Enum Class FrameType

java.lang.Object
java.lang.Enum<FrameType>
org.snpeff.interval.FrameType
All Implemented Interfaces:
Serializable, Comparable<FrameType>, Constable

public enum FrameType extends 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'
  • Enum Constant Details

  • Method Details

    • values

      public static FrameType[] 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
    • valueOf

      public static FrameType valueOf(String name)
      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 name
      NullPointerException - if the argument is null
    • convertFrame

      public int convertFrame(int frame)
    • frameFromLength

      public int frameFromLength(int length)
      Calculate frame from cds length