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

Example 21 with BEASTObject

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

the class InputTypeTest method testInputTypeCanBeSet.

/*
	 * Test that the type of an input can be determined, If not, the programmer
	 * has to manually initialise the type of the input (most easily done
	 * through a constructor of Input)
	 */
@Test
public void testInputTypeCanBeSet() throws Exception {
    List<String> beastObjectNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR);
    List<String> failingInputs = new ArrayList<String>();
    for (String beastObjectName : beastObjectNames) {
        try {
            BEASTObject beastObject = (BEASTObject) Class.forName(beastObjectName).newInstance();
            List<Input<?>> inputs = beastObject.listInputs();
            for (Input<?> input : inputs) {
                if (input.getType() == null) {
                    try {
                        input.determineClass(beastObject);
                        if (input.getType() == null) {
                            failingInputs.add(beastObject + ":" + input.getName());
                        }
                    } catch (Exception e2) {
                        failingInputs.add(beastObject + ":" + input.getName());
                    }
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
    assertTrue("Type of input could not be set for these inputs (probably requires to be set by using the appropriate constructure of Input): " + failingInputs.toString(), failingInputs.size() == 0);
}

Example 22 with BEASTObject

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

the class XMLElementNameTest method test_ReservedElementNames.

/**
 * test that Inputs that use reserved names have the correct type *
 */
@Test
public void test_ReservedElementNames() {
    // retrieve list of reserved names and their classes
    XMLParser parser = new XMLParser();
    HashMap<String, String> element2ClassMap = parser.getElement2ClassMap();
    // allow 'parameter' for any of the various parameter derivatives, not just RealParameter
    element2ClassMap.put("parameter", "beast.core.parameter.Parameter");
    // check each beastObject
    List<String> pluginNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR);
    List<String> improperInputs = new ArrayList<String>();
    for (String beastObjectName : pluginNames) {
        try {
            BEASTObject beastObject = (BEASTObject) Class.forName(beastObjectName).newInstance();
            // check each input
            List<Input<?>> inputs = beastObject.listInputs();
            for (Input<?> input : inputs) {
                if (element2ClassMap.containsKey(input.getName())) {
                    if (beastObject.getClass() == null) {
                        input.determineClass(beastObject);
                    }
                    Class<?> type = input.getType();
                    String baseType = element2ClassMap.get(input.getName());
                    if (!isDerivedType(type, baseType)) {
                        improperInputs.add(beastObjectName + "." + input.getName());
                    }
                }
            }
        } catch (InstantiationException e) {
        // ignore
        } catch (Exception e) {
        // ignore
        }
    }
    if (improperInputs.size() > 0) {
        String str = improperInputs.toString();
        str = str.replaceAll(",", "\n");
        System.err.println("Reserved element names used for wrong types in:\n" + str);
    }
    // not activated till problem with naming is solved
    assertTrue("Reserved element names used for wrong types in: " + improperInputs.toString(), improperInputs.size() == 0);
}

Example 23 with BEASTObject

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

the class JSONTest method testJSONtoXMLtoJSON.

@Test
public void testJSONtoXMLtoJSON() throws Exception {
    JSONParser parser = new JSONParser();
    BEASTObject beastObject = parser.parseFile(new File(JSON_FILE));
    JSONProducer producer = new JSONProducer();
    // .replaceAll("\\s+", " ");
    String actual = producer.toJSON(beastObject).trim();
    // .replaceAll("\\s+", " ");
    String expected = BeautiDoc.load(JSON_FILE).trim();
    assertEquals("Produced JSON differs from original", expected, actual);
}