Package jebl.evolution.characters

Class DiscreteCharacter

  • All Implemented Interfaces:
    Character
    public class DiscreteCharacter
extends java.lang.Object
implements Character
    Author:
    Stephen A. Smith

    • Constructor Summary

      Constructors 
      Constructor Description
      DiscreteCharacter​(java.lang.String name, java.lang.String desc, int numOfStates)
      Constructs a basic DiscreteCharacter object with no taxa added yet
      DiscreteCharacter​(java.lang.String name, java.lang.String desc, int numOfStates, java.util.Set<Taxon> taxa)
      Constructs a basic DiscreteCharacter object with taxa

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addTaxon​(Taxon taxon)
      add a taxon with this character
      java.lang.String getDesc()
      return the description of the character
      java.lang.String getName()
      return the name of the character
      double getNumOfStates()  
      java.util.Map<java.lang.Integer,​java.lang.String> getStateDesc()  
      java.lang.String getStateDesc​(int state)  
      java.util.Set<Taxon> getTaxa()
      get a Set of all the taxa for this character
      CharacterType getType()
      return the CharacterType of the character
      java.lang.Object getValue​(Taxon taxon)
      get a value for a taxon containing the character
      boolean isOrdered()  
      void setDesc​(java.lang.String desc)
      set the description of the character
      void setIsOrdered​(boolean isOrdered)  
      void setName​(java.lang.String name)
      set the name of the character
      void setNumOfStates​(int numOfStates)  
      void setStateDesc​(java.util.Map<java.lang.Integer,​java.lang.String> stateDesc)  

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • DiscreteCharacter

        public DiscreteCharacter​(java.lang.String name,
                         java.lang.String desc,
                         int numOfStates)
        Constructs a basic DiscreteCharacter object with no taxa added yet
        Parameters:
        name - the name of the character
        desc - the description of the character
        numOfStates - the number of possible states for the character

      • DiscreteCharacter

        public DiscreteCharacter​(java.lang.String name,
                         java.lang.String desc,
                         int numOfStates,
                         java.util.Set<Taxon> taxa)
        Constructs a basic DiscreteCharacter object with taxa
        Parameters:
        name - the name of the character
        desc - the description of the character
        numOfStates - the number of possible states for the character
        taxa - the Set containing the taxa with this character

    • Method Detail

      • setName

        public void setName​(java.lang.String name)
        Description copied from interface: Character
        set the name of the character
        Specified by:
        setName in interface Character
        Parameters:
        name - the name of the character

      • getName

        public java.lang.String getName()
        Description copied from interface: Character
        return the name of the character
        Specified by:
        getName in interface Character
        Returns:
        the name of the character

      • setDesc

        public void setDesc​(java.lang.String desc)
        Description copied from interface: Character
        set the description of the character
        Specified by:
        setDesc in interface Character
        Parameters:
        desc - the description of the character

      • getDesc

        public java.lang.String getDesc()
        Description copied from interface: Character
        return the description of the character
        Specified by:
        getDesc in interface Character
        Returns:
        the description of the character

      • getType

        public CharacterType getType()
        Description copied from interface: Character
        return the CharacterType of the character
        Specified by:
        getType in interface Character
        Returns:
        the CharacterType of the character

      • addTaxon

        public void addTaxon​(Taxon taxon)
        Description copied from interface: Character
        add a taxon with this character
        Specified by:
        addTaxon in interface Character
        Parameters:
        taxon - the taxon to add containing the character

      • getValue

        public java.lang.Object getValue​(Taxon taxon)
        Description copied from interface: Character
        get a value for a taxon containing the character
        Specified by:
        getValue in interface Character
        Parameters:
        taxon - the taxon to get the value for
        Returns:
        the Object value of the character for the given taxon

      • isOrdered

        public boolean isOrdered()
        Returns:
        whether character is ordered or not

      • setIsOrdered

        public void setIsOrdered​(boolean isOrdered)
        Parameters:
        isOrdered - set whether character is ordered or not

      • getNumOfStates

        public double getNumOfStates()
        Returns:
        the number of possible states for the character

      • setNumOfStates

        public void setNumOfStates​(int numOfStates)
        Parameters:
        numOfStates - the number of possible states for the characeter

      • getTaxa

        public java.util.Set<Taxon> getTaxa()
        Description copied from interface: Character
        get a Set of all the taxa for this character
        Specified by:
        getTaxa in interface Character
        Returns:
        a Set containing all of the taxa for this character

      • setStateDesc

        public void setStateDesc​(java.util.Map<java.lang.Integer,​java.lang.String> stateDesc)
        Parameters:
        stateDesc - a Map of the state descriptions corresponding to the values

      • getStateDesc

        public java.util.Map<java.lang.Integer,​java.lang.String> getStateDesc()
        Returns:
        the Map of the state descriptions corresponding to the values

      • getStateDesc

        public java.lang.String getStateDesc​(int state)
        Parameters:
        state - corresponding to the state
        Returns:
        state description