SimpleGapPenalty
public interface GapPenalty
Modifier and Type | Interface | Description |
---|---|---|
static class |
GapPenalty.Type |
Defines the possible types of gap penalties.
|
Modifier and Type | Method | 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
|
int getExtensionPenalty()
int getOpenPenalty()
GapPenalty.Type getType()
GapPenalty.Type
stored.void setExtensionPenalty(int gep)
gep
- gap extension penaltyvoid setOpenPenalty(int gop)
gop
- gap open penalty