Exemplo n.º 1
0
  private void insertRecord(String line) throws FormatException {
    String[] fields = line.split(",");
    if (fields.length < 9)
      throw new FormatException(
          "Too few columns in sample sheet.  Expecing at least 9 but found "
              + fields.length
              + ". Line: "
              + line);

    // Format is CSV with these columns:
    // "FCID","Lane","SampleID","SampleRef","Index","Description","Control","Recipe","Operator"
    // All text fields are quoted (all except Lane)

    // remove external quotes and whitespace from all string fields (even spaces within the quotes)
    for (int i = 0; i < fields.length; ++i) {
      quoteMatcher.reset(fields[i]);
      fields[i] = quoteMatcher.replaceAll("").trim();
    }

    Entry entry;
    try {
      entry = Entry.createEntry(fields);
    } catch (IllegalArgumentException e) {
      throw new FormatException(e.getMessage() + ". Line: " + line);
    }

    table.add(entry);
  }
Exemplo n.º 2
0
 public int addToTable(String line) {
   String[] a = line.split(splitToken);
   try {
     return addToTable(a);
   } catch (IllegalArgumentException e) {
     String msg = String.format("\"%s\" -> '%s'", e.getMessage(), line);
     throw new IllegalArgumentException(msg, e);
   }
 }
Exemplo n.º 3
0
  /**
   * Does real work; separated out so it can be efficiently called from subclass.
   *
   * @param params Request parameters
   * @param doc MathML as DOM document
   * @param result Initialised result object with blank fields
   * @param start Start time of request (milliseconds since epoch)
   * @return Return result
   * @throws IOException Any error creating image file
   */
  protected MathsImageReturn getImage(
      MathsImageParams params, Document doc, MathsImageReturn result, long start)
      throws IOException {
    initContext();

    Color fg;
    try {
      fg = convertRgb(params.getRgb());
    } catch (IllegalArgumentException e) {
      result.setError(e.getMessage());
      return result;
    }

    if (SHOWPERFORMANCE) {
      System.err.println("Setup: " + (System.currentTimeMillis() - start));
    }

    // Parse XML to JEuclid document
    DocumentElement document;
    preprocessForJEuclid(doc);
    document = DOMBuilder.getInstance().createJeuclidDom(doc);
    if (SHOWPERFORMANCE) {
      System.err.println("Parse: " + (System.currentTimeMillis() - start));
    }

    // Set layout options
    LayoutContextImpl layout = new LayoutContextImpl(LayoutContextImpl.getDefaultLayoutContext());
    layout.setParameter(Parameter.ANTIALIAS, Boolean.TRUE);
    // This size is hardcoded to go well with our default text size
    // and be one of the sizes that doesn't look too horrible.
    layout.setParameter(Parameter.MATHSIZE, params.getSize() * 15f);
    layout.setParameter(Parameter.SCRIPTSIZEMULTIPLIER, 0.86667f);
    layout.setParameter(Parameter.MATHCOLOR, fg);

    // These fonts are included with the JEuclid build so ought to work
    layout.setParameter(
        Parameter.FONTS_SERIF, Arrays.asList(new String[] {"DejaVu Serif", "Quivira"}));
    layout.setParameter(Parameter.FONTS_SCRIPT, Arrays.asList(new String[] {"Allura"}));
    layout.setParameter(Parameter.FONTS_SANSSERIF, "DejaVu Sans");
    layout.setParameter(Parameter.FONTS_MONOSPACED, "DejaVu Sans Mono");

    if (SHOWPERFORMANCE) {
      System.err.println("Layout: " + (System.currentTimeMillis() - start));
    }

    // Layout equation
    JEuclidView view = new JEuclidView(document, layout, context);
    float ascent = view.getAscentHeight();
    float descent = view.getDescentHeight();
    float width = view.getWidth();
    if (SHOWPERFORMANCE) {
      System.err.println("View: " + (System.currentTimeMillis() - start));
    }

    // Create new image to hold it
    int pixelWidth = Math.max(1, (int) Math.ceil(width)),
        pixelHeight = Math.max(1, (int) Math.ceil(ascent + descent));

    BufferedImage image = new BufferedImage(pixelWidth, pixelHeight, BufferedImage.TYPE_INT_ARGB);
    if (SHOWPERFORMANCE) {
      System.err.println("Image: " + (System.currentTimeMillis() - start));
    }
    view.draw(image.createGraphics(), 0, ascent);
    if (SHOWPERFORMANCE) {
      System.err.println("Draw: " + (System.currentTimeMillis() - start));
    }
    ByteArrayOutputStream output = new ByteArrayOutputStream();
    ImageIO.write(image, "png", output);
    if (SHOWPERFORMANCE) {
      System.err.println("PNG: " + (System.currentTimeMillis() - start));
    }

    // Save results
    result.setImage(output.toByteArray());
    result.setBaseline(BigInteger.valueOf(image.getHeight() - (int) Math.round(ascent)));
    result.setOk(true);

    if (SHOWPERFORMANCE) {
      System.err.println("End: " + (System.currentTimeMillis() - start));
    }
    return result;
  }