Class NeedlemanWunschLinearSpaceAffine

    • Constructor Detail

      • NeedlemanWunschLinearSpaceAffine

        public NeedlemanWunschLinearSpaceAffine​(Scores sub,
                                                float openGapPenalty,
                                                float extendGapPenalty)
      • NeedlemanWunschLinearSpaceAffine

        public NeedlemanWunschLinearSpaceAffine​(Scores sub,
                                                float d,
                                                float e,
                                                boolean freeGapsAtEnds)
      • NeedlemanWunschLinearSpaceAffine

        public NeedlemanWunschLinearSpaceAffine​(Scores sub,
                                                float d,
                                                float e,
                                                boolean freeGapsAtEnds,
                                                boolean applyGapExtendCostToFirstGapResidue)
        Parameters:
        applyGapExtendCostToFirstGapResidue - Generally there is an ambiguity in bioinformatics whether "gap opening" already includes the first gap character - in other words, whether a gap of length N has
             (a) a cost of gapOpen + N * gapExtend
             or
             (b) gapOpen + (N-1) * gapExtend.
             
        . applyGapExtendCostToFirstGapResidue should be true if using interpretation (a).
        sub -
        d -
        e -
        freeGapsAtEnds -
    • Method Detail

      • allocateMatrices

        public void allocateMatrices​(int n,
                                     int m)
      • doAlignment

        public void doAlignment​(java.lang.String sq1,
                                java.lang.String sq2)
        Performs the alignment. Abstract.
      • doAlignment

        public void doAlignment​(java.lang.String sq1,
                                java.lang.String sq2,
                                ProgressListener progress,
                                boolean scoreOnly)
      • doAlignment

        public void doAlignment​(java.lang.String sq1,
                                java.lang.String sq2,
                                ProgressListener progress)
      • getMemoryRequiredForAlignment

        public static long getMemoryRequiredForAlignment​(int maximumSequenceLength)
        Returns:
        the number of bytes required per residue in the longest sequence to be alignned.
      • doAlignment

        public jebl.evolution.align.AlignmentResult[] doAlignment​(jebl.evolution.align.Profile profile1,
                                                                  jebl.evolution.align.Profile profile2,
                                                                  ProgressListener progress,
                                                                  boolean scoreOnly)
      • getMatch

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

        public float getScore()
        Returns:
        score for this alignment
      • main

        public static void main​(java.lang.String[] arguments)
      • setDebug

        public void setDebug​(boolean display)
      • prepareAlignment

        public void prepareAlignment​(java.lang.String sq1,
                                     java.lang.String sq2)
        Description copied from class: Align
        Initialises the matrices for the alignment.
      • printf

        public void printf​(Output out)
        Print matrix used to calculate this alignment.
        Parameters:
        out - Output to print to.
      • 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