/**
* Method that reads a XML-file, and returns a Model that contains the information
*
* @param file
* @return
* @return
*/
public static Model readXML(String file) {
// initialize table to be filled with content of XML file
Model t = new Model();
try {
// Create file to be parsed by document parser
File xmlfile = new File(file);
// create parser
DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder();
// parse the file
Document parsedfile = parser.parse(xmlfile);
// normalize the parsed file (make it more user-friendly)
parsedfile.getDocumentElement().normalize();
NodeList cells = parsedfile.getElementsByTagName("CELL");
for (int i = 0; i < cells.getLength(); i++) {
// Get cell at list index i
Node currentcell = cells.item(i);
// read the elements "location" attributes row/column
if (Node.ELEMENT_NODE == currentcell.getNodeType()) {
Element cellinfo = (Element) currentcell;
// get the row number from node attribute
int row = Integer.parseInt(cellinfo.getAttribute("row")) - 1;
// get the column number from the node attribute
int col = Integer.parseInt(cellinfo.getAttribute("column")) - 1;
// get content from node
String content = cellinfo.getTextContent();
if (content != null) {
content = content.replace("\n", "");
}
// Make the content an Integer (if it is a number), easier
// for
// using it later on
// put content in table, with row/column inserted as x/y
t.setContent(row, col, (String) content);
}
}
} catch (ParserConfigurationException e) {
System.out.println("Fileparser could not be made");
} catch (IOException f) {
System.out.println("File could not be parsed, did you enter the correct file name?");
} catch (SAXException g) {
System.out.println("Something went wrong in parsing the file");
}
return t;
}
/**
* Gets the definitions of a word, sets the main one if necessary, and returns it.
*
* @param overwrite if true, then function will attempt to retrieve from online even if the
* definition is already set.
* @return String containing the main definition of the word.
*/
public static Word[] getWordsFromFile(ByteArrayInputStream inputStream) {
try {
// now to parse the XML
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(inputStream);
removeEmptyTextNodes(doc);
NodeList wordList = doc.getElementsByTagName("WordDefinitions");
int wordCount = wordList.getLength();
Word[] returnWords = new Word[wordCount];
for (int wordi = 0; wordi < wordCount; wordi++) {
NodeList list = ((Element) wordList.item(wordi)).getElementsByTagName("Definition");
Element wordElement = (Element) wordList.item(wordi);
String word = wordElement.getAttribute("word");
String mainDefinition = wordElement.getAttribute("mainDefinition");
int numDefinitions = list.getLength();
Definition[] wordOtherDefinitions = new Definition[numDefinitions];
for (int i = 0; i < numDefinitions; i++) {
Node node = list.item(i);
NodeList children = node.getChildNodes(); // gets each child node of the definition
// get all data
String definition = children.item(XML_DEFINITION_LOC).getTextContent();
String theWord = children.item(XML_WORD_LOC).getTextContent();
NodeList dictionaryNode = children.item(XML_DICTIONARY_BRANCH_LOC).getChildNodes();
String dictionaryId = dictionaryNode.item(XML_DICTIONARY_ID_LOC).getTextContent();
String dictionaryName = dictionaryNode.item(XML_DICTIONARY_NAME_LOC).getTextContent();
// now we've got all the data lets add it to the array
wordOtherDefinitions[i] =
new Definition(dictionaryName, dictionaryId, definition, theWord);
}
if (wordOtherDefinitions.length == 0) {
wordOtherDefinitions =
new Definition[] {new Definition("nil", "nil", "NO DEFINITION FOUND", word)};
}
Word currentWord = new Word(word, mainDefinition);
currentWord.setOtherDefinitions(wordOtherDefinitions);
returnWords[wordi] = currentWord;
}
return returnWords;
} catch (Exception ex) {
ex.printStackTrace();
return null;
}
}
/**
* XML Circuit constructor
*
* @param file the file that contains the XML description of the circuit
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
this("");
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
Document doc;
Element root;
Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();
try {
builder = factory.newDocumentBuilder();
doc = builder.parse(file);
} catch (SAXException sxe) {
throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
} catch (ParserConfigurationException pce) {
throw new CircuitLoadingException(
"Parser exception raised, parser configuration is invalid.");
} catch (IOException ioe) {
throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
}
root = (Element) doc.getElementsByTagName("Circuit").item(0);
this.setName(root.getAttribute("name"));
NodeList nl = root.getElementsByTagName("Node");
Element e;
Node n;
Class cl;
for (int i = 0; i < nl.getLength(); ++i) {
e = (Element) nl.item(i);
try {
cl = Class.forName(e.getAttribute("class"));
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
try {
n = ((Node) cl.newInstance());
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
this.nodes.add(n);
n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));
if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));
if (n instanceof giraffe.ui.CompositeNode) {
try {
((CompositeNode) n)
.load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
} catch (Exception exc) {
/* try to load from the lib */
((CompositeNode) n)
.load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
}
}
NodeList nlist = e.getElementsByTagName("Anchor");
Element el;
for (int j = 0; j < nlist.getLength(); ++j) {
el = (Element) nlist.item(j);
Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
NodeList linklist = el.getElementsByTagName("Link");
Element link;
Link l;
for (int k = 0; k < linklist.getLength(); ++k) {
link = (Element) linklist.item(k);
int id = new Integer(link.getAttribute("id"));
int index = new Integer(link.getAttribute("index"));
if (id >= this.linkID) linkID = id + 1;
if (linkstable.containsKey(id)) {
l = linkstable.get(id);
l.addLinkedAnchorAt(a, index);
a.addLink(l);
} else {
l = new Link(id);
l.addLinkedAnchorAt(a, index);
this.links.add(l);
linkstable.put(id, l);
a.addLink(l);
}
}
}
}
}
// ## operation readReactorOutputFile(ReactionModel)
public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
// #[ operation readReactorOutputFile(ReactionModel)
try {
// open output file and build the DOM tree
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/reactorOutput.xml";
File inputFile = new File(filename);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true); // validate the document with the DTD
factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(inputFile);
// get root element and its children
Element root = doc.getDocumentElement();
NodeList rootchildren = root.getChildNodes();
// header is rootchildren.item(0)
// get return message and check for successful run
Element returnmessageElement = (Element) rootchildren.item(1);
Text returnmessageText = (Text) returnmessageElement.getFirstChild();
String returnmessage = returnmessageText.toString();
returnmessage = returnmessage.trim();
if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
System.out.println("External reactor model failed!");
System.out.println("Reactor model error message: " + returnmessage);
System.exit(0);
}
// get outputvalues element and its children
Element outputvaluesElement = (Element) rootchildren.item(2);
NodeList children = outputvaluesElement.getChildNodes();
// get time
Element timeElement = (Element) children.item(0);
Text timeText = (Text) timeElement.getFirstChild();
double time = Double.parseDouble(timeText.getData());
String timeUnits = timeElement.getAttribute("units");
// get systemstate element and its children
Element systemstateElement = (Element) children.item(1);
NodeList states = systemstateElement.getChildNodes();
// get temperature and its units
Element temperatureElement = (Element) states.item(0);
String tempUnits = temperatureElement.getAttribute("units");
Text temperatureText = (Text) temperatureElement.getFirstChild();
double temp = Double.parseDouble(temperatureText.getData());
Temperature T = new Temperature(temp, tempUnits);
// get pressure and its units
Element pressureElement = (Element) states.item(1);
String presUnits = pressureElement.getAttribute("units");
Text pressureText = (Text) pressureElement.getFirstChild();
double pres = Double.parseDouble(pressureText.getData());
Pressure P = new Pressure(pres, presUnits);
// get species amounts (e.g. concentrations)
ArrayList speciesIDs = new ArrayList();
ArrayList amounts = new ArrayList();
ArrayList fluxes = new ArrayList();
String amountUnits = null;
String fluxUnits = null;
// loop thru all the species
// begin at i=2, since T and P take already the first two position of states
int nSpe = (states.getLength() - 2) / 2;
int index = 0;
LinkedHashMap inertGas = new LinkedHashMap();
for (int i = 2; i < nSpe + 2; i++) {
// get amount element and the units
Element amountElement = (Element) states.item(i);
amountUnits = amountElement.getAttribute("units");
Element fluxElement = (Element) states.item(i + nSpe);
fluxUnits = fluxElement.getAttribute("units");
// get speciesid and store in an array list
String thisSpeciesID = amountElement.getAttribute("speciesid");
// get amount (e.g. concentraion) and store in an array list
Text amountText = (Text) amountElement.getFirstChild();
double thisAmount = Double.parseDouble(amountText.getData());
if (thisAmount < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(thisAmount) < aTol) thisAmount = 0;
// else throw new NegativeConcentrationException("Negative concentration in
// reactorOutput.xml: " + thisSpeciesID);
if (thisAmount < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species "
+ thisSpeciesID
+ " has negative concentration: "
+ String.valueOf(thisAmount));
}
// get amount (e.g. concentraion) and store in an array list
Text fluxText = (Text) fluxElement.getFirstChild();
double thisFlux = Double.parseDouble(fluxText.getData());
if (thisSpeciesID.compareToIgnoreCase("N2") == 0
|| thisSpeciesID.compareToIgnoreCase("Ne") == 0
|| thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
inertGas.put(thisSpeciesID, new Double(thisAmount));
} else {
speciesIDs.add(index, thisSpeciesID);
amounts.add(index, new Double(thisAmount));
fluxes.add(index, new Double(thisFlux));
index++;
}
}
// print results for debugging purposes
/**
* System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
* System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
* i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
*/
ReactionTime rt = new ReactionTime(time, timeUnits);
LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
ss.inertGas = inertGas;
return ss;
} catch (Exception e) {
System.out.println("Error reading reactor model output: " + e.getMessage());
System.exit(0);
return null;
}
// #]
}
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;
}
/**
* 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()]);
}