org.biojava3.alignment
Class SimpleGapPenalty

java.lang.Object
  org.biojava3.alignment.SimpleGapPenalty

All Implemented Interfaces:

GapPenalty

public class SimpleGapPenalty
extends Object
implements GapPenalty

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

Author:

Mark Chapman

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava3.alignment.template.GapPenalty

GapPenalty.Type

Constructor Summary

SimpleGapPenalty()
Creates a new set of gap penalties using the defaults.

SimpleGapPenalty(short gop, short gep)
Creates a new set of gap penalties.

Method Summary

short	getExtensionPenalty() Returns penalty given when an already open gap elongates by a single element
short	getOpenPenalty() Returns penalty given when a deletion or insertion gap first opens
GapPenalty.Type	getType() Returns GapPenalty.Type stored.
static void	setDefaultExtensionPenalty(short gep) Sets the default gap extension penalty.
static void	setDefaultOpenPenalty(short gop) Sets the default gap open penalty.
void	setExtensionPenalty(short gep) Sets penalty given when an already open gap elongates by a single element
void	setOpenPenalty(short 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 Detail

SimpleGapPenalty

public SimpleGapPenalty()

Creates a new set of gap penalties using the defaults.

SimpleGapPenalty

public SimpleGapPenalty(short gop,
                        short gep)

Creates a new set of gap penalties.

Parameters:

gop - the gap open penalty

gep - the gap extension penalty

Method Detail

setDefaultExtensionPenalty

public static void setDefaultExtensionPenalty(short gep)

Sets the default gap extension penalty.

Parameters:

gep - the default gap extension penalty

setDefaultOpenPenalty

public static void setDefaultOpenPenalty(short gop)

Sets the default gap open penalty.

Parameters:

gop - the default gap open penalty

getExtensionPenalty

public short getExtensionPenalty()

Description copied from interface: GapPenalty

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

Specified by:

getExtensionPenalty in interface GapPenalty

Returns:

gap extension penalty

getOpenPenalty

public short getOpenPenalty()

Description copied from interface: GapPenalty

Returns penalty given when a deletion or insertion gap first opens

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(short 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 - gap extension penalty

setOpenPenalty

public void setOpenPenalty(short 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 - gap open penalty