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java.lang.Objectorg.biojava3.alignment.SimpleGapPenalty
public class SimpleGapPenalty
Implements a data structure for the gap penalties used during a sequence alignment routine.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava3.alignment.template.GapPenalty |
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GapPenalty.Type |
Constructor Summary | |
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SimpleGapPenalty()
Creates a new set of gap penalties using the defaults. |
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SimpleGapPenalty(short gop,
short gep)
Creates a new set 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. |
static void |
setDefaultExtensionPenalty(short gep)
Sets the default gap extension penalty. |
static void |
setDefaultOpenPenalty(short gop)
Sets the default gap open penalty. |
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 |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimpleGapPenalty()
public SimpleGapPenalty(short gop, short gep)
gop
- the gap open penaltygep
- the gap extension penaltyMethod Detail |
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public static void setDefaultExtensionPenalty(short gep)
gep
- the default gap extension penaltypublic static void setDefaultOpenPenalty(short gop)
gop
- the default gap open penaltypublic short getExtensionPenalty()
GapPenalty
getExtensionPenalty
in interface GapPenalty
public short getOpenPenalty()
GapPenalty
getOpenPenalty
in interface GapPenalty
public GapPenalty.Type getType()
GapPenalty
GapPenalty.Type
stored.
getType
in interface GapPenalty
public void setExtensionPenalty(short gep)
GapPenalty
setExtensionPenalty
in interface GapPenalty
gep
- gap extension penaltypublic void setOpenPenalty(short gop)
GapPenalty
setOpenPenalty
in interface GapPenalty
gop
- gap open penalty
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