Package org.biojava.nbio.structure.cluster

Enum SubunitClustererMethod

java.lang.Object

java.lang.Enum<SubunitClustererMethod>

org.biojava.nbio.structure.cluster.SubunitClustererMethod

All Implemented Interfaces:

Serializable, Comparable<SubunitClustererMethod>

public enum SubunitClustererMethod
extends Enum<SubunitClustererMethod>

The SubunitClustererMethod ennummerates all methods that can be used to cluster Subunit in the SubunitCluster.

Since:

5.0.0

Author:

Aleix Lafita

Enum Constant Summary

Enum Constants

Enum Constant	Description
SEQUENCE	The SEQUENCE clustering method uses the residue sequence of the Subunit to calculate sequence alignments.
SEQUENCE_STRUCTURE	The SEQUENCE_STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.
STRUCTURE	The STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

Method Summary

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

SEQUENCE

public static final SubunitClustererMethod SEQUENCE

The SEQUENCE clustering method uses the residue sequence of the Subunit to calculate sequence alignments.

Two Subunit with sufficient sequence identity and coverage are clustered together.

STRUCTURE

public static final SubunitClustererMethod STRUCTURE

The STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

Two Subunit with sufficient structural similarity and coverage are clustered together.

SEQUENCE_STRUCTURE

public static final SubunitClustererMethod SEQUENCE_STRUCTURE

The SEQUENCE_STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

Two Subunit with sufficient sequence identity and coverage are clustered together. Additionally, two Subunit with sufficient structural similarity and coverage are clustered together. If the sequence and structure clustering differ, the cluster contains pseudosymmetry (by definition).

Method Detail

values

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

Returns:

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

valueOf

public static SubunitClustererMethod 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