Transition (picard 2.18.2 API)

java.lang.Object
- java.lang.Enum<Transition>
- - picard.analysis.artifacts.Transition

All Implemented Interfaces:

Serializable, Comparable<Transition>
```
public enum Transition
extends Enum<Transition>
```
Enum representation of a transition from one base to any other.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

protected static class Transition.Base

Nested Classes
Modifier and Type	Class	Description
`protected static class`	`Transition.Base`

Enum Constant Summary

Enum Constants
Enum Constant	Description
`AtoA`
`AtoC`
`AtoG`
`AtoT`
`CtoA`
`CtoC`
`CtoG`
`CtoT`
`GtoA`
`GtoC`
`GtoG`
`GtoT`
`TtoA`
`TtoC`
`TtoG`
`TtoT`

Field Summary

Fields
Modifier and Type Field Description

protected static int[] baseIndexMap

Fields
Modifier and Type	Field	Description
`protected static int[]`	`baseIndexMap`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static Transition[]`	`altValues()`	Like values(), but ignores the ref:ref "transitions".
`char`	`call()`	Gets the call for the transition.
`Transition`	`complement()`	Return the complementary transition.
`char`	`ref()`	Gets the reference for the transition.
`String`	`toString()`
`static Transition`	`transitionOf(char ref, char call)`	Gets a the enum representing the transition from a 'reference' to a 'call' base.
`static Transition`	`valueOf(String name)`	Returns the enum constant of this type with the specified name.
`static Transition[]`	`values()`	Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, valueOf

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Enum Constant Detail
  - AtoA
```
public static final Transition AtoA
```
  - AtoC
```
public static final Transition AtoC
```
  - AtoG
```
public static final Transition AtoG
```
  - AtoT
```
public static final Transition AtoT
```
  - CtoA
```
public static final Transition CtoA
```
  - CtoC
```
public static final Transition CtoC
```
  - CtoG
```
public static final Transition CtoG
```
  - CtoT
```
public static final Transition CtoT
```
  - GtoA
```
public static final Transition GtoA
```
  - GtoC
```
public static final Transition GtoC
```
  - GtoG
```
public static final Transition GtoG
```
  - GtoT
```
public static final Transition GtoT
```
  - TtoA
```
public static final Transition TtoA
```
  - TtoC
```
public static final Transition TtoC
```
  - TtoG
```
public static final Transition TtoG
```
  - TtoT
```
public static final Transition TtoT
```
- Field Detail
  - baseIndexMap
```
protected static final int[] baseIndexMap
```
- Method Detail
  - values
```
public static Transition[] values()
```
    Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
```
for (Transition c : Transition.values())
    System.out.println(c);
```
    Returns:
    
    an array containing the constants of this enum type, in the order they are declared
  - valueOf
```
public static Transition valueOf(String name)
```
    Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
    
    Parameters:
    
    name - the name of the enum constant to be returned.
    
    Returns:
    
    the enum constant with the specified name
    
    Throws:
    
    IllegalArgumentException - if this enum type has no constant with the specified name
    
    NullPointerException - if the argument is null
  - transitionOf
```
public static Transition transitionOf(char ref,
                                      char call)
```
    Gets a the enum representing the transition from a 'reference' to a 'call' base.
    For example, a transtion from 'A' to 'T' would return AtoT.
    
    Parameters:
    
    ref - reference base (one of of {A, C, T, G}).
    
    call - call base (one of of {A, C, T, G}).
    
    Returns:
    
    enum representation for the transition.
  - altValues
```
public static Transition[] altValues()
```
    Like values(), but ignores the ref:ref "transitions".
  - complement
```
public Transition complement()
```
    Return the complementary transition. Both ref and call must be complemented.
  - ref
```
public char ref()
```
    Gets the reference for the transition.
  - call
```
public char call()
```
    Gets the call for the transition.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Enum<Transition>

Enum Transition

Nested Class Summary

Enum Constant Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

AtoA

AtoC

AtoG

AtoT

CtoA

CtoC

CtoG

CtoT

GtoA

GtoC

GtoG

GtoT

TtoA

TtoC

TtoG

TtoT

Field Detail

baseIndexMap

Method Detail

values

valueOf

transitionOf

altValues

complement

ref

call

toString