ArrayPositionMask.java

/*******************************************************************************
 * Copyright 2013 EMBL-EBI
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 ******************************************************************************/
package net.sf.cram.mask;

import java.util.Arrays;

public class ArrayPositionMask implements PositionMask {
	private int[] array;

	public ArrayPositionMask(int[] array) {
		if (array == null)
			throw new NullPointerException("Expecting a non-null array.");
		this.array = array;
		Arrays.sort(array);
	}

	@Override
	public boolean isMasked(int position) {
		return Arrays.binarySearch(array, position) > -1;
	}

	@Override
	public int[] getMaskedPositions() {
		return array;
	}

	@Override
	public boolean isEmpty() {
		return array.length == 0;
	}

	@Override
	public int getMaskedCount() {
		return array.length;
	}

	@Override
	public int getMinMaskedPosition() {
		return array.length > 0 ? array[0] : -1;
	}

	@Override
	public int getMaxMaskedPosition() {
		return array.length > 0 ? array[array.length - 1] : -1;
	}

	public static final PositionMask EMPTY_INSTANCE = new ArrayPositionMask(new int[] {});

	@Override
	public byte[] toByteArrayUsing(byte mask, byte nonMask) {
		byte[] ba = new byte[array[array.length - 1]];
		Arrays.fill(ba, nonMask);
		for (int pos : array)
			ba[pos - 1] = mask;

		return ba;
	}
}