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

Example 26 with State

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

the class BooleanParameterListTest method test1.

@Test
public void test1() throws Exception {
    BooleanParameterList parameterList = new BooleanParameterList();
    // Parameters with which to initialise list
    BooleanParameter param1 = new BooleanParameter();
    param1.initByName("value", "true false true");
    BooleanParameter param2 = new BooleanParameter();
    param2.initByName("value", "false true false");
    // Initialise parameter list
    parameterList.initByName("dimension", 3, "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(0, false);
    // Test parameter creation and modification
    Parameter<Boolean> newParam = parameterList.addNewParam();
    newParam.setValue(0, true);
    newParam.setValue(1, true);
    newParam.setValue(2, true);
    assertTrue(parameterList.get(0).getValue(0) == false);
    assertTrue(parameterList.get(0).getValue(1) == false);
    assertTrue(parameterList.get(0).getValue(2) == true);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue(0) == false);
    assertTrue(parameterList.get(1).getValue(1) == true);
    assertTrue(parameterList.get(1).getValue(2) == false);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.get(2).getValue(0) == true);
    assertTrue(parameterList.get(2).getValue(1) == true);
    assertTrue(parameterList.get(2).getValue(2) == true);
    assertTrue(parameterList.get(2).getKey() == 2);
    assertTrue(parameterList.size() == 3);
    parameterList.remove(1);
    newParam = parameterList.addNewParam();
    newParam.setValue(0, false);
    newParam.setValue(1, false);
    newParam.setValue(2, false);
    assertTrue(parameterList.get(0).getValue(0) == false);
    assertTrue(parameterList.get(0).getValue(1) == false);
    assertTrue(parameterList.get(0).getValue(2) == true);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue(0) == true);
    assertTrue(parameterList.get(1).getValue(1) == true);
    assertTrue(parameterList.get(1).getValue(2) == true);
    assertTrue(parameterList.get(1).getKey() == 2);
    assertTrue(parameterList.get(2).getValue(0) == false);
    assertTrue(parameterList.get(2).getValue(1) == false);
    assertTrue(parameterList.get(2).getValue(2) == false);
    assertTrue(parameterList.get(2).getKey() == 1);
    assertTrue(parameterList.size() == 3);
    // Test state restore
    parameterList.restore();
    assertTrue(parameterList.get(0).getValue(0) == true);
    assertTrue(parameterList.get(0).getValue(1) == false);
    assertTrue(parameterList.get(0).getValue(2) == true);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue(0) == false);
    assertTrue(parameterList.get(1).getValue(1) == true);
    assertTrue(parameterList.get(1).getValue(2) == false);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.size() == 2);
    // Test serialization
    parameterList.addNewParam(newParam);
    String xmlStr = parameterList.toXML();
    assertEquals(xmlStr, "<statenode id='null'>" + "Dimension: [3, 1], " + "Bounds: [false,true], " + "AvailableKeys: [], " + "NextKey: 3, " + "Parameters: [[true,false,true],[false,true,false],[false,false,false]], " + "ParameterKeys: [0,1,2]" + "</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);
    BooleanParameterList newParameterList = new BooleanParameterList();
    newParameterList.initAndValidate();
    newParameterList.fromXML(docNode);
    assertTrue(newParameterList.get(0).getValue(0) == true);
    assertTrue(newParameterList.get(0).getValue(1) == false);
    assertTrue(newParameterList.get(0).getValue(2) == true);
    assertTrue(newParameterList.get(0).getKey() == 0);
    assertTrue(newParameterList.get(1).getValue(0) == false);
    assertTrue(newParameterList.get(1).getValue(1) == true);
    assertTrue(newParameterList.get(1).getValue(2) == false);
    assertTrue(newParameterList.get(1).getKey() == 1);
    assertTrue(newParameterList.get(2).getValue(0) == false);
    assertTrue(newParameterList.get(2).getValue(1) == false);
    assertTrue(newParameterList.get(2).getValue(2) == false);
    assertTrue(newParameterList.get(2).getKey() == 2);
    assertTrue(newParameterList.size() == 3);
}

Example 27 with State

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

the class UniformIntegerOperatorTest method testParameterBound.

public void testParameterBound() {
    try {
        // 4 vaules {0, 1, 2, 3}
        count = new int[dimension][4];
        RealParameter parameter = new RealParameter(new Double[] { 1.0, 0.0, 2.0 });
        parameter.setLower(0.0);
        parameter.setUpper(3.0);
        State state = new State();
        state.initByName("stateNode", parameter);
        state.initialise();
        UniformOperator uniformOperator = new UniformOperator();
        uniformOperator.initByName("parameter", parameter, "howMany", 3, "weight", 1.0);
        for (int i = 0; i < 400; i++) {
            uniformOperator.proposal();
            Double[] values = parameter.getValues();
            for (int k = 0; k < values.length; k++) {
                int j = (int) (double) values[k];
                count[k][j] += 1;
            }
        }
        System.out.println("Discretized real distributions lower = 0.0, upper = 3.0");
        for (int j = 0; j < count.length; j++) {
            System.out.println("x[" + j + "] = " + Arrays.toString(count[j]));
        }
        assertTrue("Expected count[0][0-2] > 0 && count[0][3] == 0", (count[0][0] > 0) && (count[0][1] > 0) && (count[0][2] > 0) && (count[0][3] == 0));
        assertTrue("Expected count[1][0-2] > 0 && count[1][3] == 0", (count[1][0] > 0) && (count[1][1] > 0) && (count[1][2] > 0) && (count[1][3] == 0));
        assertTrue("Expected count[2][0-2] > 0 && count[2][3] == 0", (count[2][0] > 0) && (count[2][1] > 0) && (count[2][2] > 0) && (count[2][3] == 0));
    } catch (Exception e) {
        e.printStackTrace();
    }
}