org.nmdp.ngs.align

Class GapPenalties

java.lang.Object

org.nmdp.ngs.align.GapPenalties

@Immutable
public final class GapPenalties
extends Object

Gap penalties.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GapPenalties.Builder Gap penalties builder.

Method Summary

Methods

Modifier and Type	Method and Description
static GapPenalties.Builder	builder() Create and return a new gap penalties builder.
static GapPenalties	create(int match, int replace, int insert, int delete, int extend) Create and return a new gap penalties with the specified penalties.
short	delete() Return the delete penalty.
short	extend() Return the extend penalty.
short	insert() Return the insert penalty.
short	match() Return the match penalty.
short	replace() Return the replace penalty.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

match

public short match()

Return the match penalty.

Returns:

the match penalty

replace

public short replace()

Return the replace penalty.

Returns:

the replace penalty

insert

public short insert()

Return the insert penalty.

Returns:

the insert penalty

delete

public short delete()

Return the delete penalty.

Returns:

the delete penalty

extend

public short extend()

Return the extend penalty.

Returns:

the extend penalty

builder

public static GapPenalties.Builder builder()

Create and return a new gap penalties builder.

Returns:

a new gap penalties builder

create

public static GapPenalties create(int match,
                  int replace,
                  int insert,
                  int delete,
                  int extend)

Create and return a new gap penalties with the specified penalties.

Parameters:

match - match penalty

replace - replace penalty

insert - insert penalty

delete - delete penalty

extend - extend penalty

Returns:

a new gap penalties with the specified penalties