Class QuatSymmetryParameters

  • All Implemented Interfaces:
    java.io.Serializable

    public class QuatSymmetryParameters
    extends java.lang.Object
    implements java.io.Serializable
    See Also:
    Serialized Form
    • Constructor Detail

      • QuatSymmetryParameters

        public QuatSymmetryParameters()
    • Method Detail

      • getMinimumSequenceLength

        public int getMinimumSequenceLength()
        Returns:
        the minimumSequenceLength
      • setMinimumSequenceLength

        public void setMinimumSequenceLength​(int minimumSequenceLength)
        Parameters:
        minimumSequenceLength - the minimumSequenceLength to set
      • getAbsoluteMinimumSequenceLength

        public int getAbsoluteMinimumSequenceLength()
        Returns:
        the absoluteMinimumSequenceLength
      • setAbsoluteMinimumSequenceLength

        public void setAbsoluteMinimumSequenceLength​(int absoluteMinimumSequenceLength)
        Parameters:
        absoluteMinimumSequenceLength - the absoluteMinimumSequenceLength to set
      • getMinimumSequenceLengthFraction

        public double getMinimumSequenceLengthFraction()
        Returns:
        the minimumSequenceLengthFraction
      • setMinimumSequenceLengthFraction

        public void setMinimumSequenceLengthFraction​(double minimumSequenceLengthFraction)
        Parameters:
        minimumSequenceLengthFraction - the minimumSequenceLengthFraction to set
      • getSequenceIdentityThresholds

        public double[] getSequenceIdentityThresholds()
        Returns:
        the sequenceIdentityThreshold
      • setSequenceIdentityThresholds

        public void setSequenceIdentityThresholds​(double[] sequenceIdentityThresholds)
        Parameters:
        sequenceIdentityThresholds - the sequenceIdentityThresholds to set
      • getAlignmentFractionThreshold

        public double getAlignmentFractionThreshold()
        Returns:
        the alignmentFractionThreshold
      • setAlignmentFractionThreshold

        public void setAlignmentFractionThreshold​(double alignmentFractionThreshold)
        Parameters:
        alignmentFractionThreshold - the alignmentFractionThreshold to set
      • getRmsdThreshold

        public double getRmsdThreshold()
        Returns:
        the rmsdThreshold
      • setRmsdThreshold

        public void setRmsdThreshold​(double rmsdThreshold)
        Parameters:
        rmsdThreshold - the rmsdThreshold to set
      • getAngleThreshold

        public double getAngleThreshold()
      • setAngleThreshold

        public void setAngleThreshold​(double angleThreshold)
      • getHelixRmsdThreshold

        public double getHelixRmsdThreshold()
      • setHelixRmsdThreshold

        public void setHelixRmsdThreshold​(double helixRmsdThreshold)
      • getHelixRmsdToRiseRatio

        public double getHelixRmsdToRiseRatio()
        Returns:
        the helixRmsdToRiseRatio
      • setHelixRmsdToRiseRatio

        public void setHelixRmsdToRiseRatio​(double helixRmsdToRiseRatio)
        Parameters:
        helixRmsdToRiseRatio - the helixRmsdToRiseRatio to set
      • getMinimumHelixRise

        public double getMinimumHelixRise()
      • setMinimumHelixRise

        public void setMinimumHelixRise​(double minimumHelixRise)
      • getMinimumHelixAngle

        public double getMinimumHelixAngle()
      • setMinimumHelixAngle

        public void setMinimumHelixAngle​(double minimumHelixAngle)
      • getSequencePseudoSymmetryThreshold

        public double getSequencePseudoSymmetryThreshold()
      • setSequencePseudoSymmetryThreshold

        public void setSequencePseudoSymmetryThreshold​(double sequencePseudoSymmetryThreshold)
      • getMaximumLocalCombinations

        public int getMaximumLocalCombinations()
      • setMaximumLocalCombinations

        public void setMaximumLocalCombinations​(int maximumLocalCombinations)
      • getMaximumLocalResults

        public int getMaximumLocalResults()
        Returns:
        the maximumLocalResults
      • getMaximumLocalSubunits

        public int getMaximumLocalSubunits()
        Returns:
        the maximumLocalSubunits
      • setMaximumLocalSubunits

        public void setMaximumLocalSubunits​(int maximumLocalSubunits)
        Parameters:
        maximumLocalSubunits - the maximumLocalSubunits to set
      • setMaximumLocalResults

        public void setMaximumLocalResults​(int maximumLocalResults)
        Parameters:
        maximumLocalResults - the maximumLocalResults to set
      • isLocalSymmetry

        public boolean isLocalSymmetry()
      • setLocalSymmetry

        public void setLocalSymmetry​(boolean localSymmetry)
      • getLocalTimeLimit

        public double getLocalTimeLimit()
        Returns:
        the localTimeLimit
      • setLocalTimeLimit

        public void setLocalTimeLimit​(double localTimeLimit)
        Parameters:
        localTimeLimit - the localTimeLimit to set
      • isOnTheFly

        public boolean isOnTheFly()
        Returns:
        true if Jmol on the fly bioassembly generation is used
      • setOnTheFly

        public void setOnTheFly​(boolean useJmolBioAssemblies)
        Parameters:
        onTheFly - the onTheFly to set
      • isVerbose

        public boolean isVerbose()
      • setVerbose

        public void setVerbose​(boolean verbose)
      • toString

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