue(p.getValue(index) * scale);
            }
            if (outsideBounds(up)) {
                return Double.NEGATIVE_INFINITY;
            }
        }
        for (StateNode down : downInput.get()) {
            if (down instanceof RealParameter) {
                RealParameter p = (RealParameter) down;
                p.setValue(p.getValue(index) / scale);
            }
            if (outsideBounds(down)) {
                return Double.NEGATIVE_INFINITY;
            }
        }
    } else {
        try {
            for (StateNode up : upInput.get()) {
                up = up.getCurrentEditable(this);
                goingUp += up.scale(scale);
            }
            // Same below for down
            for (StateNode up : upInput.get()) {
                if (outsideBounds(up)) {
                    return Double.NEGATIVE_INFINITY;
                }
            }
            for (StateNode down : downInput.get()) {
                down = down.getCurrentEditable(this);
                goingDown += down.scale(1.0 / scale);
            }
            for (StateNode down : downInput.get()) {
                if (outsideBounds(down)) {
                    return Double.NEGATIVE_INFINITY;
                }
            }
        } catch (Exception e) {
            // scale resulted in invalid StateNode, abort proposal
            return Double.NEGATIVE_INFINITY;
        }
    }
    return (goingUp - goingDown - 2) * Math.log(scale);
}