/**
* Decodes data encoded using {@link #toHex(byte[],int,int) toHex}.
*
* @param hex data to be converted
* @param start offset
* @param len count
* @throws IOException if input does not represent hex encoded value
* @since 1.29
*/
public static byte[] fromHex(char[] hex, int start, int len) throws IOException {
if (hex == null) throw new IOException("null");
int i = hex.length;
if (i % 2 != 0) throw new IOException("odd length");
byte[] magic = new byte[i / 2];
for (; i > 0; i -= 2) {
String g = new String(hex, i - 2, 2);
try {
magic[(i / 2) - 1] = (byte) Integer.parseInt(g, 16);
} catch (NumberFormatException ex) {
throw new IOException(ex.getLocalizedMessage());
}
}
return magic;
}
private void processFrames(Element element) {
NodeList elements = element.getChildNodes();
if (elements.getLength() > 0) {
Map<String, ReferenceFrame> frames = new HashMap();
for (ReferenceFrame f : FrameManager.getFrames()) {
frames.put(f.getName(), f);
}
List<ReferenceFrame> reorderedFrames = new ArrayList();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equalsIgnoreCase(SessionElement.FRAME.getText())) {
String frameName = getAttribute((Element) childNode, SessionAttribute.NAME.getText());
ReferenceFrame f = frames.get(frameName);
if (f != null) {
reorderedFrames.add(f);
try {
String chr = getAttribute((Element) childNode, SessionAttribute.CHR.getText());
final String startString =
getAttribute((Element) childNode, SessionAttribute.START.getText())
.replace(",", "");
final String endString =
getAttribute((Element) childNode, SessionAttribute.END.getText())
.replace(",", "");
int start = ParsingUtils.parseInt(startString);
int end = ParsingUtils.parseInt(endString);
org.broad.igv.feature.Locus locus = new Locus(chr, start, end);
f.jumpTo(locus);
} catch (NumberFormatException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings |
// File Templates.
}
}
}
}
if (reorderedFrames.size() > 0) {
FrameManager.setFrames(reorderedFrames);
}
}
IGV.getInstance().resetFrames();
}