Package org.snpeff.align
Class NeedlemanWunsch
- java.lang.Object
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- org.snpeff.align.NeedlemanWunsch
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- Direct Known Subclasses:
SmithWaterman
,VcfRefAltAlign
public class NeedlemanWunsch extends java.lang.Object
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 Constructor Description NeedlemanWunsch(java.lang.String a, java.lang.String b)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
align()
java.lang.String
getAlignment()
int
getAlignmentScore()
int
getOffset()
void
setDeletion(int deletion)
void
setMatch(int match)
void
setMissMatch(int missMatch)
void
setUseSpace(boolean useSpace)
java.lang.String
toString()
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Method Detail
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align
public java.lang.String align()
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getAlignment
public java.lang.String getAlignment()
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getAlignmentScore
public int getAlignmentScore()
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getOffset
public int getOffset()
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setDeletion
public void setDeletion(int deletion)
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setMatch
public void setMatch(int match)
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setMissMatch
public void setMissMatch(int missMatch)
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setUseSpace
public void setUseSpace(boolean useSpace)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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