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

Example 21 with State

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

the class IntegerParameterListTest method test1.

@Test
public void test1() throws Exception {
    IntegerParameterList parameterList = new IntegerParameterList();
    // Parameters with which to initialise list
    IntegerParameter param1 = new IntegerParameter();
    param1.initByName("value", "2");
    IntegerParameter param2 = new IntegerParameter();
    param2.initByName("value", "3");
    // Initialise parameter list
    parameterList.initByName("initialParam", param1, "initialParam", param2);
    // Create dummy state to allow statenode editing
    State state = new State();
    state.initByName("stateNode", parameterList);
    state.initialise();
    // Test parameter value modification
    parameterList.get(0).setValue(20);
    // Test parameter creation and modification
    Parameter<Integer> newParam = parameterList.addNewParam();
    newParam.setValue(53);
    assertTrue(parameterList.get(0).getValue() == 20);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue() == 3);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.get(2).getValue() == 53);
    assertTrue(parameterList.get(2).getKey() == 2);
    assertTrue(parameterList.size() == 3);
    parameterList.remove(1);
    newParam = parameterList.addNewParam();
    newParam.setValue(42);
    assertTrue(parameterList.get(0).getValue() == 20);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue() == 53);
    assertTrue(parameterList.get(1).getKey() == 2);
    assertTrue(parameterList.get(2).getValue() == 42);
    assertTrue(parameterList.get(2).getKey() == 1);
    assertTrue(parameterList.size() == 3);
    // Test state restore
    parameterList.restore();
    assertTrue(parameterList.get(0).getValue() == 2);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue() == 3);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.size() == 2);
    // Test serialization
    String xmlStr = parameterList.toXML();
    assertEquals(xmlStr, "<statenode id='null'>" + "Dimension: [1, 1], " + "Bounds: [-2147483647,2147483646], " + "AvailableKeys: [], " + "NextKey: 2, " + "Parameters: [[2],[3]], " + "ParameterKeys: [0,1]" + "</statenode>\n");
    // Test deserialization
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    Document doc = factory.newDocumentBuilder().parse(new ByteArrayInputStream(xmlStr.getBytes()));
    doc.normalize();
    NodeList nodes = doc.getElementsByTagName("*");
    org.w3c.dom.Node docNode = nodes.item(0);
    IntegerParameterList newParameterList = new IntegerParameterList();
    newParameterList.initAndValidate();
    newParameterList.fromXML(docNode);
    assertTrue(newParameterList.get(0).getValue() == 2);
    assertTrue(newParameterList.get(0).getKey() == 0);
    assertTrue(newParameterList.get(1).getValue() == 3);
    assertTrue(newParameterList.get(1).getKey() == 1);
    assertTrue(newParameterList.size() == 2);
}

Example 22 with State

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

the class JSONParser method createBeastObject.

/**
 * create BEASTInterface either using Inputs, or using annotated constructor *
 */
private BEASTInterface createBeastObject(JSONObject node, String ID, String clazzName, List<NameValuePair> inputInfo) throws JSONParserException {
    BEASTInterface beastObject = useAnnotatedConstructor(node, ID, clazzName, inputInfo);
    if (beastObject != null) {
        return beastObject;
    }
    // create new instance using class name
    Object o = null;
    try {
        Class<?> c = Class.forName(clazzName);
        o = c.newInstance();
    } catch (InstantiationException e) {
        // created for instance because it is abstract
        throw new JSONParserException(node, "Cannot instantiate class. Please check the spec attribute.", 1006);
    } catch (ClassNotFoundException e) {
    // ignore -- class was found in beastObjectNames before
    } catch (IllegalAccessException e) {
        // T O D O Auto-generated catch block
        e.printStackTrace();
        throw new JSONParserException(node, "Cannot access class. Please check the spec attribute.", 1011);
    }
    // set id
    beastObject = (BEASTInterface) o;
    beastObject.setID(ID);
    // hack required to make log-parsing easier
    if (o instanceof State) {
        state = (State) o;
    }
    // process inputs for annotated constructors
    for (NameValuePair pair : inputInfo) {
        setInput(node, beastObject, pair.name, pair.value);
    }
    // fill in missing inputs, if an input provider is available
    try {
        if (requiredInputProvider != null) {
            for (Input<?> input : beastObject.listInputs()) {
                if (input.get() == null && input.getRule() == Validate.REQUIRED) {
                    Object o2 = requiredInputProvider.createInput(beastObject, input, partitionContext);
                    if (o2 != null) {
                        input.setValue(o2, beastObject);
                    }
                }
            }
        }
    } catch (Exception e) {
        throw new JSONParserException(node, e.getMessage(), 1008);
    }
    // sanity check: all attributes should be valid input names
    if (!(beastObject instanceof Map)) {
        for (String name : node.keySet()) {
            if (!(name.equals("id") || name.equals("idref") || name.equals("spec") || name.equals("name"))) {
                try {
                    beastObject.getInput(name);
                } catch (Exception e) {
                    throw new JSONParserException(node, e.getMessage(), 1009);
                }
            }
        }
    }
    // make sure object o is in outputs of inputs
    for (NameValuePair pair : inputInfo) {
        if (pair.value instanceof BEASTInterface) {
            ((BEASTInterface) pair.value).getOutputs().add((BEASTInterface) o);
        }
    }
    register(node, beastObject);
    return beastObject;
}

Example 23 with State

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

the class DeltaExchangeOperatorTest method testCanOperate.

@Test
public void testCanOperate() {
    // Test whether a validly initialised operator may make proposals
    State state = new State();
    RealParameter parameter = new RealParameter(new Double[] { 1., 1., 1., 1. });
    state.initByName("stateNode", parameter);
    state.initialise();
    DeltaExchangeOperator d = new DeltaExchangeOperator();
    // proposals
    try {
        d.initByName("parameter", parameter);
    } catch (RuntimeException e) {
        return;
    }
    d.proposal();
}

Example 24 with State

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

the class IntRandomWalkOperatorTest method instantiate.

public void instantiate(int dimension, int upper, int runs, Integer[] windowSizes) {
    for (int r = 0; r < runs; r++) {
        for (Integer windowSize : windowSizes) {
            try {
                int[][] count = new int[dimension][upper + 1];
                Integer[] init = new Integer[dimension];
                Arrays.fill(init, 0);
                IntegerParameter parameter = new IntegerParameter(init);
                parameter.setLower(0);
                parameter.setUpper(upper);
                State state = new State();
                state.initByName("stateNode", parameter);
                state.initialise();
                IntRandomWalkOperator operator = new IntRandomWalkOperator();
                operator.initByName("parameter", parameter, "windowSize", windowSize, "weight", 1.0);
                for (int i = 0; i < 1000000 * (upper + 1); i++) {
                    operator.proposal();
                    Integer[] values = parameter.getValues();
                    for (int k = 0; k < values.length; k++) {
                        int j = values[k];
                        count[k][j] += 1;
                    }
                }
                System.out.print("Distribution lower = 0, upper = " + upper + " windowSize = " + windowSize);
                for (int j = 0; j < count.length; j++) {
                // System.out.println("x[" +j + "] = " + Arrays.toString(count[j]));
                }
                int sum = 0;
                for (int i = 0; i < dimension; i++) {
                    for (int k = 0; k < count[i].length; k++) {
                        sum += Math.abs(count[i][k] - 1000000);
                    }
                }
                System.out.println(" Average deviation: " + sum / (dimension * (upper + 1)));
                assertTrue("average deviation (" + sum / (dimension * (upper + 1)) + ") exceeds 10000", sum / (dimension * (upper + 1)) < 10000);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 25 with State

use of beast.core.State 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;
}