Package org.snpeff.align
Class VcfRefAltAlign
- java.lang.Object
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- org.snpeff.align.NeedlemanWunsch
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- org.snpeff.align.VcfRefAltAlign
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public class VcfRefAltAlign extends NeedlemanWunsch
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment Only used for short strings (algorithm is not optimized)- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
MAX_SIZE
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Constructor Summary
Constructors Constructor Description VcfRefAltAlign(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()
Variant.VariantType
getVariantType()
void
setVariantType(Variant.VariantType variantType)
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Methods inherited from class org.snpeff.align.NeedlemanWunsch
getAlignment, getAlignmentScore, getOffset, setDeletion, setMatch, setMissMatch, setUseSpace, toString
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Field Detail
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MAX_SIZE
public static final int MAX_SIZE
- See Also:
- Constant Field Values
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Method Detail
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align
public java.lang.String align()
- Overrides:
align
in classNeedlemanWunsch
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getVariantType
public Variant.VariantType getVariantType()
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setVariantType
public void setVariantType(Variant.VariantType variantType)
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