Package org.snpeff.align
Class NeedlemanWunschOverlap
- java.lang.Object
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- org.snpeff.align.NeedlemanWunschOverlap
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public class NeedlemanWunschOverlap extends java.lang.Object
Needleman-Wunsch algorithm for string alignment (short strings, since it's not memory optimized)- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description NeedlemanWunschOverlap(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
calcAlignment()
int
calcAlignmentScore()
Calculate score matrixint
getAligmentScore()
java.lang.String
getAlignment()
void
setDeletion(int deletion)
void
setMatch(int match)
void
setMissMatch(int missMatch)
java.lang.String
toString()
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Method Detail
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align
public java.lang.String align()
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calcAlignment
public java.lang.String calcAlignment()
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calcAlignmentScore
public int calcAlignmentScore()
Calculate score matrix
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getAligmentScore
public int getAligmentScore()
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getAlignment
public java.lang.String getAlignment()
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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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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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