htsjdk.samtools.CigarElement Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import java.io.Serializable;
/**
* One component of a cigar string. The component comprises the operator, and the number of bases to which
* the operator applies.
*/
public class CigarElement implements Serializable {
public static final long serialVersionUID = 1L;
private final int length;
private final CigarOperator operator;
public CigarElement(final int length, final CigarOperator operator) {
if (length < 0) throw new IllegalArgumentException(String.format("Cigar element being constructed with negative length: %d and operation: %s" , length, operator.name()));
this.length = length;
this.operator = operator;
}
public int getLength() {
return length;
}
public CigarOperator getOperator() {
return operator;
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (!(o instanceof CigarElement)) return false;
final CigarElement that = (CigarElement) o;
if (length != that.length) return false;
if (operator != that.operator) return false;
return true;
}
@Override
public int hashCode() {
int result = length;
result = 31 * result + (operator != null ? operator.hashCode() : 0);
return result;
}
@Override
public String toString() {
return String.valueOf(this.length)+this.operator;
}
}