mesquite.categ.lib
Class MProteinAdjustable

java.lang.Object
  mesquite.lib.characters.MCharactersStates
      mesquite.categ.lib.MCategoricalStates
          mesquite.categ.lib.MCategoricalDistribution
              mesquite.categ.lib.MCategoricalAdjustable
                  mesquite.categ.lib.MProteinAdjustable

All Implemented Interfaces:

Annotatable, MAdjustableDistribution, MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

public class MProteinAdjustable
extends MCategoricalAdjustable

Field Summary

Fields inherited from class mesquite.categ.lib.MCategoricalStates

extraFrequencies, frequencies

Fields inherited from class mesquite.lib.characters.MCharactersStates

data, totalCreated

Constructor Summary

MProteinAdjustable()

MProteinAdjustable(Taxa taxa)

MProteinAdjustable(Taxa taxa, int numChars, int numTaxa)

Method Summary

MCharactersHistory	adjustHistorySize(Tree tree, MCharactersHistory charStates) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
long	getAllStates() returns the union of all state sets
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterDistribution	getCharacterDistribution(int ic) return CharacterDistribution object for character ic
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.MCategoricalAdjustable

deassignStates, getAnnotation, getNumChars, getNumTaxa, getState, setAnnotation, setCharacterState, setParentData, setSize, setState, tradeStatesBetweenTaxa, transferFrom

Methods inherited from class mesquite.categ.lib.MCategoricalDistribution

getStateRaw

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, getName, 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.MAdjustableDistribution

setTaxa

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.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MProteinAdjustable

public MProteinAdjustable(Taxa taxa,
                          int numChars,
                          int numTaxa)

MProteinAdjustable

public MProteinAdjustable(Taxa taxa)

MProteinAdjustable

public MProteinAdjustable()

Method Detail

getCharacterDistribution

public CharacterDistribution getCharacterDistribution(int ic)

Description copied from class: MCategoricalAdjustable

return CharacterDistribution object for character ic

Specified by:

getCharacterDistribution in interface MCharactersDistribution

Overrides:

getCharacterDistribution in class MCategoricalAdjustable

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 MCategoricalAdjustable

getAllStates

public long getAllStates()

returns the union of all state sets

Overrides:

getAllStates in class MCategoricalStates

adjustHistorySize

public MCharactersHistory adjustHistorySize(Tree tree,
                                            MCharactersHistory charStates)

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

Specified by:

adjustHistorySize in interface MCharactersDistribution

Overrides:

adjustHistorySize in class MCategoricalDistribution