/**
   * 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;
   }
 }
Exemple #3
0
  /**
   * 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);
          }
        }
      }
    }
  }
Exemple #4
0
  // ## 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>&nbsp;</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>&nbsp;</td>\n</tr>");

        j++;
      }

      int k = 0;
      for (Test test : suite.tests) {

        k++;
      }

      this.resultsWriter.write("</tbody></table>\n</td><td>&nbsp;</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()]);
 }