Class MDSetParameters


  • @PublicAPI
    public class MDSetParameters
    extends Object
    Parameters settings for MDSet-s. The main purpose of this class is the support for dissimilarity calculations over MDSet objects. The dissimilarity coefficient of two MDSet objects is defined as the weighted sum of component-wise dissimilarity coefficients. Weights of components are stored in this class, along with the metric indices used as default metric. This is allows by MDSet.getDissimilarity( final Object other ) perform calculations with the required metric (not only the default one).
    Since:
    JChem 2.0
    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int[] metricIndex
      metric index by component
      protected float[] userDataWeights
      user data weights
      protected float[] weights
      component weights
    • Constructor Summary

      Constructors 
      Constructor Description
      MDSetParameters()
      Crates an empty object.
      MDSetParameters​(float[] weights, float[] userDataWeights, int[] metricIndex)
      Creates and initializes an object with the given weights and metric indices.
      MDSetParameters​(float[] weights, int[] metricIndex)
      Creates and initializes an object with the given weights and metric indices.
      MDSetParameters​(int nComponents)
      Creates an object of the given size.
      MDSetParameters​(int nComponents, int nUserData)
      Creates an object of the given size.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getMetricIndex​(int index)
      Gets the index of the metric used by a component to calculate the dissimilarity coefficient.
      float getUserDataWeight​(int index)
      Gets the weight of a userData component.
      float getWeight​(int index)
      Gets the weight of a component.
      void setMetricIndex​(int componentIndex, int mi)
      Sets the index of metric used in the dissimilarity calculation by an individual component.
      void setMetricIndices​(int[] metricIndices)
      Sets the index of metric of components.
      void setSize​(int nComponents)
      Sets the size, number of components of an empty MDSetParameters object.
      void setSize​(int nComponents, int nUserData)
      Sets the size, number of components and number of userData values of an empty MDSetParameters object.
      void setUserDataWeight​(int index, float w)
      Sets the weight of an individual user data component.
      void setUserDataWeights​(float[] weights)
      Sets the weights for userData.
      void setWeight​(int componentIndex, float w)
      Sets the weight of an individual component.
      void setWeights​(float[] weights)
      Sets the weights.
      int size()
      Get the size of the associated MDSet instance.
    • Field Detail

      • weights

        protected float[] weights
        component weights
      • userDataWeights

        protected float[] userDataWeights
        user data weights
      • metricIndex

        protected int[] metricIndex
        metric index by component
    • Constructor Detail

      • MDSetParameters

        public MDSetParameters()
        Crates an empty object.
      • MDSetParameters

        public MDSetParameters​(int nComponents)
        Creates an object of the given size.
        Parameters:
        nComponents - number of components in the MDSet
      • MDSetParameters

        public MDSetParameters​(int nComponents,
                               int nUserData)
        Creates an object of the given size.
        Parameters:
        nComponents - number of components in the MDSet
        nUserData - number of further floating point values
      • MDSetParameters

        public MDSetParameters​(float[] weights,
                               int[] metricIndex)
        Creates and initializes an object with the given weights and metric indices.
        Parameters:
        weights - weights of every components used in MDSet.getDissimilarity( final Object other )
        metricIndex - index of metrices of components to be used in MDSet.getDissimilarity( final Object other )
      • MDSetParameters

        public MDSetParameters​(float[] weights,
                               float[] userDataWeights,
                               int[] metricIndex)
        Creates and initializes an object with the given weights and metric indices.
        Parameters:
        weights - weights of every components used in MDSet.getDissimilarity( final Object other )
        userDataWeights - weights of every components of user data
        metricIndex - index of metrices of components to be used in MDSet.getDissimilarity( final Object other )
    • Method Detail

      • setSize

        public void setSize​(int nComponents)
        Sets the size, number of components of an empty MDSetParameters object.
        Parameters:
        nComponents - number of components in the MDSet
      • setSize

        public void setSize​(int nComponents,
                            int nUserData)
        Sets the size, number of components and number of userData values of an empty MDSetParameters object.
        Parameters:
        nComponents - number of components in the MDSet
        nUserData - number of further floating point values
      • setWeights

        public void setWeights​(float[] weights)
        Sets the weights.
        Parameters:
        weights - weights of every components used in MDSet.getDissimilarity( final Object other )
      • setUserDataWeights

        public void setUserDataWeights​(float[] weights)
        Sets the weights for userData.
        Parameters:
        weights - weights of every components used in MDSet.getDissimilarity( final Object other )
      • setMetricIndices

        public void setMetricIndices​(int[] metricIndices)
        Sets the index of metric of components.
        Parameters:
        metricIndices - index of metrices of components to be used in MDSet.getDissimilarity( final Object other )
      • setWeight

        public void setWeight​(int componentIndex,
                              float w)
        Sets the weight of an individual component.
        Parameters:
        componentIndex - index of the component
        w - the weight of this component in MDSet.getDissimilarity( final Object other )
      • setUserDataWeight

        public void setUserDataWeight​(int index,
                                      float w)
        Sets the weight of an individual user data component.
        Parameters:
        index - index of the component
        w - the weight of this user data component
      • setMetricIndex

        public void setMetricIndex​(int componentIndex,
                                   int mi)
        Sets the index of metric used in the dissimilarity calculation by an individual component.
        Parameters:
        componentIndex - index of the component
        mi - index of the metric of this component in MDSet.getDissimilarity( final Object other )
      • size

        public int size()
        Get the size of the associated MDSet instance.
        Returns:
        number of components in the MDSet
      • getWeight

        public float getWeight​(int index)
        Gets the weight of a component.
        Parameters:
        index - index of a component
        Returns:
        the weight of the component
      • getUserDataWeight

        public float getUserDataWeight​(int index)
        Gets the weight of a userData component.
        Parameters:
        index - index of a component
        Returns:
        the weight of the component
      • getMetricIndex

        public int getMetricIndex​(int index)
        Gets the index of the metric used by a component to calculate the dissimilarity coefficient.
        Parameters:
        index - index of a component
        Returns:
        the index of the metric used by the specified component