FastaByteArrayMaskFactory.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.nio.IntBuffer;

public class FastaByteArrayMaskFactory implements ReadMaskFactory<String> {
	public static final byte DEFAULT_MASK_BYTE = 'x';
	public static final byte DEFAULT_NON_MASK_BYTE = '_';
	public static final int DEFAULT_BUFFER_SIZE = 1024;

	private byte maskByte;
	private IntBuffer buf;

	public FastaByteArrayMaskFactory(byte maskByte, int bufSize) {
		this.maskByte = maskByte;
		this.buf = IntBuffer.allocate(bufSize);
	}

	public FastaByteArrayMaskFactory(byte maskByte) {
		this(maskByte, DEFAULT_BUFFER_SIZE);
	}

	public FastaByteArrayMaskFactory() {
		this(DEFAULT_MASK_BYTE, DEFAULT_BUFFER_SIZE);
	}

	@Override
	public PositionMask createMask(String line) throws ReadMaskFormatException {
		if (line.length() == 0)
			return ArrayPositionMask.EMPTY_INSTANCE;

		byte[] data = line.getBytes();

		buf.clear();
		for (int i = 0; i < data.length; i++)
			if (data[i] == maskByte)
				buf.put(i + 1);
			else if (data[i] == '\n')
				throw new ReadMaskFormatException("New line not allowed inside of mask line: "
						+ line.substring(0, Math.min(10, line.length())));

		buf.flip();
		int[] array = new int[buf.limit()];
		buf.get(array);

		return new ArrayPositionMask(array);
	}
}