Package jebl.evolution.align

Class Align

java.lang.Object
jebl.evolution.align.Align
Direct Known Subclasses:
MaximalSegmentPair, NeedlemanWunsch, NeedlemanWunschAffine, NeedlemanWunschLinearSpace, NeedlemanWunschLinearSpaceAffine, NonOverlapMultipleLocalAffine, OldNeedlemanWunschAffine, OverlapAlign, SmithWaterman, SmithWatermanLinearSpace, SmithWatermanLinearSpaceAffine
public abstract class Align extends Object

  • Constructor Details

    • Align

      public Align(Scores sub, float d)

  • Method Details

    • doAlignment

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

    • prepareAlignment

      public abstract void prepareAlignment(String seq1, String seq2)
      Initialises the matrices for the alignment.
      Parameters:
      seq1 -
      seq2 -

    • setGapOpen

      public void setGapOpen(float d)

    • setScores

      public void setScores(Scores sub)

    • getMatch

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

    • formatScore

      public String formatScore(float val)
      Parameters:
      val -
      Returns:
      float value of string val

    • doMatch

      public void doMatch(Output out, String msg, boolean outputFMatrix)
      Print the score, the F matrix, and the alignment
      Parameters:
      out - output to print to
      msg - message printed at start
      outputFMatrix - print the score matrix

    • traceback

      public void traceback(TracebackPlotter plotter)

    • doMatch

      public void doMatch(Output out, String msg)
      Print the score and the alignment
      Parameters:
      out - output to print to
      msg - msg printed at the start

    • next

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

    • getScore

      public abstract float getScore()
      Returns:
      the score of the best alignment

    • printf

      public abstract void printf(Output out)
      Print the matrix (matrices) used to compute the alignment
      Parameters:
      out - output to print to