org.biojava.nbio.alignment.template

Interface GapPenalty

All Known Implementing Classes:

SimpleGapPenalty

public interface GapPenalty

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

Author:

Mark Chapman

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	GapPenalty.Type Defines the possible types of gap penalties.

Method Summary

Modifier and Type	Method and Description
int	getExtensionPenalty() Returns penalty given when an already open gap elongates by a single element
int	getOpenPenalty() Returns penalty given when a deletion or insertion gap first opens
GapPenalty.Type	getType() Returns GapPenalty.Type stored.
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

Method Detail

getExtensionPenalty

int getExtensionPenalty()

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

Returns:

gap extension penalty

getOpenPenalty

int getOpenPenalty()

Returns penalty given when a deletion or insertion gap first opens

Returns:

gap open penalty

getType

GapPenalty.Type getType()

Returns GapPenalty.Type stored.

Returns:

gap penalty type

setExtensionPenalty

void setExtensionPenalty(int gep)

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

Parameters:

gep - gap extension penalty

setOpenPenalty

void setOpenPenalty(int gop)

Sets penalty given when a deletion or insertion gap first opens

Parameters:

gop - gap open penalty