Package org.snpeff.interval
Enum Class FrameType
- All Implemented Interfaces:
Serializable
,Comparable<FrameType>
,Constable
Type of frame calculations
Internally, we use GFF style frame calculation for Exon / Transcript
Technically, these are 'frame' and 'phase' which are calculated in different ways
UCSC type: Indicated the coding base number modulo 3. This is the 'classical' definition of frame.
GFF/GTF type: Indicates the number of bases that should be removed from the beginning
of this feature to reach the first base of the next codon.
0) indicates that the feature begins with a whole codon at the 5' most base.
1) means that there is one extra base (the third base of a codon) before the first whole codon and
2) means that there are two extra bases (the second and third bases of the codon) before the first codon
Sometimes this is called 'phase' instead of frame, to distinguish form
the previous definition.
Valid numbers are {-1, 0, 1, 2}, where -1 indicates 'unknown'
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum Constants -
Method Summary
Modifier and TypeMethodDescriptionint
convertFrame
(int frame) int
frameFromLength
(int length) Calculate frame from cds lengthstatic FrameType
Returns the enum constant of this class with the specified name.static FrameType[]
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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GFF
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UCSC
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PHASE
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FRAME
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UNKNOWN
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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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convertFrame
public int convertFrame(int frame) -
frameFromLength
public int frameFromLength(int length) Calculate frame from cds length
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