Class FatCatParameters

    • Constructor Detail

      • FatCatParameters

        public FatCatParameters()
    • Method Detail

      • getFragLen

        public java.lang.Integer getFragLen()
      • setFragLen

        public void setFragLen​(java.lang.Integer fragLen)
      • getFragLenSq

        public int getFragLenSq()
      • setFragLenSq

        public void setFragLenSq​(int fragLenSq)
      • getRmsdCut

        public java.lang.Double getRmsdCut()
        The cutoff to be used during AFP detection
        Returns:
        rmsdCut parameter
      • setRmsdCut

        public void setRmsdCut​(java.lang.Double rmsdCut)
        The cutoff to be used during AFP detection
        Parameters:
        rmsdCut -
      • getDisCut

        public java.lang.Double getDisCut()
        Get the distance cutoff used during AFP chain connectivity checks
        Returns:
        distance Cutoff
      • setDisCut

        public void setDisCut​(java.lang.Double disCut)
      • getAfpDisCut

        public double getAfpDisCut()
      • setAfpDisCut

        public void setAfpDisCut​(double afpDisCut)
      • getAfpDisCut0

        public double getAfpDisCut0()
      • setAfpDisCut0

        public void setAfpDisCut0​(double afpDisCut0)
      • getDisSmooth

        public double getDisSmooth()
      • setDisSmooth

        public void setDisSmooth​(double disSmooth)
      • getMisCut

        public int getMisCut()
      • setMisCut

        public void setMisCut​(int misCut)
      • getMaxGap

        public int getMaxGap()
      • setMaxGap

        public void setMaxGap​(int maxGap)
      • getMaxGapFrag

        public int getMaxGapFrag()
      • setMaxGapFrag

        public void setMaxGapFrag​(int maxGapFrag)
      • getDisFilter

        public double getDisFilter()
      • setDisFilter

        public void setDisFilter​(double disFilter)
      • getBadRmsd

        public double getBadRmsd()
      • setBadRmsd

        public void setBadRmsd​(double badRmsd)
      • getMaxTra

        public java.lang.Integer getMaxTra()
        get the maximum number of Twists that are allowed...
        Returns:
        max nr of allowed twists
      • setMaxTra

        public void setMaxTra​(java.lang.Integer maxTra)
        set the maximum number of Twists that are allowed...
        Parameters:
        maxTra -
      • getGapCreate

        public double getGapCreate()
      • setGapCreate

        public void setGapCreate​(double gapCreate)
      • getGapExtend

        public double getGapExtend()
      • setGapExtend

        public void setGapExtend​(double gapExtend)
      • getMisScore

        public double getMisScore()
      • setMisScore

        public void setMisScore​(double misScore)
      • getTorsionPenalty

        public double getTorsionPenalty()
      • setTorsionPenalty

        public void setTorsionPenalty​(double torsionPenalty)
      • getMaxPenalty

        public double getMaxPenalty()
      • setMaxPenalty

        public void setMaxPenalty​(double maxPenalty)
      • getResScore

        public double getResScore()
      • setResScore

        public void setResScore​(double resScore)
      • getFragScore

        public double getFragScore()
      • setFragScore

        public void setFragScore​(double fragScore)
      • getSparse

        public int getSparse()
      • setSparse

        public void setSparse​(int sparse)
      • 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
      • toString

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

        public boolean isOptimizeAlignment()
        Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. NB: Not implemented in jFatCat
        Returns:
        optimizeAlignment
      • setOptimizeAlignment

        public void setOptimizeAlignment​(boolean optimizeAlignment)
        Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. NB: Not implemented in jFatCat
        Parameters:
        optimizeAlignment -