/**
* Return the query, resulting array may contain rubbish entries at the end. Assumes the caller
* knows what it is doing!
*
* @param id read id
* @param frame read frame
* @return amino acid sequence
* @exception IOException if an I/O error occurs.
*/
byte[] query(final int id, final int frame) throws IOException {
if (mQueryReader == null) {
return EMPTY;
} else if (mQueryReader.type() == SequenceType.DNA) {
// In this situation, use precomputed array to store intermediate nt version
final int length = mQueryReader.read(id, mWorkSpace);
// Convert to protein in situ
final Frame frames = ProteinOutputProcessor.FRAMES_MAPPING[frame + 3];
final int limit = (length - Math.abs(frame) + 1) / 3;
for (int j = 0, i = 0; j < limit; j++, i += 3) {
mWorkSpaceProtein[j] = frames.code(mWorkSpace, length, i);
}
return mWorkSpaceProtein;
} else {
return mQueryReader.read(id);
}
}
byte[] template(final int id) throws IOException {
if (id != mCachedTemplateId) {
if (mTemplateReader == null) {
mCachedTemplate = EMPTY;
} else {
mCachedTemplate = mTemplateReader.read(id);
}
mCachedTemplateId = id;
}
return mCachedTemplate;
}