@Override
protected Index doInBackground() throws Exception {
int binSize = IgvTools.LINEAR_BIN_SIZE;
FeatureCodec codec =
CodecFactory.getCodec(
file.getAbsolutePath(), GenomeManager.getInstance().getCurrentGenome());
if (codec != null) {
try {
Index index = IndexFactory.createLinearIndex(file, codec, binSize);
if (index != null) {
IgvTools.writeTribbleIndex(index, idxFile.getAbsolutePath());
}
return index;
} catch (TribbleException.MalformedFeatureFile e) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Files must be sorted by start position prior to indexing.<br>");
buf.append(e.getMessage());
buf.append(
"<br><br>Note: igvtools can be used to sort the file, select \"File > Run igvtools...\".");
MessageUtils.showMessage(buf.toString());
}
} else {
throw new DataLoadException("Unknown File Type", file.getAbsolutePath());
}
return null;
}
public Object getIndex() {
if (worker == null || !worker.isDone()) {
return null;
} else {
try {
return worker.get();
} catch (Exception ex) {
MessageUtils.showMessage(ex.getMessage());
}
return null;
}
}
private void notifyGenomesAddedRemoved(List<GenomeListItem> selectedValues, boolean added) {
if (selectedValues == null || selectedValues.size() == 0) return;
int size = selectedValues.size();
String msg = "";
if (size == 1) {
msg += selectedValues.get(0) + " genome";
} else {
msg += size + " genomes";
}
if (added) {
msg += " added to";
} else {
msg += " removed from";
}
msg += " list";
MessageUtils.setStatusBarMessage(msg);
}
