/**
* Unmarshall a Genotype instance from a given XML Element representation. Its population of
* Chromosomes will be unmarshalled from the Chromosome sub-elements.
*
* @param a_activeConfiguration the current active Configuration object that is to be used during
* construction of the Genotype and Chromosome instances
* @param a_xmlElement the XML Element representation of the Genotype
* @return a new Genotype instance, complete with a population of Chromosomes, setup with the data
* from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws InvalidConfigurationException if the given Configuration is in an inconsistent state
* @throws UnsupportedRepresentationException if the actively configured Gene implementation does
* not support the string representation of the alleles used in the given XML document
* @throws GeneCreationException if there is a problem creating or populating a Gene instance
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public static Genotype getGenotypeFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, InvalidConfigurationException,
UnsupportedRepresentationException, GeneCreationException {
// Sanity check. Make sure the XML element isn't null and that it
// actually represents a genotype.
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENOTYPE_TAG))) {
throw new ImproperXMLException(
"Unable to build Genotype instance from XML Element: "
+ "given Element is not a 'genotype' element.");
}
// Fetch all of the nested chromosome elements and convert them
// into Chromosome instances.
// ------------------------------------------------------------
NodeList chromosomes = a_xmlElement.getElementsByTagName(CHROMOSOME_TAG);
int numChromosomes = chromosomes.getLength();
Population population = new Population(a_activeConfiguration, numChromosomes);
for (int i = 0; i < numChromosomes; i++) {
population.addChromosome(
getChromosomeFromElement(a_activeConfiguration, (Element) chromosomes.item(i)));
}
// Construct a new Genotype with the chromosomes and return it.
// ------------------------------------------------------------
return new Genotype(a_activeConfiguration, population);
}
/**
* Searches the children of an element looking for a Text node. If it finds one, it returns it.
*
* @param element The element whose children will be searched
* @return The text for the element, or null if there is none
*/
public static String getElementString(Element element) {
NodeList nodes = element.getChildNodes();
int numNodes = nodes.getLength();
for (int i = 0; i < numNodes; i++) {
Node node = nodes.item(i);
if (node instanceof Text) {
return ((Text) node).getData();
}
}
return null;
}
/**
* Reads the children of an XML element and matches them to properties of a bean.
*
* @param ob The bean to receive the values
* @param element The element the corresponds to the bean
* @throws IOException If there is an error reading the document
*/
public void readObject(Object ob, Element element) throws IOException {
// If the object is null, skip the element
if (ob == null) {
return;
}
try {
BeanInfo info = (BeanInfo) beanCache.get(ob.getClass());
if (info == null) {
// Get the bean info for the object
info = Introspector.getBeanInfo(ob.getClass(), Object.class);
beanCache.put(ob.getClass(), info);
}
// Get the object's properties
PropertyDescriptor[] props = info.getPropertyDescriptors();
// Get the attributes of the node
NamedNodeMap attrs = element.getAttributes();
// Get the children of the XML element
NodeList nodes = element.getChildNodes();
int numNodes = nodes.getLength();
for (int i = 0; i < props.length; i++) {
// Treat indexed properties a little differently
if (props[i] instanceof IndexedPropertyDescriptor) {
readIndexedProperty(ob, (IndexedPropertyDescriptor) props[i], nodes, attrs);
} else {
readProperty(ob, props[i], nodes, attrs);
}
}
} catch (IntrospectionException exc) {
throw new IOException(
"Error getting bean info for " + ob.getClass().getName() + ": " + exc.toString());
}
}
public Command executeStep(Element stepRow) throws Exception {
Command command = new Command();
NodeList stepFields = stepRow.getElementsByTagName("td");
String cmd = stepFields.item(0).getTextContent().trim();
command.cmd = cmd;
ArrayList<String> argList = new ArrayList<String>();
if (stepFields.getLength() == 1) {
// skip comments
command.result = "OK";
return command;
}
for (int i = 1; i < stepFields.getLength(); i++) {
String content = stepFields.item(i).getTextContent();
content = content.replaceAll(" +", " ");
content = content.replace('\u00A0', ' ');
content = content.trim();
argList.add(content);
}
String args[] = argList.toArray(new String[0]);
command.args = args;
if (this.verbose) {
System.out.println(cmd + " " + Arrays.asList(args));
}
try {
command.result = this.commandProcessor.doCommand(cmd, args);
command.error = false;
} catch (Exception e) {
command.result = e.getMessage();
command.error = true;
}
command.failure = command.error && !cmd.startsWith("verify");
if (this.verbose) {
System.out.println(command.result);
}
return command;
}
private Object deserialize(Node node, boolean setProperty, boolean popBean) throws Exception {
Object object = null;
currentType = null;
currentNode = node;
currentName = node.getNodeName();
boolean isNull = false;
NamedNodeMap attrs = node.getAttributes();
String arrayType = null;
for (int i = 0; i < attrs.getLength(); i++) {
String nodeName = attrs.item(i).getNodeName();
String nodeValue = attrs.item(i).getNodeValue();
if (nodeName.equals(NamespaceConstants.NSPREFIX_SCHEMA_XSI + ":" + Constants.ATTR_TYPE))
currentType = new StringBuffer(nodeValue).delete(0, nodeValue.indexOf(':') + 1).toString();
else if (nodeName.equals(
NamespaceConstants.NSPREFIX_SOAP_ENCODING + ":" + Constants.ATTR_ARRAY_TYPE))
arrayType = new StringBuffer(nodeValue).delete(0, nodeValue.indexOf(':') + 1).toString();
else if (nodeName.equals(NamespaceConstants.NSPREFIX_SCHEMA_XSI + ":null"))
isNull = nodeValue.equals("true");
}
Class cls = null;
if (currentType != null) cls = getXsdTypeClass(currentType);
// Handle array, Vector, ArrayList, LinkedList, Hashtable,
// Properties, and HashMap data types
if ((cls != null)
&& ((cls == java.lang.reflect.Array.class)
|| (cls == Vector.class)
|| (cls == ArrayList.class)
|| (cls == LinkedList.class)
|| (cls == Hashtable.class)
|| (cls == Properties.class)
|| (cls == HashMap.class)
|| (cls == SortedMap.class))) {
parentNode = currentNode;
String name = node.getNodeName();
// Handle arrays
if (cls == java.lang.reflect.Array.class) {
int a = arrayType.indexOf("[");
int b = arrayType.indexOf("]");
String s = arrayType.substring(a + 1, b);
int arrayLen = Integer.valueOf(s).intValue();
arrayType = arrayType.substring(0, a);
// check if the array element is a standard Java class
Class arrayClass = getXsdTypeClass(arrayType);
// otherwise try to get the class of the bean
if (arrayClass == null)
arrayClass = getClassOfBean((ClassLoader) classLoaderStrategy, arrayType);
object = java.lang.reflect.Array.newInstance(arrayClass, arrayLen);
} else {
// Construct the list or map type
Constructor ct = cls.getConstructor((Class[]) null);
object = ct.newInstance((Object[]) null);
}
// deserialize the elements of the array, list, or map
NodeList childNodes = node.getChildNodes();
int arrayIndex = -1;
Node childNode = null;
Object nodeObj = null;
for (int i = 0; i < childNodes.getLength(); i++) {
childNode = childNodes.item(i);
if (childNode.getNodeType() == Node.ELEMENT_NODE) {
if ((cls == java.lang.reflect.Array.class)
|| (cls == Vector.class)
|| (cls == ArrayList.class)
|| (cls == LinkedList.class)) {
nodeObj = deserialize(childNode, false, true);
if (nodeObj != null) {
if (cls == java.lang.reflect.Array.class)
java.lang.reflect.Array.set(object, ++arrayIndex, nodeObj);
else ((List) object).add(nodeObj);
}
} else if ((cls == Hashtable.class)
|| (cls == Properties.class)
|| (cls == HashMap.class)
|| (cls == SortedMap.class)) {
if (childNode.getLocalName().equals("item")) {
NodeList htNodes = childNode.getChildNodes();
if (htNodes.getLength() == 2) {
Object hashKey = deserialize(htNodes.item(0), false, false);
Object hashValue = deserialize(htNodes.item(1), false, true);
((Map) object).put(hashKey, hashValue);
}
}
}
}
}
setBeanProperty(name, object);
// Handle everything else (primitives & POJOs)
} else {
// recurse on each of the child nodes
NodeList childNodes = node.getChildNodes();
if ((childNodes != null) && (childNodes.getLength() > 0)) {
for (int i = 0; i < childNodes.getLength(); i++) {
Node childNode = childNodes.item(i);
if (childNode.getNodeType() == Node.ELEMENT_NODE) {
if (currentType != null)
createObject(
node,
currentName,
currentPackage,
currentType,
childNode.getNodeValue(),
setProperty);
parentNode = node;
object = deserialize(childNode, true, true);
} else if ((childNode.getNodeType() == Node.TEXT_NODE) && (currentType != null)) {
object =
createObject(
node,
currentName,
currentPackage,
currentType,
childNode.getNodeValue(),
setProperty);
}
currentType = null;
}
} else {
if (!isNull)
object = createObject(node, currentName, currentPackage, currentType, null, setProperty);
}
if (node.getParentNode() != parentNode) {
parentNode = node.getParentNode();
if (popBean) {
Object bean = popBeanOffStack();
if (bean != null) object = bean;
}
}
}
return object;
}
public boolean runTest(Test test) throws Exception {
String filename = test.file.toString();
if (this.verbose) {
System.out.println(
"Running "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
this.document = parseDocument(filename);
if (this.baseUrl == null) {
NodeList links = this.document.getElementsByTagName("link");
if (links.getLength() != 0) {
Element link = (Element) links.item(0);
setBaseUrl(link.getAttribute("href"));
}
}
if (this.verbose) {
System.out.println("Base URL=" + this.baseUrl);
}
Node body = this.document.getElementsByTagName("body").item(0);
Element resultContainer = document.createElement("div");
resultContainer.setTextContent("Result: ");
Element resultElt = document.createElement("span");
resultElt.setAttribute("id", "result");
resultElt.setIdAttribute("id", true);
resultContainer.appendChild(resultElt);
body.insertBefore(resultContainer, body.getFirstChild());
Element executionLogContainer = document.createElement("div");
executionLogContainer.setTextContent("Execution Log:");
Element executionLog = document.createElement("div");
executionLog.setAttribute("id", "log");
executionLog.setIdAttribute("id", true);
executionLog.setAttribute("style", "white-space: pre;");
executionLogContainer.appendChild(executionLog);
body.appendChild(executionLogContainer);
NodeList tableRows = document.getElementsByTagName("tr");
Element theadRow = (Element) tableRows.item(0);
test.name = theadRow.getTextContent();
appendCellToRow(theadRow, "Result");
this.commandProcessor =
new HtmlCommandProcessor(this.host, this.port, this.browser, this.baseUrl);
String resultState;
String resultLog;
test.result = true;
try {
this.commandProcessor.start();
test.commands = new Command[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element stepRow = (Element) tableRows.item(i);
Command command = executeStep(stepRow);
appendCellToRow(stepRow, command.result);
test.commands[i - 1] = command;
if (command.error) {
test.result = false;
}
if (command.failure) {
test.result = false;
// break;
}
}
resultState = test.result ? "PASSED" : "FAILED";
resultLog = (test.result ? "Test Complete" : "Error");
this.commandProcessor.stop();
} catch (Exception e) {
test.result = false;
resultState = "ERROR";
resultLog = "Failed to initialize session\n" + e;
e.printStackTrace();
}
document.getElementById("result").setTextContent(resultState);
Element log = document.getElementById("log");
log.setTextContent(log.getTextContent() + resultLog + "\n");
return test.result;
}
public boolean runSuite(String filename) throws Exception {
if (this.verbose) {
System.out.println(
"Running test suite "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
TestSuite suite = new TestSuite();
long start = System.currentTimeMillis();
suite.numTestPasses = 0;
suite.file = new File(filename);
File suiteDirectory = suite.file.getParentFile();
this.document = parseDocument(filename);
Element table = (Element) this.document.getElementsByTagName("table").item(0);
NodeList tableRows = table.getElementsByTagName("tr");
Element tableNameRow = (Element) tableRows.item(0);
suite.name = tableNameRow.getTextContent();
suite.result = true;
suite.tests = new Test[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element tableRow = (Element) tableRows.item(i);
Element cell = (Element) tableRow.getElementsByTagName("td").item(0);
Element link = (Element) cell.getElementsByTagName("a").item(0);
Test test = new Test();
test.label = link.getTextContent();
test.file = new File(suiteDirectory, link.getAttribute("href"));
SeleniumHtmlClient subclient = new SeleniumHtmlClient();
subclient.setHost(this.host);
subclient.setPort(this.port);
subclient.setBrowser(this.browser);
// subclient.setResultsWriter(this.resultsWriter);
subclient.setBaseUrl(this.baseUrl);
subclient.setVerbose(this.verbose);
subclient.runTest(test);
if (test.result) {
suite.numTestPasses++;
}
suite.result &= test.result;
suite.tests[i - 1] = test;
}
long end = System.currentTimeMillis();
suite.totalTime = (end - start) / 1000;
if (this.resultsWriter != null) {
this.resultsWriter.write("<html><head>\n");
this.resultsWriter.write("<style type='text/css'>\n");
this.resultsWriter.write(
"body, table {font-family: Verdana, Arial, sans-serif;font-size: 12;}\n");
this.resultsWriter.write("table {border-collapse: collapse;border: 1px solid #ccc;}\n");
this.resultsWriter.write("th, td {padding-left: 0.3em;padding-right: 0.3em;}\n");
this.resultsWriter.write("a {text-decoration: none;}\n");
this.resultsWriter.write(".title {font-style: italic;}");
this.resultsWriter.write(".selected {background-color: #ffffcc;}\n");
this.resultsWriter.write(".status_done {background-color: #eeffee;}\n");
this.resultsWriter.write(".status_passed {background-color: #ccffcc;}\n");
this.resultsWriter.write(".status_failed {background-color: #ffcccc;}\n");
this.resultsWriter.write(
".breakpoint {background-color: #cccccc;border: 1px solid black;}\n");
this.resultsWriter.write("</style>\n");
this.resultsWriter.write("<title>" + suite.name + "</title>\n");
this.resultsWriter.write("</head><body>\n");
this.resultsWriter.write("<h1>Test suite results </h1>\n\n");
this.resultsWriter.write("<table>\n");
this.resultsWriter.write(
"<tr>\n<td>result:</td>\n<td>" + (suite.result ? "passed" : "failed") + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>totalTime:</td>\n<td>" + suite.totalTime + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestTotal:</td>\n<td>" + suite.tests.length + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestPasses:</td>\n<td>" + suite.numTestPasses + "</td>\n</tr>\n");
int numTestFailures = suite.tests.length - suite.numTestPasses;
this.resultsWriter.write(
"<tr>\n<td>numTestFailures:</td>\n<td>" + numTestFailures + "</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandPasses:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandFailures:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandErrors:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Version:</td>\n<td>2.24</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Revision:</td>\n<td>.1</td>\n</tr>\n");
// test suite
this.resultsWriter.write("<tr>\n<td>\n");
this.resultsWriter.write(
"<table id=\"suiteTable\" class=\"selenium\" border=\"1\" cellpadding=\"1\" cellspacing=\"1\"><tbody>\n");
this.resultsWriter.write(
"<tr class=\"title "
+ (suite.result ? "status_passed" : "status_failed")
+ "\"><td><b>Test Suite</b></td></tr>\n");
int i = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr class=\""
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td><a href=\"#testresult"
+ i
+ "\">"
+ test.name
+ "</a></td></tr>");
i++;
}
this.resultsWriter.write(
"</tbody></table>\n</td>\n<td> </td>\n</tr>\n</table>\n<table>");
int j = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr><td><a name=\"testresult" + j + "\">" + test.file + "</a><br/><div>\n");
this.resultsWriter.write("<table border=\"1\" cellpadding=\"1\" cellspacing=\"1\">\n");
this.resultsWriter.write(
"<thead>\n<tr class=\"title "
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td rowspan=\"1\" colspan=\"3\">"
+ test.name
+ "</td></tr>");
this.resultsWriter.write("</thead><tbody>\n");
for (Command command : test.commands) {
boolean result = command.result.startsWith("OK");
boolean isAssert = command.cmd.startsWith("assert") || command.cmd.startsWith("verify");
;
if (!isAssert) {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_done" : "") + "\">\n<td>\n");
} else {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_passed" : "status_failed") + "\">\n<td>\n");
}
this.resultsWriter.write(command.cmd);
this.resultsWriter.write("</td>\n");
if (command.args != null) {
for (String arg : Arrays.asList(command.args)) {
this.resultsWriter.write("<td>" + arg + "</td>\n");
}
}
}
this.resultsWriter.write("</tr>\n");
this.resultsWriter.write("</tbody></table>\n");
this.resultsWriter.write("</div></td>\n<td> </td>\n</tr>");
j++;
}
int k = 0;
for (Test test : suite.tests) {
k++;
}
this.resultsWriter.write("</tbody></table>\n</td><td> </td>\n</tr>\n</table>\n");
this.resultsWriter.write("</body></html>");
}
return suite.result;
}
/**
* Reads XML element(s) into an indexed bean property by first locating the XML element(s)
* corresponding to this property.
*
* @param ob The bean whose property is being set
* @param desc The property that will be set
* @param nodes The list of XML items that may contain the property
* @throws IOException If there is an error reading the document
*/
public void readIndexedProperty(
Object ob, IndexedPropertyDescriptor desc, NodeList nodes, NamedNodeMap attrs)
throws IOException {
// Create a vector to hold the property values
Vector v = new Vector();
int numAttrs = attrs.getLength();
for (int i = 0; i < numAttrs; i++) {
// See if this attribute matches the property name
if (namesMatch(desc.getName(), attrs.item(i).getNodeName())) {
// Get the property value
Object obValue = getObjectValue(desc, attrs.item(i).getNodeValue());
if (obValue != null) {
// Add the value to the list of values to be set
v.addElement(obValue);
}
}
}
int numNodes = nodes.getLength();
for (int i = 0; i < numNodes; i++) {
Node node = nodes.item(i);
// Skip non-element nodes
if (!(node instanceof Element)) continue;
Element element = (Element) node;
// See if this element tag matches the property name
if (namesMatch(desc.getName(), element.getTagName())) {
// Get the property value
Object obValue = getObjectValue(desc, element);
if (obValue != null) {
// Add the value to the list of values to be set
v.addElement(obValue);
}
}
}
// Get the method used to set the property value
Method setter = desc.getWriteMethod();
// If this property has no setter, don't write it
if (setter == null) return;
// Create a new array of property values
Object propArray = Array.newInstance(desc.getPropertyType().getComponentType(), v.size());
// Copy the vector into the array
v.copyInto((Object[]) propArray);
try {
// Store the array of property values
setter.invoke(ob, new Object[] {propArray});
} catch (InvocationTargetException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
}
}
/**
* Reads an XML element into a bean property by first locating the XML element corresponding to
* this property.
*
* @param ob The bean whose property is being set
* @param desc The property that will be set
* @param nodes The list of XML items that may contain the property
* @throws IOException If there is an error reading the document
*/
public void readProperty(Object ob, PropertyDescriptor desc, NodeList nodes, NamedNodeMap attrs)
throws IOException {
int numAttrs = attrs.getLength();
for (int i = 0; i < numAttrs; i++) {
// See if the attribute name matches the property name
if (namesMatch(desc.getName(), attrs.item(i).getNodeName())) {
// Get the method used to set this property
Method setter = desc.getWriteMethod();
// If this object has no setter, don't bother writing it
if (setter == null) continue;
// Get the value of the property
Object obValue = getObjectValue(desc, attrs.item(i).getNodeValue());
if (obValue != null) {
try {
// Set the property value
setter.invoke(ob, new Object[] {obValue});
} catch (InvocationTargetException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
}
}
return;
}
}
int numNodes = nodes.getLength();
Vector arrayBuild = null;
for (int i = 0; i < numNodes; i++) {
Node node = nodes.item(i);
// If this node isn't an element, skip it
if (!(node instanceof Element)) continue;
Element element = (Element) node;
// See if the tag name matches the property name
if (namesMatch(desc.getName(), element.getTagName())) {
// Get the method used to set this property
Method setter = desc.getWriteMethod();
// If this object has no setter, don't bother writing it
if (setter == null) continue;
// Get the value of the property
Object obValue = getObjectValue(desc, element);
// 070201 MAW: Modified from change submitted by Steve Poulson
if (setter.getParameterTypes()[0].isArray()) {
if (arrayBuild == null) {
arrayBuild = new Vector();
}
arrayBuild.addElement(obValue);
// 070201 MAW: Go ahead and read through the rest of the nodes in case
// another one matches the array. This has the effect of skipping
// over the "return" statement down below
continue;
}
if (obValue != null) {
try {
// Set the property value
setter.invoke(ob, new Object[] {obValue});
} catch (InvocationTargetException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException(
"Error setting property " + desc.getName() + ": " + exc.toString());
}
}
return;
}
}
// If we build a vector of array members, convert the vector into
// an array and save it in the property
if (arrayBuild != null) {
// Get the method used to set this property
Method setter = desc.getWriteMethod();
if (setter == null) return;
Object[] obValues = (Object[]) Array.newInstance(desc.getPropertyType(), arrayBuild.size());
arrayBuild.copyInto(obValues);
try {
setter.invoke(ob, new Object[] {obValues});
} catch (InvocationTargetException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
}
return;
}
}
/**
* Unmarshall a Chromosome instance from a given XML Element representation.
*
* @param a_activeConfiguration current Configuration object
* @param a_xmlElement the XML Element representation of the Chromosome
* @return a new Chromosome instance setup with the data from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws UnsupportedRepresentationException if the actively configured Gene implementation does
* not support the string representation of the alleles used in the given XML document
* @throws GeneCreationException if there is a problem creating or populating a Gene instance
* @author Neil Rotstan
* @since 1.0
*/
public static Gene[] getGenesFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, UnsupportedRepresentationException, GeneCreationException {
// Do some sanity checking. Make sure the XML Element isn't null and
// that it in fact represents a set of genes.
// -----------------------------------------------------------------
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENES_TAG))) {
throw new ImproperXMLException(
"Unable to build Chromosome instance from XML Element: "
+ "given Element is not a 'genes' element.");
}
List genes = Collections.synchronizedList(new ArrayList());
// Extract the nested gene elements.
// ---------------------------------
NodeList geneElements = a_xmlElement.getElementsByTagName(GENE_TAG);
if (geneElements == null) {
throw new ImproperXMLException(
"Unable to build Gene instances from XML Element: "
+ "'"
+ GENE_TAG
+ "'"
+ " sub-elements not found.");
}
// For each gene, get the class attribute so we know what class
// to instantiate to represent the gene instance, and then find
// the child text node, which is where the string representation
// of the allele is located, and extract the representation.
// -------------------------------------------------------------
int numberOfGeneNodes = geneElements.getLength();
for (int i = 0; i < numberOfGeneNodes; i++) {
Element thisGeneElement = (Element) geneElements.item(i);
thisGeneElement.normalize();
// Fetch the class attribute and create an instance of that
// class to represent the current gene.
// --------------------------------------------------------
String geneClassName = thisGeneElement.getAttribute(CLASS_ATTRIBUTE);
Gene thisGeneObject;
Class geneClass = null;
try {
geneClass = Class.forName(geneClassName);
try {
Constructor constr = geneClass.getConstructor(new Class[] {Configuration.class});
thisGeneObject = (Gene) constr.newInstance(new Object[] {a_activeConfiguration});
} catch (NoSuchMethodException nsme) {
// Try it by calling method newGeneInternal.
// -----------------------------------------
Constructor constr = geneClass.getConstructor(new Class[] {});
thisGeneObject = (Gene) constr.newInstance(new Object[] {});
thisGeneObject =
(Gene)
PrivateAccessor.invoke(
thisGeneObject, "newGeneInternal", new Class[] {}, new Object[] {});
}
} catch (Throwable e) {
throw new GeneCreationException(geneClass, e);
}
// Find the text node and fetch the string representation of
// the allele.
// ---------------------------------------------------------
NodeList children = thisGeneElement.getChildNodes();
int childrenSize = children.getLength();
String alleleRepresentation = null;
for (int j = 0; j < childrenSize; j++) {
Element alleleElem = (Element) children.item(j);
if (alleleElem.getTagName().equals(ALLELE_TAG)) {
alleleRepresentation = alleleElem.getAttribute("value");
}
if (children.item(j).getNodeType() == Node.TEXT_NODE) {
// We found the text node. Extract the representation.
// ---------------------------------------------------
alleleRepresentation = children.item(j).getNodeValue();
break;
}
}
// Sanity check: Make sure the representation isn't null.
// ------------------------------------------------------
if (alleleRepresentation == null) {
throw new ImproperXMLException(
"Unable to build Gene instance from XML Element: "
+ "value (allele) is missing representation.");
}
// Now set the value of the gene to that reflect the
// string representation.
// -------------------------------------------------
try {
thisGeneObject.setValueFromPersistentRepresentation(alleleRepresentation);
} catch (UnsupportedOperationException e) {
throw new GeneCreationException(
"Unable to build Gene because it does not support the "
+ "setValueFromPersistentRepresentation() method.");
}
// Finally, add the current gene object to the list of genes.
// ----------------------------------------------------------
genes.add(thisGeneObject);
}
return (Gene[]) genes.toArray(new Gene[genes.size()]);
}
