Package org.snpeff.align

Class NeedlemanWunsch

java.lang.Object
org.snpeff.align.NeedlemanWunsch
Direct Known Subclasses:
SmithWaterman, VcfRefAltAlign
public class NeedlemanWunsch extends Object
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
Author:
pcingola

  • Constructor Details

    • NeedlemanWunsch

      public NeedlemanWunsch(String a, String b)

  • Method Details

    • align

      public String align()

    • getAlignment

      public String getAlignment()

    • 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

      public String toString()
      Overrides:
      toString in class Object