de.jstacs.algorithms.alignment

Enum Alignment.AlignmentType

java.lang.Object

java.lang.Enum<Alignment.AlignmentType>

de.jstacs.algorithms.alignment.Alignment.AlignmentType

All Implemented Interfaces:

Serializable, Comparable<Alignment.AlignmentType>

Enclosing class:

Alignment

public static enum Alignment.AlignmentType
extends Enum<Alignment.AlignmentType>

Author:

Jens Keilwagen

Enum Constant Summary

Enum Constants

Enum Constant and Description
FREE_SHIFT The free shift alignment allows gaps at the begin and at the end of both sequence without any costs.
GLOBAL The global version of an alignment aligns two complete sequences.
LOCAL The local version of an alignment aligns a subsequence of the first sequence with a subsequence of the second sequence.
SEMI_GLOBAL The semi global version of an alignment allows gaps at the begin and at the end of the second sequence without any costs.

Method Summary

Methods

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

GLOBAL

public static final Alignment.AlignmentType GLOBAL

The global version of an alignment aligns two complete sequences.

SEMI_GLOBAL

public static final Alignment.AlignmentType SEMI_GLOBAL

The semi global version of an alignment allows gaps at the begin and at the end of the second sequence without any costs.

FREE_SHIFT

public static final Alignment.AlignmentType FREE_SHIFT

The free shift alignment allows gaps at the begin and at the end of both sequence without any costs. Be aware that the match cost should be negative.

LOCAL

public static final Alignment.AlignmentType LOCAL

The local version of an alignment aligns a subsequence of the first sequence with a subsequence of the second sequence.

Method Detail

values

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

Returns:

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

valueOf

public static Alignment.AlignmentType 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