Class CeParameters

    • Field Detail

      • winSize

        protected int winSize
      • rmsdThr

        protected double rmsdThr
      • rmsdThrJoin

        protected double rmsdThrJoin
      • maxOptRMSD

        protected double maxOptRMSD
      • maxGapSize

        protected int maxGapSize
      • showAFPRanges

        protected boolean showAFPRanges
      • sideChainScoringType

        protected int sideChainScoringType
      • DEFAULT_GAP_EXTENSION

        protected static final double DEFAULT_GAP_EXTENSION
        See Also:
        Constant Field Values
      • DEFAULT_SUBSTITUTION_MATRIX

        protected static final java.lang.String DEFAULT_SUBSTITUTION_MATRIX
        See Also:
        Constant Field Values
      • gapOpen

        protected double gapOpen
      • gapExtension

        protected double gapExtension
      • distanceIncrement

        protected double distanceIncrement
      • oRmsdThr

        protected double oRmsdThr
      • maxNrIterationsForOptimization

        protected int maxNrIterationsForOptimization
      • seqWeight

        protected double seqWeight
    • Constructor Detail

      • CeParameters

        public CeParameters()
    • Method Detail

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • getWinSize

        public java.lang.Integer getWinSize()
        The window size to look at
        Returns:
        window size
      • setWinSize

        public void setWinSize​(java.lang.Integer winSize)
      • getRmsdThr

        public java.lang.Double getRmsdThr()
        RMSD Threshold
        Returns:
        RMSD threshold
      • setRmsdThr

        public void setRmsdThr​(java.lang.Double rmsdThr)
      • getRmsdThrJoin

        public java.lang.Double getRmsdThrJoin()
        RMSD threshold for joining of AFPs
        Returns:
        rmsd threshold
      • setRmsdThrJoin

        public void setRmsdThrJoin​(java.lang.Double rmsdThrJoin)
      • setScoringStrategy

        public void setScoringStrategy​(CeParameters.ScoringStrategy scoringStrategy)
        Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.
        Parameters:
        scoringStrategy -
      • setMaxGapSize

        public void setMaxGapSize​(java.lang.Integer maxGapSize)
        Set the Max gap size parameter. Default 30. For unlimited gaps set to -1
        Parameters:
        maxGapSize -
      • getMaxGapSize

        public java.lang.Integer getMaxGapSize()
        the Max gap size parameter G . default is 30, which was described to obtained empirically in the CE paper. the larger the max gap size, the longer the compute time, but in same cases drastically improved results. Set to -1 for unlimited gap size.
        Returns:
        max gap size parameter
      • getUserConfigParameters

        public java.util.List<java.lang.String> getUserConfigParameters()
        Description copied from interface: ConfigStrucAligParams
        get the list of parameters that the user can change through the user interface. Parameter names are the same names as the corresponding Get/Set methods.
        Specified by:
        getUserConfigParameters in interface ConfigStrucAligParams
        Returns:
        list of parameters
      • isShowAFPRanges

        public boolean isShowAFPRanges()
        Returns:
        whether information about AFPs should be printed
      • setShowAFPRanges

        public void setShowAFPRanges​(boolean showAFPRanges)
      • setMaxOptRMSD

        public void setMaxOptRMSD​(java.lang.Double param)
        set the maximum RMSD cutoff to be applied during alignment optimization. (default: 99 = unlimited)
        Parameters:
        param - maxOptRMSD
      • getMaxOptRMSD

        public java.lang.Double getMaxOptRMSD()
        Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
        Returns:
        maxOptRMSD
      • getGapOpen

        public java.lang.Double getGapOpen()
      • setGapOpen

        public void setGapOpen​(java.lang.Double gapOpen)
      • getGapExtension

        public java.lang.Double getGapExtension()
      • setGapExtension

        public void setGapExtension​(java.lang.Double gapExtension)
      • getDistanceIncrement

        public java.lang.Double getDistanceIncrement()
      • setDistanceIncrement

        public void setDistanceIncrement​(java.lang.Double distanceIncrement)
      • getORmsdThr

        public java.lang.Double getORmsdThr()
        Get the Original RMSD threshold from which the alignment optimization is started
        Returns:
        oRMSDThreshold
      • setORmsdThr

        public void setORmsdThr​(java.lang.Double oRmsdThr)
        Set the Original RMSD threshold from which the alignment optimization is started
        Parameters:
        oRmsdThr - the threshold
      • getMaxNrIterationsForOptimization

        public int getMaxNrIterationsForOptimization()
        Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
        Parameters:
        maxNrIterationsForOptimization -
      • setMaxNrIterationsForOptimization

        public void setMaxNrIterationsForOptimization​(int maxNrIterationsForOptimization)
        Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
        Parameters:
        maxNrIterationsForOptimization -
      • getSeqWeight

        public double getSeqWeight()
        Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.
        Returns:
        seqWeight the weight factor (default 0)
      • setSeqWeight

        public void setSeqWeight​(double seqWeight)
        Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.
        Parameters:
        seqWeight - the weight factor (default 0)
      • getSubstitutionMatrix

        public SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix()
        Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)
        Returns:
        substitutionMatrix
      • setSubstitutionMatrix

        public void setSubstitutionMatrix​(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)
        Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)
        Parameters:
        substitutionMatrix -