de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Enum HMMFactory.HMMType

java.lang.Object

java.lang.Enum<HMMFactory.HMMType>

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.HMMType

All Implemented Interfaces:

Serializable, Comparable<HMMFactory.HMMType>

Enclosing class:

HMMFactory

public static enum HMMFactory.HMMType
extends Enum<HMMFactory.HMMType>

This enum defines some standard architecture of profile HMMs.

Author:

Jan Grau, Jens Keilwagen

See Also:

HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet, HMMType, boolean, int, int, AlphabetContainer, double, boolean, boolean, double[][])

Enum Constant Summary

Enum Constants

Enum Constant and Description
PLAN7 The PLAN7 architecture without connections between delete and insert states
PLAN8D Architecture similar to PLAN7 but with connections from insert to delete states of the next layer
PLAN8I Architecture similar to PLAN7 but with connections from delete to insert states of the same layer
PLAN9 The PLAN9 architecture, where each state has transitions to the insert state of the same layer and the delete and match states of the next layer

Method Summary

Methods

Modifier and Type	Method and Description
static HMMFactory.HMMType	valueOf(String name) Returns the enum constant of this type with the specified name.
static HMMFactory.HMMType[]	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

PLAN7

public static final HMMFactory.HMMType PLAN7

The PLAN7 architecture without connections between delete and insert states

PLAN9

public static final HMMFactory.HMMType PLAN9

The PLAN9 architecture, where each state has transitions to the insert state of the same layer and the delete and match states of the next layer

PLAN8I

public static final HMMFactory.HMMType PLAN8I

Architecture similar to PLAN7 but with connections from delete to insert states of the same layer

PLAN8D

public static final HMMFactory.HMMType PLAN8D

Architecture similar to PLAN7 but with connections from insert to delete states of the next layer

Method Detail

values

public static HMMFactory.HMMType[] 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 (HMMFactory.HMMType c : HMMFactory.HMMType.values())
    System.out.println(c);

Returns:

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

valueOf

public static HMMFactory.HMMType 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