org.biojava3.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

static class

GapPenalty.Type Defines the possible types 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.
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

Method Detail

getExtensionPenalty

short getExtensionPenalty()

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

Returns:

gap extension penalty

getOpenPenalty

short 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(short gep)

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

Parameters:

gep - gap extension penalty

setOpenPenalty

void setOpenPenalty(short gop)

Sets penalty given when a deletion or insertion gap first opens

Parameters:

gop - gap open penalty