Package org.biojava.nbio.alignment

Class SimpleGapPenalty

java.lang.Object

org.biojava.nbio.alignment.SimpleGapPenalty

All Implemented Interfaces:

Serializable, GapPenalty

public class SimpleGapPenalty
extends Object
implements GapPenalty, Serializable

Implements a data structure for the gap penalties used during a sequence alignment routine.

Author:

Mark Chapman

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.alignment.template.GapPenalty

GapPenalty.Type

Constructor Summary

Constructors

Constructor	Description
SimpleGapPenalty()	Creates a new set of gap penalties using the defaults.
SimpleGapPenalty(int gop, int gep)	Creates a new set of gap penalties.

Method Summary

Modifier and Type	Method	Description
int	getExtensionPenalty()	Returns the negative of the extension penalty passed to the constructor.
int	getOpenPenalty()	Returns the negative of the opening penalty passed to the constructor.
GapPenalty.Type	getType()	Returns GapPenalty.Type stored.
static void	setDefaultExtensionPenalty(int gep)	Sets the default gap extension penalty.
static void	setDefaultOpenPenalty(int gop)	Sets the default gap open penalty.
void	setExtensionPenalty(int gep)	Sets penalty given when an already open gap elongates by a single element
void	setOpenPenalty(int gop)	Sets penalty given when a deletion or insertion gap first opens

Methods inherited from class java.lang.Object

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

Constructor Details

SimpleGapPenalty

public SimpleGapPenalty()

Creates a new set of gap penalties using the defaults.

SimpleGapPenalty

public SimpleGapPenalty(int gop,
 int gep)

Creates a new set of gap penalties.

Parameters:

gop - the gap open penalty; should be nonnegative

gep - the gap extension penalty; should be nonnegative

Method Details

setDefaultExtensionPenalty

public static void setDefaultExtensionPenalty(int gep)

Sets the default gap extension penalty.

Parameters:

gep - the default gap extension penalty

setDefaultOpenPenalty

public static void setDefaultOpenPenalty(int gop)

Sets the default gap open penalty.

Parameters:

gop - the default gap open penalty

getExtensionPenalty

public int getExtensionPenalty()

Returns the negative of the extension penalty passed to the constructor.

Specified by:

getExtensionPenalty in interface GapPenalty

Returns:

gap extension penalty

getOpenPenalty

public int getOpenPenalty()

Returns the negative of the opening penalty passed to the constructor.

Specified by:

getOpenPenalty in interface GapPenalty

Returns:

gap open penalty

getType

public GapPenalty.Type getType()

Description copied from interface: GapPenalty

Returns GapPenalty.Type stored.

Specified by:

getType in interface GapPenalty

Returns:

gap penalty type

setExtensionPenalty

public void setExtensionPenalty(int gep)

Description copied from interface: GapPenalty

Sets penalty given when an already open gap elongates by a single element

Specified by:

setExtensionPenalty in interface GapPenalty

Parameters:

gep - Should be nonnegative

setOpenPenalty

public void setOpenPenalty(int gop)

Description copied from interface: GapPenalty

Sets penalty given when a deletion or insertion gap first opens

Specified by:

setOpenPenalty in interface GapPenalty

Parameters:

gop - Should be nonnegative