Package org.biojavax.ga.util

Class WeightedSet

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable, java.util.Collection, java.util.Set
    public class WeightedSet
extends java.util.AbstractSet
implements java.io.Serializable

    Inspred by the BioJava Distribution objects the WeightedSet is a map from a Key to a Weight. Unlike Distributions the Keys do not have to be Symbols. In the GA package the WeightedMap is useful for sampling Organisms according to their fitness.

    When Symbols are added or their weights are set then the weights are internally normalized to 1

    Since:
    1.5
    Version:
    1.0
    Author:
    Mark Schreiber
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      WeightedSet()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean add​(java.lang.Object o)
      Adds a new Object with a weight of zero.
      boolean addAll​(java.util.Collection c)  
      java.util.Map asMap()
      Converts the Set to a map from key Objects to Double weights.
      void clear()  
      boolean contains​(java.lang.Object o)  
      boolean containsAll​(java.util.Collection c)  
      protected double getTotalWeight()
      The total weight that has been added to this Set.
      double getWeight​(java.lang.Object o)
      Determines the normalized weight for o
      boolean isEmpty()  
      java.util.Iterator iterator()
      Returns an unmodifiable iterator over the keys of the set.
      boolean remove​(java.lang.Object o)  
      boolean retainAll​(java.util.Collection c)  
      java.lang.Object sample()
      Randomly samples an Object from the Set according to its weight.
      void setWeight​(java.lang.Object o, double w)
      Sets the weight of an Object.
      int size()  
      java.lang.Object[] toArray()  

      • Methods inherited from class java.util.AbstractSet

        equals, hashCode, removeAll

      • Methods inherited from class java.util.AbstractCollection

        toArray, toString

      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, notify, notifyAll, wait, wait, wait

      • Methods inherited from interface java.util.Collection

        parallelStream, removeIf, stream, toArray

      • Methods inherited from interface java.lang.Iterable

        forEach

      • Methods inherited from interface java.util.Set

        spliterator, toArray

    • Constructor Detail

      • WeightedSet

        public WeightedSet()

    • Method Detail

      • asMap

        public java.util.Map asMap()
        Converts the Set to a map from key Objects to Double weights.
        Returns:
        a Map with all the key-weight mappings. Weights are not normalized in this map.

      • sample

        public java.lang.Object sample()
        Randomly samples an Object from the Set according to its weight.
        Returns:
        the Object sampled.

      • getWeight

        public double getWeight​(java.lang.Object o)
                 throws java.util.NoSuchElementException
        Determines the normalized weight for o
        Parameters:
        o - the Object you want to know the weight of
        Returns:
        the normalized weight
        Throws:
        java.util.NoSuchElementException - if o is not found in this set

      • getTotalWeight

        protected double getTotalWeight()
        The total weight that has been added to this Set.
        Returns:
        the total weight (the value that can be used for normalizing)

      • setWeight

        public void setWeight​(java.lang.Object o,
                      double w)
        Sets the weight of an Object. If the Object is not in this Set then it is added.
        Parameters:
        o - the Object
        w - the weight.
        Throws:
        java.lang.IllegalArgumentException - if w is < 0.0

      • contains

        public boolean contains​(java.lang.Object o)
        Specified by:
        contains in interface java.util.Collection
        Specified by:
        contains in interface java.util.Set
        Overrides:
        contains in class java.util.AbstractCollection

      • remove

        public boolean remove​(java.lang.Object o)
        Specified by:
        remove in interface java.util.Collection
        Specified by:
        remove in interface java.util.Set
        Overrides:
        remove in class java.util.AbstractCollection

      • isEmpty

        public boolean isEmpty()
        Specified by:
        isEmpty in interface java.util.Collection
        Specified by:
        isEmpty in interface java.util.Set
        Overrides:
        isEmpty in class java.util.AbstractCollection

      • retainAll

        public boolean retainAll​(java.util.Collection c)
        Specified by:
        retainAll in interface java.util.Collection
        Specified by:
        retainAll in interface java.util.Set
        Overrides:
        retainAll in class java.util.AbstractCollection

      • add

        public boolean add​(java.lang.Object o)
        Adds a new Object with a weight of zero. Equivalent to setWeight(o, 0.0);
        Specified by:
        add in interface java.util.Collection
        Specified by:
        add in interface java.util.Set
        Overrides:
        add in class java.util.AbstractCollection
        Parameters:
        o - the object to add.
        Returns:
        true if this Object has not been added before.

      • size

        public int size()
        Specified by:
        size in interface java.util.Collection
        Specified by:
        size in interface java.util.Set
        Specified by:
        size in class java.util.AbstractCollection

      • containsAll

        public boolean containsAll​(java.util.Collection c)
        Specified by:
        containsAll in interface java.util.Collection
        Specified by:
        containsAll in interface java.util.Set
        Overrides:
        containsAll in class java.util.AbstractCollection

      • toArray

        public java.lang.Object[] toArray()
        Specified by:
        toArray in interface java.util.Collection
        Specified by:
        toArray in interface java.util.Set
        Overrides:
        toArray in class java.util.AbstractCollection

      • clear

        public void clear()
        Specified by:
        clear in interface java.util.Collection
        Specified by:
        clear in interface java.util.Set
        Overrides:
        clear in class java.util.AbstractCollection

      • iterator

        public java.util.Iterator iterator()
        Returns an unmodifiable iterator over the keys of the set.
        Specified by:
        iterator in interface java.util.Collection
        Specified by:
        iterator in interface java.lang.Iterable
        Specified by:
        iterator in interface java.util.Set
        Specified by:
        iterator in class java.util.AbstractCollection
        Returns:
        an Iterator

      • addAll

        public boolean addAll​(java.util.Collection c)
        Specified by:
        addAll in interface java.util.Collection
        Specified by:
        addAll in interface java.util.Set
        Overrides:
        addAll in class java.util.AbstractCollection