Enum IntensityTransform

    • Enum Constant Detail

      • NONE

        public static final IntensityTransform NONE
        No transformation has been applied to the spot intensities.
      • LOG2

        public static final IntensityTransform LOG2
        Spot intensities are stored as base-2 logged values
      • LOG10

        public static final IntensityTransform LOG10
        Spot intensities are stored as base-10 logged values
    • Field Detail

      • LN2

        private static final double LN2
      • value

        private final int value
        The integer value of this transform.
      • displayValue

        private final String displayValue
        Returned by the toString method.
      • isTransformed

        private final boolean isTransformed
        If the intensities are transformed or not.
    • Constructor Detail

      • IntensityTransform

        private IntensityTransform​(int value,
                                   String displayValue,
                                   boolean isTransformed,
                                   Formula.AverageMethod averageMethod)
        Creates a new intensity transform. Used internal only.
        Parameters:
        value - The integer value of this location.
    • Method Detail

      • values

        public static IntensityTransform[] 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 (IntensityTransform c : IntensityTransform.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static IntensityTransform valueOf​(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:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null
      • fromValue

        public static IntensityTransform fromValue​(int value)
        Get the SpotDataTransform object when you know the integer code.
        Parameters:
        value - The integer value.
        Returns:
        The transform for the integer value.
      • getValue

        public int getValue()
        Get the integer value that is used when storing a transform in the database.
        Returns:
        The integer value for this transform
      • isTransformed

        public boolean isTransformed()
        Does this intensity transformation represents a transformation that has modified the spot intensity values or not?
        Returns:
        TRUE if the intensity values are transformed, FALSE if they are not
      • getAverageMethod

        public Formula.AverageMethod getAverageMethod()
        Get the averaging method to use when averaging values that has been transformed with the specified transformation.
        Returns:
        An average method
      • unTransform

        public abstract Expression unTransform​(Expression transformed)
        Un-transform an expression representing a transformed intensity value so that it represents a raw intensity value. This method may return the same expression if no transformation is needed.
        Parameters:
        transformed - The transformed expression
      • unTransform

        public abstract double unTransform​(double transformed)
        Un-transform a transformed intensity value back to a regular intensity value.
        Parameters:
        transformed - The transformed value
      • transform

        public abstract Expression transform​(Expression e)
        Transform an expression representing a "normal" intensity value so that it represents the transformed intensity value. This method may return the same expression if no transformation is needed.
        Parameters:
        e - The regular expression
        Since:
        3.2.4
      • transform

        public abstract double transform​(double value)
        Transform a "normal" intensity value to the transformed value.
        Parameters:
        value - The regular value
        Since:
        3.2.4
      • getMACalculator

        public abstract MACalculator getMACalculator()
        Get a MA calculator implementation that is suitable for calculating MA-values for the given source data type.
        Since:
        3.2.4