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Class mesquite.lib.CharacterStates 

java.lang.Object
   |
   +----mesquite.lib.CharacterStates
public abstract class CharacterStates
extends java.lang.Object
implements mesquite.lib.CharacterStatesHolder, mesquite.lib.Listable
Stores the character states at a series of terminal taxa or nodes in a tree. The class on which particular classes implementing CharacterDistribution and CharacterHistory are based.

Variable Index

o characterNumber
o data
o totalCreated

Constructor Index

o CharacterStates(Taxa)

Method Index

o checkIllegalNode(int, int)
o firstIsGreater(int, int)
o getCharacterDataClass()
o getCharacterState(CharacterState, int)
o getDefaultModel(MesquiteProject, String)
o getName()
returns name
o getNumNodes()
o getNumTaxa()
o getParentCharacter()
returns parent character of this CharacterStates
o getParentData()
returns parent data of this CharacterStates.
o getStateClass()
o getTaxa()
returns taxa object
o isInapplicable(int)
o isUnassigned(int)
o logStates()
o makeCharacterState()
o setName(String)
sets name
o setParentCharacter(int)
sets the parent character number from which this CharacterDistribution is derived or related.
o setParentData(CharacterData)
sets the parent CharacterData from which this CharacterDistribution is derived or related
o setTaxa(Taxa)
sets taxa object
o statesEqual(int, int)
o toExternal(int)
Translates internal numbering system of characters to external (currently, 0 based to 1 based
o toInternal(int)
Translates external numbering system of characters to internal (currently, 1 based to 0 based
o toString(int)

Variables

o data 
 protected mesquite.lib.CharacterData data
o characterNumber 
 protected int characterNumber
o totalCreated 
 public static long totalCreated

Constructors

o CharacterStates 
 public CharacterStates(mesquite.lib.Taxa taxa)

Methods

o makeCharacterState 
 public mesquite.lib.CharacterState makeCharacterState()
o getTaxa 
 public mesquite.lib.Taxa getTaxa()
returns taxa object

o setTaxa 
 public void setTaxa(mesquite.lib.Taxa taxa)
sets taxa object

o getName 
 public java.lang.String getName()
returns name

o setName 
 public void setName(java.lang.String name)
sets name

o getParentData 
 public mesquite.lib.CharacterData getParentData()
returns parent data of this CharacterStates. There is not a corresponding set procedure because the parent data is set either by the constructor (for Embedded distributions) or by a set procedure (for History or Adjustables)

o getParentCharacter 
 public int getParentCharacter()
returns parent character of this CharacterStates

o checkIllegalNode 
 protected boolean checkIllegalNode(int node,
                                    int where)
o setParentData 
 public void setParentData(mesquite.lib.CharacterData cd)
sets the parent CharacterData from which this CharacterDistribution is derived or related

o setParentCharacter 
 public void setParentCharacter(int ic)
sets the parent character number from which this CharacterDistribution is derived or related.

o toExternal 
 public static int toExternal(int i)
Translates internal numbering system of characters to external (currently, 0 based to 1 based

o toInternal 
 public static int toInternal(int i)
Translates external numbering system of characters to internal (currently, 1 based to 0 based

o getCharacterState 
 public abstract mesquite.lib.CharacterState getCharacterState(mesquite.lib.CharacterState cs,
                                                               int N)
o logStates 
 public abstract void logStates()
o getStateClass 
 public abstract java.lang.Class getStateClass()
o isUnassigned 
 public abstract boolean isUnassigned(int N)
o getCharacterDataClass 
 public abstract java.lang.Class getCharacterDataClass()
o firstIsGreater 
 public abstract boolean firstIsGreater(int N,
                                        int M)
o statesEqual 
 public abstract boolean statesEqual(int n,
                                     int m)
o getNumNodes 
 public abstract int getNumNodes()
o toString 
 public abstract java.lang.String toString(int taxon)
o getNumTaxa 
 public abstract int getNumTaxa()
o isInapplicable 
 public abstract boolean isInapplicable(int N)
o getDefaultModel 
 public abstract mesquite.lib.CharacterModel getDefaultModel(mesquite.lib.MesquiteProject proj,
                                                             java.lang.String paradigm)

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