de.jstacs.motifDiscovery
Enum SignificantMotifOccurrencesFinder.RandomSeqType

java.lang.Object
  java.lang.Enum<SignificantMotifOccurrencesFinder.RandomSeqType>
      de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder.RandomSeqType

All Implemented Interfaces:

Serializable, Comparable<SignificantMotifOccurrencesFinder.RandomSeqType>

Enclosing class:

SignificantMotifOccurrencesFinder

public static enum SignificantMotifOccurrencesFinder.RandomSeqType
extends Enum<SignificantMotifOccurrencesFinder.RandomSeqType>

Author:

Jan Grau, Jens Keilwagen

Enum Constant Summary

BACKGROUND
A enum constant that indicates to use the a background set to determine the significance level.

hMM0
A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 0 to determine the significance level.

hMM1
A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 1 to determine the significance level.

hMM2
A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 3 to determine the significance level.

hMM3
A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 3 to determine the significance level.

hMM4
A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 4 to determine the significance level.

hMM5
A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 5 to determine the significance level.

PERMUTED
A enum constant that indicates to use permuted instances of the sequence to determine the significance level.

Method Summary

int	getOrder() This method returns the Markov order.
static SignificantMotifOccurrencesFinder.RandomSeqType	valueOf(String name) Returns the enum constant of this type with the specified name.
static SignificantMotifOccurrencesFinder.RandomSeqType[]	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

Enum Constant Detail

BACKGROUND

public static final SignificantMotifOccurrencesFinder.RandomSeqType BACKGROUND

A enum constant that indicates to use the a background set to determine the significance level.

PERMUTED

public static final SignificantMotifOccurrencesFinder.RandomSeqType PERMUTED

A enum constant that indicates to use permuted instances of the sequence to determine the significance level.

hMM0

public static final SignificantMotifOccurrencesFinder.RandomSeqType hMM0

A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 0 to determine the significance level.

hMM1

public static final SignificantMotifOccurrencesFinder.RandomSeqType hMM1

A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 1 to determine the significance level.

hMM2

public static final SignificantMotifOccurrencesFinder.RandomSeqType hMM2

A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 3 to determine the significance level.

hMM3

public static final SignificantMotifOccurrencesFinder.RandomSeqType hMM3

A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 3 to determine the significance level.

hMM4

public static final SignificantMotifOccurrencesFinder.RandomSeqType hMM4

A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 4 to determine the significance level.

hMM5

public static final SignificantMotifOccurrencesFinder.RandomSeqType hMM5

A enum constant that indicates to use sequences drawn from a homogeneous Markov model of order 5 to determine the significance level.

Method Detail

values

public static SignificantMotifOccurrencesFinder.RandomSeqType[] 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 (SignificantMotifOccurrencesFinder.RandomSeqType c : SignificantMotifOccurrencesFinder.RandomSeqType.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static SignificantMotifOccurrencesFinder.RandomSeqType 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

getOrder

public int getOrder()

This method returns the Markov order.

Returns:

the Markov order