/**
   * Carries out preprocessing that makes JEuclid handle the document better.
   *
   * @param doc Document
   */
  static void preprocessForJEuclid(Document doc) {
    // underbrace and overbrace
    NodeList list = doc.getElementsByTagName("mo");
    for (int i = 0; i < list.getLength(); i++) {
      Element mo = (Element) list.item(i);
      String parentName = ((Element) mo.getParentNode()).getTagName();
      if (parentName == null) {
        continue;
      }
      if (parentName.equals("munder") && isTextChild(mo, "\ufe38")) {
        mo.setAttribute("stretchy", "true");
        mo.removeChild(mo.getFirstChild());
        mo.appendChild(doc.createTextNode("\u23df"));
      } else if (parentName.equals("mover") && isTextChild(mo, "\ufe37")) {
        mo.setAttribute("stretchy", "true");
        mo.removeChild(mo.getFirstChild());
        mo.appendChild(doc.createTextNode("\u23de"));
      }
    }

    // menclose for long division doesn't allow enough top padding. Oh, and
    // <mpadded> isn't implemented. And there isn't enough padding to left of
    // the bar either. Solve by adding an <mover> with just an <mspace> over#
    // the longdiv, contained within an mrow that adds a <mspace> before it.
    list = doc.getElementsByTagName("menclose");
    for (int i = 0; i < list.getLength(); i++) {
      Element menclose = (Element) list.item(i);
      // Only for longdiv
      if (!"longdiv".equals(menclose.getAttribute("notation"))) {
        continue;
      }
      Element mrow = doc.createElementNS(WebMathsService.NS, "mrow");
      Element mover = doc.createElementNS(WebMathsService.NS, "mover");
      Element mspace = doc.createElementNS(WebMathsService.NS, "mspace");
      Element mspaceW = doc.createElementNS(WebMathsService.NS, "mspace");
      boolean previousElement = false;
      for (Node previous = menclose.getPreviousSibling();
          previous != null;
          previous = previous.getPreviousSibling()) {
        if (previous.getNodeType() == Node.ELEMENT_NODE) {
          previousElement = true;
          break;
        }
      }
      if (previousElement) {
        mspaceW.setAttribute("width", "4px");
      }
      menclose.getParentNode().insertBefore(mrow, menclose);
      menclose.getParentNode().removeChild(menclose);
      mrow.appendChild(mspaceW);
      mrow.appendChild(mover);
      mover.appendChild(menclose);
      mover.appendChild(mspace);
    }
  }
Exemple #2
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  /**
   * Reads in a decision stored in XML.
   *
   * @param decN - the XML element.
   */
  public void fromXML(Element decN) {
    this.fromXML = true;

    RationaleDB db = RationaleDB.getHandle();

    String rid = decN.getAttribute("rid");
    id = Integer.parseInt(rid.substring(2));

    name = decN.getAttribute("name");

    type = DecisionType.fromString(decN.getAttribute("type"));

    devPhase = Phase.fromString(decN.getAttribute("phase"));

    status = DecisionStatus.fromString(decN.getAttribute("status"));

    Node child = decN.getFirstChild();
    importHelper(child);

    Node nextNode = child.getNextSibling();
    while (nextNode != null) {
      importHelper(nextNode);
      nextNode = nextNode.getNextSibling();
    }

    db.addPatternDecisionFromXML(this);
  }
  /**
   * @param sourceFile File to read from
   * @return List of String objects with the shas
   */
  public static FileRequestFileContent readRequestFile(final File sourceFile) {
    if (!sourceFile.isFile() || !(sourceFile.length() > 0)) {
      return null;
    }
    Document d = null;
    try {
      d = XMLTools.parseXmlFile(sourceFile.getPath());
    } catch (final Throwable t) {
      logger.log(Level.SEVERE, "Exception in readRequestFile, during XML parsing", t);
      return null;
    }

    if (d == null) {
      logger.log(Level.SEVERE, "Could'nt parse the request file");
      return null;
    }

    final Element rootNode = d.getDocumentElement();

    if (rootNode.getTagName().equals(TAG_FrostFileRequestFile) == false) {
      logger.severe(
          "Error: xml request file does not contain the root tag '"
              + TAG_FrostFileRequestFile
              + "'");
      return null;
    }

    final String timeStampStr = XMLTools.getChildElementsTextValue(rootNode, TAG_timestamp);
    if (timeStampStr == null) {
      logger.severe("Error: xml file does not contain the tag '" + TAG_timestamp + "'");
      return null;
    }
    final long timestamp = Long.parseLong(timeStampStr);

    final List<Element> nodelist = XMLTools.getChildElementsByTagName(rootNode, TAG_shaList);
    if (nodelist.size() != 1) {
      logger.severe("Error: xml request files must contain only one element '" + TAG_shaList + "'");
      return null;
    }

    final Element rootShaNode = nodelist.get(0);

    final List<String> shaList = new LinkedList<String>();
    final List<Element> xmlKeys = XMLTools.getChildElementsByTagName(rootShaNode, TAG_sha);
    for (final Element el : xmlKeys) {

      final Text txtname = (Text) el.getFirstChild();
      if (txtname == null) {
        continue;
      }

      final String sha = txtname.getData();
      shaList.add(sha);
    }

    final FileRequestFileContent content = new FileRequestFileContent(timestamp, shaList);
    return content;
  }
  /** used for cut and paste. */
  public void addObjectFromClipboard(String a_value) throws CircularIncludeException {
    Reader reader = new StringReader(a_value);
    Document document = null;
    try {
      document = UJAXP.getDocument(reader);
    } catch (Exception e) {
      e.printStackTrace();
      return;
    } // try-catch

    Element root = document.getDocumentElement();
    if (!root.getNodeName().equals("clipboard")) {
      return;
    } // if

    Node child;
    for (child = root.getFirstChild(); child != null; child = child.getNextSibling()) {
      if (!(child instanceof Element)) {
        continue;
      } // if
      Element element = (Element) child;

      IGlyphFactory factory = GlyphFactory.getFactory();

      if (XModule.isMatch(element)) {
        EModuleInvoke module = (EModuleInvoke) factory.createXModule(element);
        addModule(module);
        continue;
      } // if

      if (XContour.isMatch(element)) {
        EContour contour = (EContour) factory.createXContour(element);
        addContour(contour);
        continue;
      } // if

      if (XInclude.isMatch(element)) {
        EIncludeInvoke include = (EIncludeInvoke) factory.createXInclude(element);
        addInclude(include);
        continue;
      } // if
    } // while
  }
Exemple #5
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  // ## 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;
    }

    // #]
  }