Examples with RealParameterList beast.core.parameter.RealParameterList used on opensource projects

Example 1 with RealParameterList

use of beast.core.parameter.RealParameterList in project beast2 by CompEvol.

the class RealParameterListTest method test1.

@Test
public void test1() throws Exception {
    RealParameterList parameterList = new RealParameterList();
    // Parameters with which to initialise list
    RealParameter param1 = new RealParameter();
    param1.initByName("value", "2");
    RealParameter param2 = new RealParameter();
    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(20.0);
    // Test parameter creation and modification
    Parameter<Double> newParam = parameterList.addNewParam();
    newParam.setValue(53.0);
    assertEquals(parameterList.get(0).getValue(), 20.0, 1e-15);
    assertEquals(parameterList.get(0).getKey(), 0);
    assertEquals(parameterList.get(1).getValue(), 3.0, 1e-15);
    assertEquals(parameterList.get(1).getKey(), 1);
    assertEquals(parameterList.get(2).getValue(), 53.0, 1e-15);
    assertEquals(parameterList.get(2).getKey(), 2);
    assertEquals(parameterList.size(), 3);
    parameterList.remove(1);
    newParam = parameterList.addNewParam();
    newParam.setValue(42.0);
    assertEquals(parameterList.get(0).getValue(), 20.0, 1e-15);
    assertEquals(parameterList.get(0).getKey(), 0, 1e-15);
    assertEquals(parameterList.get(1).getValue(), 53.0, 1e-15);
    assertEquals(parameterList.get(1).getKey(), 2, 1e-15);
    assertEquals(parameterList.get(2).getValue(), 42.0, 1e-15);
    assertEquals(parameterList.get(2).getKey(), 1);
    assertEquals(parameterList.size(), 3);
    // Test state restore
    parameterList.restore();
    assertEquals(parameterList.get(0).getValue(), 2.0, 1e-15);
    assertEquals(parameterList.get(0).getKey(), 0);
    assertEquals(parameterList.get(1).getValue(), 3.0, 1e-15);
    assertEquals(parameterList.get(1).getKey(), 1);
    assertEquals(parameterList.size(), 2);
    // Test serialization
    String xmlStr = parameterList.toXML();
    assertEquals(xmlStr, "<statenode id='null'>" + "Dimension: [1, 1], " + "Bounds: [-Infinity,Infinity], " + "AvailableKeys: [], NextKey: 2, " + "Parameters: [[2.0],[3.0]], " + "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);
    RealParameterList newParameterList = new RealParameterList();
    newParameterList.initAndValidate();
    newParameterList.fromXML(docNode);
    assertEquals(newParameterList.get(0).getValue(), 2.0, 1e-15);
    assertEquals(newParameterList.get(0).getKey(), 0);
    assertEquals(newParameterList.get(1).getValue(), 3.0, 1e-15);
    assertEquals(newParameterList.get(1).getKey(), 1);
    assertEquals(newParameterList.size(), 2);
}