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public interface GapPenalty
Defines a data structure for the gap penalties used during a sequence alignment routine.
Nested Class Summary | |
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static class |
GapPenalty.Type
Defines the possible types of gap penalties. |
Method Summary | |
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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 |
Method Detail |
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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
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