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