net.sf.basedb.core
Enum IntensityTransform

java.lang.Object
  java.lang.Enum<IntensityTransform>
      net.sf.basedb.core.IntensityTransform

All Implemented Interfaces:

Serializable, Comparable<IntensityTransform>

public enum IntensityTransform
extends Enum<IntensityTransform>

Gives information in what way spot intensities has been transformed before they were stored in the database.

Version:

2.12

Author:

Nicklas

Enum Constant Summary

LOG10
Spot intensities are stored as base-10 logged values

LOG2
Spot intensities are stored as base-2 logged values

NONE
No transformation has been applied to the spot intensities.

Field Summary

private Formula.AverageMethod	averageMethod
private String	displayValue Returned by the toString method.
private boolean	isTransformed If the intensities are transformed or not.
private int	value The integer value of this transform.
private static Map<Integer,IntensityTransform>	valueMapping Maps an integer to a transform.

Method Summary

static IntensityTransform	fromValue(int value) Get the SpotDataTransform object when you know the integer code.
Formula.AverageMethod	getAverageMethod() Get the averaging method to use when averaging values that has been transformed with the specified transformation.
int	getValue() Get the integer value that is used when storing a transform in the database.
boolean	isTransformed() Does this intensity transformation represents a transformation that has modified the spot intensity values or not?
String	toString()
abstract double	unTransform(double transformed) Un-transform a transformed intensity value back to a regular intensity value.
abstract Expression	unTransform(Expression transformed) Un-transform an expression representing a transformed intensity value so that it represents a raw intensity value.
static IntensityTransform	valueOf(String name) Returns the enum constant of this type with the specified name.
static IntensityTransform[]	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, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

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

valueMapping

private static final Map<Integer,IntensityTransform> valueMapping

Maps an integer to a transform.

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.

averageMethod

private final Formula.AverageMethod averageMethod

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

toString

public String toString()

Overrides:

toString in class Enum<IntensityTransform>

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