htsjdk.samtools.cram.encoding.readfeatures.RefSkip Maven / Gradle / Ivy
/**
* ****************************************************************************
* 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 htsjdk.samtools.cram.encoding.readfeatures;
import java.io.Serializable;
/**
* A read feature representing a reference skip similar to {@link htsjdk.samtools.CigarOperator#N}.
*/
public class RefSkip implements Serializable, ReadFeature {
private int position;
private int length;
public static final byte operator = 'N';
public RefSkip() {
}
public RefSkip(final int position, final int length) {
this.position = position;
this.length = length;
}
@Override
public byte getOperator() {
return operator;
}
@Override
public int getPosition() {
return position;
}
@Override
public void setPosition(final int position) {
this.position = position;
}
public int getLength() {
return length;
}
public void setLength(final int length) {
this.length = length;
}
@Override
public boolean equals(final Object obj) {
if (!(obj instanceof RefSkip))
return false;
final RefSkip refSkip = (RefSkip) obj;
return position == refSkip.position && length == refSkip.length;
}
@Override
public String toString() {
return String.valueOf((char) operator) + '@' + position + '+' + length;
}
}