Package jebl.evolution.align

Class Align

    • Constructor Summary

      Constructors 
      Constructor Description
      Align​(Scores sub, float d)  

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      abstract void doAlignment​(java.lang.String sq1, java.lang.String sq2)
      Performs the alignment, abstract.
      void doMatch​(Output out, java.lang.String msg)
      Print the score and the alignment
      void doMatch​(Output out, java.lang.String msg, boolean outputFMatrix)
      Print the score, the F matrix, and the alignment
      java.lang.String formatScore​(float val)  
      java.lang.String[] getMatch()  
      abstract float getScore()  
      Traceback next​(Traceback tb)
      Get the next state in the traceback
      abstract void prepareAlignment​(java.lang.String seq1, java.lang.String seq2)
      Initialises the matrices for the alignment.
      abstract void printf​(Output out)
      Print the matrix (matrices) used to compute the alignment
      void setGapOpen​(float d)  
      void setScores​(Scores sub)  
      void traceback​(TracebackPlotter plotter)  

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Align

        public Align​(Scores sub,
             float d)

    • Method Detail

      • doAlignment

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

      • prepareAlignment

        public abstract void prepareAlignment​(java.lang.String seq1,
                                      java.lang.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 java.lang.String[] getMatch()
        Returns:
        two-element array containing an alignment with maximal score

      • formatScore

        public java.lang.String formatScore​(float val)
        Parameters:
        val -
        Returns:
        float value of string val

      • doMatch

        public void doMatch​(Output out,
                    java.lang.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

      • doMatch

        public void doMatch​(Output out,
                    java.lang.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