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