Package org.snpeff.align
Class NeedlemanWunsch
java.lang.Object
org.snpeff.align.NeedlemanWunsch
- Direct Known Subclasses:
SmithWaterman
,VcfRefAltAlign
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionalign()
int
int
void
setDeletion
(int deletion) void
setMatch
(int match) void
setMissMatch
(int missMatch) void
setUseSpace
(boolean useSpace) toString()
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Constructor Details
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NeedlemanWunsch
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Method Details
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align
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getAlignment
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getAlignmentScore
public int getAlignmentScore() -
getOffset
public int getOffset() -
setDeletion
public void setDeletion(int deletion) -
setMatch
public void setMatch(int match) -
setMissMatch
public void setMissMatch(int missMatch) -
setUseSpace
public void setUseSpace(boolean useSpace) -
toString
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