Class CeUserArgumentProcessor.CeStartupParams

    • Field Detail

      • maxGapSize

        protected int maxGapSize
      • winSize

        protected int winSize
      • maxOptRMSD

        protected double maxOptRMSD
      • gapOpen

        protected double gapOpen
      • gapExtension

        protected double gapExtension
      • showAFPRanges

        protected boolean showAFPRanges
    • Constructor Detail

      • CeStartupParams

        public CeStartupParams()
    • Method Detail

      • getWinSize

        public int getWinSize()
      • setWinSize

        public void setWinSize​(int winSize)
      • getGapOpen

        public double getGapOpen()
      • setGapOpen

        public void setGapOpen​(double gapOpen)
      • getGapExtension

        public double getGapExtension()
      • setGapExtension

        public void setGapExtension​(double gapExtension)
      • getMaxGapSize

        public int getMaxGapSize()
        CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30
        Returns:
        the maximum gap size G parameter.
      • setMaxGapSize

        public void setMaxGapSize​(int maxGapSize)
        CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30
        Parameters:
        maxGapSize -
      • isShowAFPRanges

        public boolean isShowAFPRanges()
      • setShowAFPRanges

        public void setShowAFPRanges​(boolean showAFP)
      • getMaxOptRMSD

        public java.lang.Double getMaxOptRMSD()
        (jCE specific): maximum RMSD that shall be calculated for the alignment.
        Returns:
        maxOptRMSD parameter
      • setMaxOptRMSD

        public void setMaxOptRMSD​(java.lang.Double maxOptRMSD)
        (jCE specific): maximum RMSD that shall be calculated for the alignment.
        Parameters:
        maxOptRMSD - max RMSD to calculate