Package jebl.evolution.characters

Class DiscreteCharacter

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

  • Constructor Details

    • DiscreteCharacter

      public DiscreteCharacter(String name, 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(String name, String desc, int numOfStates, 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 Details

    • setName

      public void setName(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 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(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 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 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 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(Map<Integer,String> stateDesc)
      Parameters:
      stateDesc - a Mapinvalid input: '<'Integer, String> of the state descriptions corresponding to the values

    • getStateDesc

      public Map<Integer,String> getStateDesc()
      Returns:
      the Mapinvalid input: '<'Integer, String> of the state descriptions corresponding to the values

    • getStateDesc

      public String getStateDesc(int state)
      Parameters:
      state - corresponding to the state
      Returns:
      state description