Package picard.analysis.artifacts
Enum Class Transition
- All Implemented Interfaces:
Serializable
,Comparable<Transition>
,Constable
Enum representation of a transition from one base to any other.
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Nested Class Summary
Nested ClassesNested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum Constants -
Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionstatic Transition[]
Like values(), but ignores the ref:ref "transitions".char
call()
Gets the call for the transition.Return the complementary transition.char
ref()
Gets the reference for the transition.toString()
static Transition
transitionOf
(char ref, char call) Gets a the enum representing the transition from a 'reference' to a 'call' base.static Transition
Returns the enum constant of this class with the specified name.static Transition[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.
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Enum Constant Details
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AtoA
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AtoC
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AtoG
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AtoT
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CtoA
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CtoC
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CtoG
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CtoT
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GtoA
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GtoC
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GtoG
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GtoT
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TtoA
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TtoC
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TtoG
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TtoT
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Field Details
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baseIndexMap
protected static final int[] baseIndexMap
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Method Details
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values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
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valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class has no constant with the specified nameNullPointerException
- if the argument is null
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transitionOf
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.
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altValues
Like values(), but ignores the ref:ref "transitions". -
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
- Overrides:
toString
in classEnum<Transition>
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