htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore 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;
import java.util.Objects;
/**
* A read feature representing a single quality score in a read.
*/
public class BaseQualityScore implements Serializable, ReadFeature {
private int position;
private byte qualityScore;
public static final byte operator = 'Q';
public BaseQualityScore(final int position, final byte qualityScore) {
this.position = position;
this.qualityScore = qualityScore;
}
@Override
public byte getOperator() {
return operator;
}
@Override
public int getPosition() {
return position;
}
@Override
public void setPosition(final int position) {
this.position = position;
}
public byte getQualityScore() {
return qualityScore;
}
public void setQualityScore(final byte qualityScore) {
this.qualityScore = qualityScore;
}
@Override
public String toString() {
return new StringBuilder().append((char) operator).append('@')
.append(position).append('#').appendCodePoint(qualityScore).toString();
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
BaseQualityScore that = (BaseQualityScore) o;
return position == that.position &&
qualityScore == that.qualityScore;
}
@Override
public int hashCode() {
return Objects.hash(position, qualityScore);
}
}