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);
}
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);
}
}
/**
* 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;
}
