Package htsjdk.samtools

Class SAMBinaryTagAndValue

java.lang.Object

htsjdk.samtools.SAMBinaryTagAndValue

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

SAMBinaryTagAndUnsignedArrayValue

public class SAMBinaryTagAndValue
extends Object
implements Serializable

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 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].

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected SAMBinaryTagAndValue	next
static final long	serialVersionUID
final short	tag
final Object	value

Constructor Summary

Constructors

Constructor	Description
SAMBinaryTagAndValue(short tag, Object value)

Method Summary

Modifier and Type	Method	Description
protected Object	cloneValue()
SAMBinaryTagAndValue	copy()	Creates and returns a shallow copy of the list of tag/values.
SAMBinaryTagAndValue	deepCopy()	Creates and returns a deep copy of the list of tag/values.
boolean	equals(Object o)
SAMBinaryTagAndValue	find(short tag)	Returns the SAMBinaryTagAndValue that contains the required tag, or null if not contained.
SAMBinaryTagAndValue	getNext()
int	hashCode()
SAMBinaryTagAndValue	insert(SAMBinaryTagAndValue attr)	Inserts an item into the ordered list of attributes and returns the head of the list/sub-list
protected static boolean	isAllowedAttributeValue(Object value)
boolean	isUnsignedArray()
SAMBinaryTagAndValue	remove(short tag)	Removes a tag from the list and returns the new head of the list/sub-list.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Details

serialVersionUID

public static final long serialVersionUID

See Also:

• Constant Field Values

tag

public final short tag

value

public final Object value

next

protected SAMBinaryTagAndValue next

Constructor Details

SAMBinaryTagAndValue

public SAMBinaryTagAndValue(short tag,
 Object value)

Parameters:

tag - tagname (in binary form) for this attribute

value - value for this attribute (must be of a type that implements Serializable or else serialization will fail). Cannot be null.

Method Details

isAllowedAttributeValue

protected static boolean isAllowedAttributeValue(Object value)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

copy

public SAMBinaryTagAndValue copy()

Creates and returns a shallow copy of the list of tag/values.

deepCopy

public SAMBinaryTagAndValue deepCopy()

Creates and returns a deep copy of the list of tag/values.

cloneValue

protected Object cloneValue()

getNext

public SAMBinaryTagAndValue getNext()

insert

public SAMBinaryTagAndValue insert(SAMBinaryTagAndValue attr)

Inserts an item into the ordered list of attributes and returns the head of the list/sub-list

remove

public SAMBinaryTagAndValue remove(short tag)

Removes a tag from the list and returns the new head of the list/sub-list.

find

public SAMBinaryTagAndValue find(short tag)

Returns the SAMBinaryTagAndValue that contains the required tag, or null if not contained.

isUnsignedArray

public boolean isUnsignedArray()