org.biojava3.alignment
public class SimpleGapPenalty extends java.lang.Object implements GapPenalty
GapPenalty.Type
Constructor and Description |
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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.
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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
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short |
getOpenPenalty()
Returns penalty given when a deletion or insertion gap first opens
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GapPenalty.Type |
getType()
Returns
GapPenalty.Type stored. |
static void |
setDefaultExtensionPenalty(short gep)
Sets the default gap extension penalty.
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static void |
setDefaultOpenPenalty(short gop)
Sets the default gap open penalty.
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void |
setExtensionPenalty(short gep)
Sets penalty given when an already open gap elongates by a single element
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void |
setOpenPenalty(short gop)
Sets penalty given when a deletion or insertion gap first opens
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public SimpleGapPenalty()
public SimpleGapPenalty(short gop, short gep)
gop
- the gap open penaltygep
- the gap extension penaltypublic 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