htsjdk.samtools.cram.ref

Class ReferenceContext

java.lang.Object

htsjdk.samtools.cram.ref.ReferenceContext

All Implemented Interfaces:

java.lang.Comparable<ReferenceContext>

public class ReferenceContext
extends java.lang.Object
implements java.lang.Comparable<ReferenceContext>

ReferenceContext defines how a given Slice or Container relates to a reference sequence. There are 3 types of reference context: single-reference context, which is backed by an accompanying reference sequence ID, UNMAPPED_UNPLACED_ID/ReferenceContextType.UNMAPPED_UNPLACED_TYPE which indicates an unmapped/unplaced context, and MULTIPLE_REFERENCE_ID/ReferenceContextType.MULTIPLE_REFERENCE_TYPE) which indicates a multiple reference context.

Field Summary

Fields

Modifier and Type	Field and Description
static ReferenceContext	MULTIPLE_REFERENCE_CONTEXT
static int	MULTIPLE_REFERENCE_ID
static int	UNINITIALIZED_REFERENCE_ID
static ReferenceContext	UNMAPPED_UNPLACED_CONTEXT
static int	UNMAPPED_UNPLACED_ID

Constructor Summary

Constructors

Constructor and Description
ReferenceContext(int referenceContextID) Create a ReferenceContext from a value that is either a valid sequence ID, or a reference context sentinel value: 0 or greater for single reference -1 for unmapped-unplaced -2 for multiple reference

Method Summary

Modifier and Type	Method and Description
int	compareTo(ReferenceContext o)
boolean	equals(java.lang.Object o)
int	getReferenceContextID() Get the ReferenceContext sequence ID, or, for unmapped or multiple context, a sentinel value suitable for serialization: 0 or greater for single reference -1 for unmapped -2 for multiple reference
int	getReferenceSequenceID() Get the valid reference sequence ID.
ReferenceContextType	getType() Get the ReferenceContext type: SINGLE_REFERENCE_TYPE, UNMAPPED_UNPLACED_TYPE, or MULTIPLE_REFERENCE_TYPE
int	hashCode()
boolean	isMappedSingleRef() Determine if this ReferenceContext represents a single reference.
boolean	isMultiRef() Determine if this ReferenceContext represents: - reads placed on multiple references - or a combination of placed and unplaced reads?
boolean	isUnmappedUnplaced() Determine if this ReferenceContext represents unmapped-unplaced ?
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

UNMAPPED_UNPLACED_ID

public static final int UNMAPPED_UNPLACED_ID

See Also:

Constant Field Values

MULTIPLE_REFERENCE_ID

public static final int MULTIPLE_REFERENCE_ID

See Also:

Constant Field Values

UNINITIALIZED_REFERENCE_ID

public static final int UNINITIALIZED_REFERENCE_ID

See Also:

Constant Field Values

MULTIPLE_REFERENCE_CONTEXT

public static final ReferenceContext MULTIPLE_REFERENCE_CONTEXT

UNMAPPED_UNPLACED_CONTEXT

public static final ReferenceContext UNMAPPED_UNPLACED_CONTEXT

Constructor Detail

ReferenceContext

public ReferenceContext(int referenceContextID)

Create a ReferenceContext from a value that is either a valid sequence ID, or a reference context sentinel value: 0 or greater for single reference -1 for unmapped-unplaced -2 for multiple reference

Parameters:

referenceContextID - the sequence ID or sentinel value for constructing this ReferenceContext

Method Detail

getType

public ReferenceContextType getType()

Get the ReferenceContext type: SINGLE_REFERENCE_TYPE, UNMAPPED_UNPLACED_TYPE, or MULTIPLE_REFERENCE_TYPE

Returns:

the ReferenceContextType enum

getReferenceContextID

public int getReferenceContextID()

Get the ReferenceContext sequence ID, or, for unmapped or multiple context, a sentinel value suitable for serialization: 0 or greater for single reference -1 for unmapped -2 for multiple reference

Returns:

the sequence ID

getReferenceSequenceID

public int getReferenceSequenceID()

Get the valid reference sequence ID. May only be called if this is reference context of type single-reference (other reference context types don't have a valid sequence ID), otherwise see getReferenceContextID().

Returns:

the sequence ID for this reference context

Throws:

CRAMException - if this is not a single-ref reference context

isUnmappedUnplaced

public boolean isUnmappedUnplaced()

Determine if this ReferenceContext represents unmapped-unplaced ?

Returns:

true if the ReferenceContext is ReferenceContextTypeUNMAPPED_UNPLACED_TYPE.

isMultiRef

public boolean isMultiRef()

Determine if this ReferenceContext represents: - reads placed on multiple references - or a combination of placed and unplaced reads?

Returns:

true if the ReferenceContext is

isMappedSingleRef

public boolean isMappedSingleRef()

Determine if this ReferenceContext represents a single reference.

Returns:

true if this ReferenceContext represents

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

compareTo

public int compareTo(ReferenceContext o)

Specified by:

compareTo in interface java.lang.Comparable<ReferenceContext>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object