@Override public void size(final int size) { list.size(size); } @Override
@Override public long size64() { return list.size(); } @Override
@Override public void size(final int size) { synchronized (sync) { list.size(size); } } @Override
@Override public void size(final long size) { list.size(intIndex(size)); } @Override
@Override public boolean addAll(final int index, final ByteList l) { ensureIndex(index); final int n = l.size(); if (n == 0) return false; grow(size + n); if (index != size) System.arraycopy(a, index, a, index + n, size - index); l.getElements(0, a, index, n); size += n; assert size <= a.length; return true; } @Override
/** * Shuffles the specified list using the specified pseudorandom number * generator. * * @param l * the list to be shuffled. * @param random * a pseudorandom number generator. * @return {@code l}. */ public static ByteList shuffle(final ByteList l, final Random random) { for (int i = l.size(); i-- != 0;) { final int p = random.nextInt(i + 1); final byte t = l.getByte(i); l.set(i, l.getByte(p)); l.set(p, t); } return l; } /**
int deletionPosition = var.getPosition() - 1; leftBases = leftBases.subList(0, deletionPosition); rightBases = rightBases.subList(deletionPosition, rightBases.size()); rightScores = rightScores.subList(deletionPosition, rightScores.size()); leftBases.toByteArray(new byte[leftBases.size()]), leftScores.toByteArray(new byte[leftScores.size()])); AlignmentBlock right = new AlignmentBlockImpl(block.getStart() + leftBases.size() + var.getFrom().length(), rightBases.toByteArray(new byte[rightBases.size()]), rightScores.toByteArray(new byte[rightScores.size()]));