BoundSAMRecordIterator.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.select;


import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;

class BoundSAMRecordIterator implements SAMRecordIterator {
	private SAMRecordIterator delegate;
	private long firstRecord = 0, lastRecord = Long.MAX_VALUE;
	private long counter = 0;

	public BoundSAMRecordIterator(SAMRecordIterator delegate, long firstRecord, long lastRecord) {
		this.delegate = delegate;
		this.firstRecord = firstRecord;
		this.lastRecord = lastRecord;
	}

	@Override
	public void close() {
		delegate.close();
	}

	@Override
	public boolean hasNext() {
		while (delegate.hasNext() && counter < firstRecord) {
			next();
		}
		return counter < lastRecord && delegate.hasNext();
	}

	@Override
	public SAMRecord next() {
		counter++;
		return delegate.next();
	}

	@Override
	public void remove() {
		delegate.remove();
	}

	@Override
	public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) {
		return delegate.assertSorted(sortOrder);
	}

}