/*
* 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;
/**
* Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
* SAMRecord stores tag name and value in this form, because much String creation is avoided this way.
* See SAMTagUtil to convert the tag to String form.
*
* @author alecw@broadinstitute.org
*/
public class SAMBinaryTagAndValue {
public final short tag;
public final Object value;
protected SAMBinaryTagAndValue next = null;
public SAMBinaryTagAndValue(final short tag, final Object value) {
this.tag = tag;
this.value = value;
}
@Override public boolean equals(final Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
return typeSafeEquals((SAMBinaryTagAndValue) o);
}
/** Type safe equals method that recurses down the list looking for equality. */
private boolean typeSafeEquals(final SAMBinaryTagAndValue that) {
if (this.tag != that.tag) return false;
if ((this.value == null) ? that.value == null : this.value.equals(that.value)) {
if (this.next == null) return that.next == null;
else return this.next.equals(that.next);
}
else {
return false;
}
}
@Override
public int hashCode() {
int result = (int) tag;
result = 31 * result + value.hashCode();
return result;
}
/** Creates and returns a deep copy of the list of tag/values. */
public SAMBinaryTagAndValue copy() {
final SAMBinaryTagAndValue retval = new SAMBinaryTagAndValue(this.tag, this.value);
if (next != null) retval.next = next.copy();
return retval;
}
// The methods below are for implementing a light-weight, single-direction linked list
public SAMBinaryTagAndValue getNext() { return this.next; }
/** Inserts at item into the ordered list of attributes and returns the head of the list/sub-list */
public SAMBinaryTagAndValue insert(final SAMBinaryTagAndValue attr) {
if (attr == null) return this;
if (attr.next != null) throw new IllegalStateException("Can only insert single tag/value combinations.");
if (attr.tag < this.tag) {
// attr joins the list ahead of this element
attr.next = this;
return attr;
}
else if (this.tag == attr.tag) {
// attr replaces this in the list
attr.next = this.next;
return attr;
}
else if (this.next == null) {
// attr gets stuck on the end
this.next = attr;
return this;
}
else {
// attr gets inserted somewhere in the tail
this.next = this.next.insert(attr);
return this;
}
}
/** Removes a tag from the list and returns the new head of the list/sub-list. */
public SAMBinaryTagAndValue remove(final short tag) {
if (this.tag == tag) return this.next;
else {
if (this.next != null) this.next = this.next.remove(tag);
return this;
}
}
/** Returns the SAMBinaryTagAndValue that contains the required tag, or null if not contained. */
public SAMBinaryTagAndValue find(final short tag) {
if (this.tag == tag) return this;
else if (this.tag > tag || this.next == null) return null;
else return this.next.find(tag);
}
public boolean isUnsignedArray() {
return false;
}
}