IntegerListMaskFactory.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 IntegerListMaskFactory implements ReadMaskFactory<String> {
	public static final String DEFAULT_DEMLIITER = " ";
	public static final int DEFAULT_BUFFER_SIZE = 1024;

	private String delimiter;
	private IntBuffer buf;

	public IntegerListMaskFactory(String delimiter, int bufSize) {
		if (delimiter == null)
			throw new NullPointerException("Delimiter is null.");
		if (bufSize < 1)
			throw new IllegalAccessError("Buffer size must be greater then 0.");

		this.delimiter = delimiter;
		this.buf = IntBuffer.allocate(bufSize);
	}

	public IntegerListMaskFactory(String delimiter) {
		this(delimiter, DEFAULT_BUFFER_SIZE);
	}

	public IntegerListMaskFactory() {
		this(DEFAULT_DEMLIITER, DEFAULT_BUFFER_SIZE);
	}

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

		buf.clear();
		try {
			for (String chunk : line.split(delimiter))
				buf.put(Integer.valueOf(chunk));
		} catch (NumberFormatException e) {
			throw new ReadMaskFormatException(
					"Expecting integers in " + line.substring(0, Math.min(10, line.length())), e);
		}
		buf.flip();
		int[] array = new int[buf.limit()];
		buf.get(array);
		PositionMask mask = new ArrayPositionMask(array);

		return mask;
	}

}