org.biojava.nbio.alignment.template

Enum GapPenalty.Type

java.lang.Object

java.lang.Enum<GapPenalty.Type>

org.biojava.nbio.alignment.template.GapPenalty.Type

All Implemented Interfaces:

Serializable, Comparable<GapPenalty.Type>

Enclosing interface:

GapPenalty

public static enum GapPenalty.Type
extends Enum<GapPenalty.Type>

Defines the possible types of gap penalties. This is:

• CONSTANT, if static and the extension penalty is 0
• LINEAR, if static and the open penalty is 0
• AFFINE, if static but neither CONSTANT nor LINEAR
• DYNAMIC, if penalty values change during alignment

Enum Constant Summary

Enum Constants

Enum Constant and Description
AFFINE
CONSTANT
DYNAMIC
LINEAR

Method Summary

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

CONSTANT

public static final GapPenalty.Type CONSTANT

LINEAR

public static final GapPenalty.Type LINEAR

AFFINE

public static final GapPenalty.Type AFFINE

DYNAMIC

public static final GapPenalty.Type DYNAMIC

Method Detail

values

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

Returns:

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

valueOf

public static GapPenalty.Type 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