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