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

Example 6 with BEASTObject

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

the class BeautiDoc method determineLinks.

// methods for dealing with linking
void determineLinks() {
    if (!allowLinking) {
        return;
    }
    linked.clear();
    for (BEASTInterface beastObject : posteriorPredecessors) {
        Map<String, Integer> outputIDs = new HashMap<>();
        for (Object output : beastObject.getOutputs()) {
            if (posteriorPredecessors.contains(output)) {
                String id = ((BEASTInterface) output).getID();
                if (id.indexOf('.') >= 0) {
                    id = id.substring(0, id.indexOf('.'));
                    if (outputIDs.containsKey(id)) {
                        outputIDs.put(id, outputIDs.get(id) + 1);
                    } else {
                        outputIDs.put(id, 1);
                    }
                }
            }
        }
        for (Object output : beastObject.getOutputs()) {
            if (posteriorPredecessors.contains(output)) {
                String id = ((BEASTInterface) output).getID();
                if (id.indexOf('.') >= 0) {
                    id = id.substring(0, id.indexOf('.'));
                    if (outputIDs.get(id) > 1) {
                        addLink(beastObject, (BEASTInterface) output);
                    }
                }
            }
        }
        // add parameters that have more than 1 outputs into susbtitution models
        if (beastObject instanceof Parameter<?>) {
            for (Object output : beastObject.getOutputs()) {
                if (posteriorPredecessors.contains(output)) {
                    if (output instanceof SubstitutionModel) {
                        int nrOfSubstModelsInOutput = 0;
                        try {
                            for (Input<?> input : ((BEASTInterface) output).listInputs()) {
                                if (input.get() != null && input.get().equals(beastObject)) {
                                    nrOfSubstModelsInOutput++;
                                }
                            }
                        } catch (Exception e) {
                        // ignore
                        }
                        if (nrOfSubstModelsInOutput > 1) {
                            addLink(beastObject, (BEASTInterface) output);
                        }
                    }
                }
            }
        }
    }
    hasLinkedAtLeastOnce = false;
    for (Input<?> input : linked) {
        if (input.getType().isAssignableFrom(RealParameter.class)) {
            hasLinkedAtLeastOnce = true;
            break;
        }
    }
}

Example 7 with BEASTObject

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

the class BeautiBase method traceLogAsString.

String traceLogAsString() {
    Logger logger = (Logger) doc.pluginmap.get("tracelog");
    List<BEASTObject> logs = logger.loggersInput.get();
    return "assertTraceLogEqual" + pluginListAsString(logs);
}

Example 8 with BEASTObject

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

the class DocMaker method getType.

// getHTML
/**
 * determine type of input of a plug in with name name
 */
String getType(BEASTObject beastObject, String name) {
    try {
        Field[] fields = beastObject.getClass().getFields();
        for (int i = 0; i < fields.length; i++) {
            if (fields[i].getType().isAssignableFrom(Input.class)) {
                final Input<?> input = (Input<?>) fields[i].get(beastObject);
                if (input.getName().equals(name)) {
                    Type t = fields[i].getGenericType();
                    Type[] genericTypes = ((ParameterizedType) t).getActualTypeArguments();
                    if (input.getType() != null) {
                        return (input.getType().isAssignableFrom(BEASTObject.class) ? "<a href='" + input.getType().getName() + ".html'>" : "") + input.getType().getName() + (input.get() != null && input.get() instanceof List<?> ? "***" : "") + (input.getType().isAssignableFrom(BEASTObject.class) ? "</a>" : "");
                    }
                    if (input.get() != null && input.get() instanceof List<?>) {
                        Type[] genericTypes2 = ((ParameterizedType) genericTypes[0]).getActualTypeArguments();
                        Class<?> _class = (Class<?>) genericTypes2[0];
                        Object o = null;
                        try {
                            o = Class.forName(_class.getName()).newInstance();
                        } catch (Exception e) {
                        }
                        if (o != null && o instanceof BEASTObject) {
                            return "<a href='" + _class.getName() + ".html'>" + _class.getName() + "***</a>";
                        } else {
                            return _class.getName() + "***";
                        }
                    } else {
                        Class<?> genericType = (Class<?>) genericTypes[0];
                        Class<?> _class = genericType;
                        Object o = null;
                        try {
                            o = Class.forName(_class.getName()).newInstance();
                        } catch (Exception e) {
                        }
                        if (o != null && o instanceof BEASTObject) {
                            return "<a href='" + _class.getName() + ".html'>" + _class.getName() + "</a>";
                        } else {
                            return _class.getName();
                        }
                    }
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
    return "?";
}

Example 9 with BEASTObject

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

the class CompoundValuable method initAndValidate.

@Override
public void initAndValidate() {
    // determine dimension
    int dimension = 0;
    for (BEASTObject beastObject : m_values.get()) {
        if (!(beastObject instanceof Function)) {
            throw new IllegalArgumentException("Input does not implement Valuable");
        }
        dimension += ((Function) beastObject).getDimension();
    }
    m_fValues = new double[dimension];
}

Example 10 with BEASTObject

use of beast.core.BEASTObject 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;
}