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/*
* 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;
import java.util.Arrays;
/**
* 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.
*
* Values associated with attribute tags must be of a type that implements {@link Serializable} or else
* serialization will fail. Accepted types are String, scalar types Short, Integer, Character, Float,
* and Long (see below); array types byte[], short[], int[] and float[]. Cannot be null.
*
* Long valued attributes are constrained to the range [Integer.MIN_VALUE, BinaryCodec.MAX_UINT],
* which includes the entire range of signed ints [Integer.MIN_VALUE, Integer.MAX_VALUE] and
* the entire range of unsigned ints that can be stored per the BAM spec [0, (Integer.MAX_VALUE * 2) + 1].
*
* @author [email protected]
*/
public class SAMBinaryTagAndValue implements Serializable {
public static final long serialVersionUID = 1L;
public final short tag;
public final Object value;
protected SAMBinaryTagAndValue next = null;
/**
* @param tag tagname (in binary form) for this attribute
* @param value value for this attribute (must be of a type that implements {@link Serializable}
* or else serialization will fail). Cannot be null.
*/
public SAMBinaryTagAndValue(final short tag, final Object value) {
if (null == value) {
throw new IllegalArgumentException("SAMBinaryTagAndValue value may not be null");
}
if (!isAllowedAttributeValue(value)) {
throw new IllegalArgumentException("Attribute type " + value.getClass() + " not supported. Tag: " +
SAMTag.makeStringTag(tag));
}
this.tag = tag;
this.value = value;
}
// Inspect the proposed value to determine if it is an allowed value type,
// and if the value is in range.
protected static boolean isAllowedAttributeValue(final Object value) {
if (value instanceof Byte ||
value instanceof Short ||
value instanceof Integer ||
value instanceof String ||
value instanceof Character ||
value instanceof Float ||
value instanceof byte[] ||
value instanceof short[] ||
value instanceof int[] ||
value instanceof float[]) {
return true;
}
// A special case for Longs: we require Long values to fit into either a uint32_t or an int32_t,
// as that is what the BAM spec allows.
if (value instanceof Long) {
return SAMUtils.isValidUnsignedIntegerAttribute((Long) value)
|| ((Long) value >= Integer.MIN_VALUE && (Long) value <= Integer.MAX_VALUE);
}
return false;
}
@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.valueEquals(that)) {
if (this.next == null) return that.next == null;
else return this.next.equals(that.next);
}
else {
return false;
}
}
private boolean valueEquals(SAMBinaryTagAndValue that) {
if (this.value instanceof byte[]) {
return that.value instanceof byte[] ?
Arrays.equals((byte[])this.value, (byte[])that.value) : false;
}
else if (this.value instanceof short[]) {
return that.value instanceof short[] ?
Arrays.equals((short[])this.value, (short[])that.value) : false;
}
else if (this.value instanceof int[]) {
return that.value instanceof int[] ?
Arrays.equals((int[])this.value, (int[])that.value) : false;
}
else if (this.value instanceof float[]) {
return that.value instanceof float[] ?
Arrays.equals((float[])this.value, (float[])that.value) : false;
}
else {
// otherwise, the api limits the remaining possible value types to
// immutable (String or boxed primitive) types
return this.value.equals(that.value);
}
}
@Override
public int hashCode() {
int valueHash;
if (this.value instanceof byte[]) {
valueHash = Arrays.hashCode((byte[])this.value);
}
else if (this.value instanceof short[]) {
valueHash = Arrays.hashCode((short[])this.value);
}
else if (this.value instanceof int[]) {
valueHash = Arrays.hashCode((int[])this.value);
}
else if (this.value instanceof float[]) {
valueHash = Arrays.hashCode((float[])this.value);
}
else {
// otherwise, the api limits the remaining possible value types to
// immutable (String or boxed primitive) types
valueHash = value.hashCode();
}
return 31 * tag + valueHash;
}
/** Creates and returns a shallow 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;
}
/** Creates and returns a deep copy of the list of tag/values. */
public SAMBinaryTagAndValue deepCopy() {
final SAMBinaryTagAndValue retval = new SAMBinaryTagAndValue(this.tag, cloneValue());
if (next != null) {
retval.next = next.deepCopy();
}
return retval;
}
/* Create and return a clone of value object */
protected Object cloneValue() {
Object valueClone;
if (value instanceof byte[]) {
valueClone = ((byte[]) value).clone();
}
else if (value instanceof short[]) {
valueClone = ((short[]) value).clone();
}
else if (value instanceof int[]) {
valueClone = ((int[]) value).clone();
}
else if (value instanceof float[]) {
valueClone = ((float[]) value).clone();
}
else {
// otherwise, the api limits the remaining possible value types to
// immutable (String or boxed primitive) types
valueClone = value;
}
return valueClone;
}
// The methods below are for implementing a light-weight, single-direction linked list
public SAMBinaryTagAndValue getNext() { return this.next; }
/** Inserts an 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;
}
}
