Package org.snpeff.interval
Enum FrameType
- java.lang.Object
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- java.lang.Enum<FrameType>
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- org.snpeff.interval.FrameType
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Comparable<FrameType>
public enum FrameType extends java.lang.Enum<FrameType>
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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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
convertFrame(int frame)
int
frameFromLength(int length)
Calculate frame from cds lengthstatic FrameType
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static FrameType[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Method Detail
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values
public static FrameType[] 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 (FrameType c : FrameType.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static FrameType valueOf(java.lang.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:
java.lang.IllegalArgumentException
- if this enum type has no constant with the specified namejava.lang.NullPointerException
- if the argument is null
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convertFrame
public int convertFrame(int frame)
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frameFromLength
public int frameFromLength(int length)
Calculate frame from cds length
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