Enum FrameType

  • 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'
    • 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 length
      static 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.
      • Methods inherited from class java.lang.Enum

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

        getClass, notify, notifyAll, wait, wait, wait
    • Method Detail

      • 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
      • 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 name
        java.lang.NullPointerException - if the argument is null
      • convertFrame

        public int convertFrame​(int frame)
      • frameFromLength

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