/**
* Get the records representing the data to be displayed for the given range.
*
* @param ref e.g. "chr1"
* @param r the range of bases to be displayed
* @param ignored historical only; no longer used
* @return List of records to be displayed for the given range
* @throws IOException
*/
@Override
public List<GenericContinuousRecord> getRecords(
String ref, RangeAdapter r, Resolution ignored, RecordFilterAdapter filt) throws IOException {
List<GenericContinuousRecord> data = new ArrayList<GenericContinuousRecord>();
if (!savantFile.containsDataForReference(ref)) {
ref = MiscUtils.homogenizeSequence(ref);
if (!savantFile.containsDataForReference(ref)) {
return data;
}
}
Level lev = getBestLevel(refnameToLevelsIndex.get(ref), (Range) r);
LOG.debug(
"Chose "
+ lev.resolution
+ " as the best for range ("
+ r.getFrom()
+ "-"
+ r.getTo()
+ ")");
int rangeEnd = r.getTo() + 1;
long seekPos = lev.offset + (r.getFrom() - 1) / lev.resolution * recordSize;
if (savantFile.seek(ref, seekPos) >= 0) {
LOG.debug("Sought to " + seekPos + " to find data for " + r.getFrom());
for (int pos = r.getFrom(); pos <= rangeEnd; pos += lev.resolution) {
data.add(GenericContinuousRecord.valueOf(ref, pos, savantFile.readFloat()));
if (savantFile.getFilePointer()
>= savantFile.getHeaderOffset()
+ savantFile.getReferenceOffset(ref)
+ lev.offset
+ lev.size) {
// We've read all the data available for this level. The rest of the
// range will have no data.
LOG.debug(
"File position "
+ savantFile.getFilePointer()
+ " was past end of level ("
+ (savantFile.getHeaderOffset()
+ savantFile.getReferenceOffset(ref)
+ lev.offset
+ lev.size)
+ ").");
break;
}
}
}
return data;
}
@Override
public void close() {
try {
if (savantFile != null) savantFile.close();
} catch (IOException ignore) {
}
}
@Override
public URI getURI() {
return savantFile.getURI();
}
@Override
public Set<String> getReferenceNames() {
return savantFile.getReferenceMap().keySet();
}
