java.lang.Object
- htsjdk.samtools.cram.ref.ReferenceContext

All Implemented Interfaces:

Comparable<ReferenceContext>
```
public class ReferenceContext
extends Object
implements 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	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	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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`compareTo(ReferenceContext o)`
`boolean`	`equals(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 ?
`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 refernce 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(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - compareTo
```
public int compareTo(ReferenceContext o)
```
    Specified by:
    
    compareTo in interface Comparable<ReferenceContext>
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class ReferenceContext

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

UNMAPPED_UNPLACED_ID

MULTIPLE_REFERENCE_ID

UNINITIALIZED_REFERENCE_ID

MULTIPLE_REFERENCE_CONTEXT

UNMAPPED_UNPLACED_CONTEXT

Constructor Detail

ReferenceContext

Method Detail

getType

getReferenceContextID

getReferenceSequenceID

isUnmappedUnplaced

isMultiRef

isMappedSingleRef

equals

hashCode

compareTo

toString