@Override
protected Fasta advance() {
Fasta f = null;
for (; ; ) {
if (!in.hasNext()) return null;
String line = in.next();
if (line.trim().isEmpty()) continue;
if (!line.startsWith(">"))
throw new RuntimeException("Expected '>'. Bad fasta line :" + line);
f = new Fasta();
f.name = line.substring(1);
break;
}
StringBuilder sb = new StringBuilder();
while (in.hasNext()) {
String line = in.peek();
if (line.trim().isEmpty()) {
in.next();
continue;
}
if (line.startsWith(">")) break; // new sequence
sb.append(in.next().trim());
}
f.sequence = sb.toString();
return f;
}
/**
* Returns a list of VariantContext records from a VCF file
*
* @param vcfFile VCF file
* @throws IOException if the file does not exist or can not be opened
* @return list of VariantContext records
*/
private static List<VariantContext> getVariantContexts(final File vcfFile) throws IOException {
final VCFCodec codec = new VCFCodec();
final FileInputStream s = new FileInputStream(vcfFile);
final LineIterator lineIteratorVCF =
codec.makeSourceFromStream(new PositionalBufferedStream(s));
codec.readHeader(lineIteratorVCF);
final List<VariantContext> VCs = new ArrayList<>();
while (lineIteratorVCF.hasNext()) {
final String line = lineIteratorVCF.next();
Assert.assertFalse(line == null);
VCs.add(codec.decode(line));
}
return VCs;
}
/**
* Returns a list of attribute values from a VCF file
*
* @param vcfFile VCF file
* @param attributeName attribute name
* @throws IOException if the file does not exist or can not be opened
* @return list of attribute values
*/
private List<String> getAttributeValues(final File vcfFile, final String attributeName)
throws IOException {
final VCFCodec codec = new VCFCodec();
final FileInputStream s = new FileInputStream(vcfFile);
final LineIterator lineIteratorVCF =
codec.makeSourceFromStream(new PositionalBufferedStream(s));
codec.readHeader(lineIteratorVCF);
List<String> attributeValues = new ArrayList<String>();
while (lineIteratorVCF.hasNext()) {
final String line = lineIteratorVCF.next();
Assert.assertFalse(line == null);
final VariantContext vc = codec.decode(line);
for (final Genotype g : vc.getGenotypes()) {
if (g.hasExtendedAttribute(attributeName)) {
attributeValues.add((String) g.getExtendedAttribute(attributeName));
}
}
}
return attributeValues;
}
private void scan(Graphics2D g, InputStream input) throws IOException {
Set<String> unknownC = new HashSet<String>();
Pattern tab = Pattern.compile("[\t]");
LineIterator in = new LineIteratorImpl(LineReaderUtil.fromBufferedStream(input));
while (in.hasNext()) {
String line = in.next();
String tokens[] = tab.split(line, 5);
if (tokens.length < 4) {
warning("Ignoring " + line);
continue;
}
SAMSequenceRecord rec = this.context.getDictionary().getSequence(tokens[0]);
if (rec == null) {
warning("unknown chromosome " + tokens[0]);
continue;
}
String country = tokens[3].toLowerCase().replaceAll("[ ]", "");
Shape shape = this.country2shape.get(country);
if (shape == null) {
if (!unknownC.contains(country)) {
unknownC.add(country);
warning("unknown country " + country);
}
continue;
}
seen.incr(country);
int midpos = (Integer.parseInt(tokens[1]) + Integer.parseInt(tokens[2])) / 2;
// country center
Point2D.Double pt1 =
new Point2D.Double(shape.getBounds2D().getCenterX(), shape.getBounds2D().getCenterY());
// circle point
Point2D pt3 = this.context.convertPositionToPoint(tokens[0], midpos, getRadiusInt());
double angle = this.context.convertPositionToRadian(rec, midpos);
double angle2 = angle -= Math.PI / 10.0;
double distance13 =
context
.getCenter()
.distance(
new Point2D.Double(
(pt1.getX() + pt3.getX()) / 2.0, (pt1.getY() + pt3.getY()) / 2.0));
// mid point
Point2D pt2 =
new Point2D.Double(
context.getCenterX() + distance13 * Math.cos(angle2),
context.getCenterX() + distance13 * Math.sin(angle2));
Composite old = g.getComposite();
Stroke olds = g.getStroke();
g.setStroke(new BasicStroke(0.8f));
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.02f));
g.setColor(Color.DARK_GRAY);
GeneralPath p = new GeneralPath();
p.moveTo(pt1.getX(), pt1.getY());
p.quadTo(pt2.getX(), pt2.getY(), pt3.getX(), pt3.getY());
p.closePath();
g.draw(p);
g.setComposite(old);
g.setStroke(olds);
}
CloserUtil.close(in);
}
