DefaultReadMaskFactory.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.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.regex.Pattern;

public class DefaultReadMaskFactory implements ReadMaskFactory<String> {

	private static ReadMaskFactory<String> detectReadMaskFormat(InputStream is) throws IOException {
		BufferedReader bis = new BufferedReader(new InputStreamReader(is));
		String line = null;

		Pattern intMaskPattern = Pattern.compile("^[0-9\\s]+$");
		Pattern fastaMaskPattern = Pattern.compile("^[" + FastaByteArrayMaskFactory.DEFAULT_MASK_BYTE
				+ FastaByteArrayMaskFactory.DEFAULT_NON_MASK_BYTE + "]+$");
		while ((line = bis.readLine()) != null) {
			if (line.length() == 0)
				continue;
			boolean intFormatMatches = intMaskPattern.matcher(line).matches();
			boolean fastaFormatMatches = fastaMaskPattern.matcher(line).matches();

			if (intFormatMatches && fastaFormatMatches)
				continue;

			if (intFormatMatches)
				return new IntegerListMaskFactory();

			return new FastaByteArrayMaskFactory();
		}
		return null;
	}

	@Override
	public PositionMask createMask(String line) throws ReadMaskFormatException {
		return null;
	}

}