mesquite.categ.lib
Class MProteinEmbedded

java.lang.Object
  mesquite.lib.characters.MCharactersStates
      mesquite.categ.lib.MCategoricalStates
          mesquite.categ.lib.MCategoricalDistribution
              mesquite.categ.lib.MCategoricalEmbedded
                  mesquite.categ.lib.MProteinEmbedded

All Implemented Interfaces:

MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

public class MProteinEmbedded
extends MCategoricalEmbedded

Field Summary

Fields inherited from class mesquite.categ.lib.MCategoricalStates

extraFrequencies, frequencies

Fields inherited from class mesquite.lib.characters.MCharactersStates

data, totalCreated

Constructor Summary

MProteinEmbedded(CharacterData data)

Method Summary

long	getAllStates() returns the union of all state sets
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterState	getCharacterState(CharacterState cs, int ic, int it) get CharacterState at node N
java.lang.String	getDataTypeName() returns the name of the type of data stored
java.lang.Class	getStateClass() Indicates the type of character stored
MAdjustableDistribution	makeBlankAdjustable() return blank adjustable MCharactersDistribution if this same type
CharacterData	makeCharacterData(CharMatrixManager manager, Taxa taxa) return CharacterData filled with same values as this matrix

Methods inherited from class mesquite.categ.lib.MCategoricalEmbedded

getCharacterDistribution, getName, getNumChars, getNumTaxa, getState, getStateRaw

Methods inherited from class mesquite.categ.lib.MCategoricalDistribution

adjustHistorySize

Methods inherited from class mesquite.categ.lib.MCategoricalStates

copyExtraFrequencies, copyFrequencies, disposeExtraFrequencies, disposeFrequencies, extraFrequenciesExist, frequenciesExist, getExtraFrequencies, getExtraFrequency, getFrequencies, getFrequency, getNumExtraFreqCateg, getNumFreqCateg, setExtraFrequencies, setExtraFrequencies, setFrequencies, setFrequencies

Methods inherited from class mesquite.lib.characters.MCharactersStates

checkIllegalNode, getBasisTree, getNumNodes, getParentData, getTaxa, isCurrentlyIncluded, matrixToString, setBasisTree, setName, setTaxa

Methods inherited from class java.lang.Object

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

Methods inherited from interface mesquite.lib.characters.MCharactersDistribution

getBasisTree, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

getNumNodes, getParentData, getTaxa, isCurrentlyIncluded

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MProteinEmbedded

public MProteinEmbedded(CharacterData data)

Method Detail

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface MCharactersStatesHolder

Overrides:

getStateClass in class MCategoricalStates

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

returns the corresponding CharacterData subclass

Specified by:

getCharacterDataClass in interface MCharactersStatesHolder

Overrides:

getCharacterDataClass in class MCategoricalStates

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Specified by:

getDataTypeName in interface MCharactersStatesHolder

Overrides:

getDataTypeName in class MCategoricalStates

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int ic,
                                        int it)

get CharacterState at node N

Specified by:

getCharacterState in interface MCharactersStatesHolder

Overrides:

getCharacterState in class MCategoricalStates

makeBlankAdjustable

public MAdjustableDistribution makeBlankAdjustable()

return blank adjustable MCharactersDistribution if this same type

Specified by:

makeBlankAdjustable in interface MCharactersDistribution

Overrides:

makeBlankAdjustable in class MCategoricalDistribution

makeCharacterData

public CharacterData makeCharacterData(CharMatrixManager manager,
                                       Taxa taxa)

return CharacterData filled with same values as this matrix

Specified by:

makeCharacterData in interface MCharactersDistribution

Overrides:

makeCharacterData in class MCategoricalDistribution

getAllStates

public long getAllStates()

returns the union of all state sets

Overrides:

getAllStates in class MCategoricalStates