Package jebl.evolution.align

Class NeedlemanWunschAffine

java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.NeedlemanWunschAffine
public class NeedlemanWunschAffine extends Align

  • Constructor Details

    • NeedlemanWunschAffine

      public NeedlemanWunschAffine(Scores sub, float d, float e)

  • Method Details

    • doAlignment

      public void doAlignment(String sq1, String sq2)
      Performs the alignment. Abstract.
      Parameters:
      sq1 -
      sq2 -

    • allocateMatrices

      public void allocateMatrices(int n, int m)

    • prepareAlignment

      public void prepareAlignment(String sq1, String sq2)
      Description copied from class: Align
      Initialises the matrices for the alignment.
      Parameters:
      sq1 -
      sq2 -

    • doAlignment

      public void doAlignment(String sequence1, String sequence2, int startType, int endType)

    • doAlignment

      public void doAlignment(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType)

    • doAlignment

      public void doAlignment(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType, boolean freeStartGap, boolean freeEndGap)

    • appendMatch

      public void appendMatch(jebl.evolution.align.AlignmentResult result1, jebl.evolution.align.AlignmentResult result2)

    • getMatch

      public String[] getMatch()
      Overrides:
      getMatch in class Align
      Returns:
      two-element array containing an alignment with maximal score

    • getMatch

      public String[] getMatch(char[] sq1, char[] sq2)

    • getScore

      public float getScore()
      Returns:
      score for this alignment

    • setGapExtend

      public void setGapExtend(float e)

    • next

      public Traceback next(Traceback tb)
      Get the next state in the traceback
      Overrides:
      next in class Align
      Parameters:
      tb - current Traceback
      Returns:
      next Traceback

    • printf

      public void printf(Output out)
      Print matrix used to calculate this alignment.
      Specified by:
      printf in class Align
      Parameters:
      out - Output to print to.