mesquite.genesis.lib
Class CharRatesModel

java.lang.Object
  mesquite.lib.Listened
      mesquite.lib.Attachable
          mesquite.lib.Associable
              mesquite.lib.AssociableWithSpecs
                  mesquite.lib.FileElement
                      mesquite.lib.characters.CharacterModel
                          mesquite.lib.characters.CharacterSubmodel
                              mesquite.genesis.lib.ProbSubModel
                                  mesquite.genesis.lib.CharRatesModel

All Implemented Interfaces:

Annotatable, Commandable, CompatibilityChecker, Doomable, Explainable, FileDirtier, HNode, HTMLDescribable, Identifiable, Listable, Listenable, MesquiteListener, Renamable, Selectionable, Showable

Direct Known Subclasses:

CharRatesCodePos, CharRatesEqual, CharRatesGamma, CharRatesGammaInvar, CharRatesInvar

public abstract class CharRatesModel
extends ProbSubModel

A class that provides for a site-to-site rate variation model.

Field Summary

Fields inherited from class mesquite.lib.characters.CharacterModel

MesquiteNEXUSFormat, NEXUSFormat, XMLFormat

Fields inherited from class mesquite.lib.FileElement

assignedIDNumber, assignedIDString, classesCreated, classesFinalized, countsOfClasses, countsOfClassesDisposed, DIRTY, doomed, IN_USE, OK, totalCreated, totalDisposed, totalFinalized

Fields inherited from class mesquite.lib.AssociableWithSpecs

SPECSSET_CHANGED

Fields inherited from class mesquite.lib.Associable

comment, comments, numParts, rememberDefaultOrder, selected, versionNumber

Fields inherited from class mesquite.lib.Listened

allListeners, classes, classesNotified, listenersRemaining, notifications

Fields inherited from interface mesquite.lib.MesquiteListener

ANNOTATION_ADDED, ANNOTATION_CHANGED, ANNOTATION_DELETED, ASSOCIATED_CHANGED, BRANCHES_REARRANGED, BRANCHLENGTHS_CHANGED, COMMAND_CANCELLED, DATA_CHANGED, ELEMENT_CHANGED, ITEMS_ADDED, NAMES_CHANGED, OBJECT_DESTROYED, PARTS_ADDED, PARTS_CHANGED, PARTS_DELETED, PARTS_MOVED, SELECTION_CHANGED, TAXA_SUBSTITUTED, TEXTFIELD_EDITED, UNKNOWN, VALUE_CHANGED

Fields inherited from interface mesquite.lib.HNode

MOUSEDOWN, MOUSEEXIT, MOUSEMOVE

Fields inherited from interface mesquite.lib.HTMLDescribable

verbose

Constructor Summary

CharRatesModel()

CharRatesModel(java.lang.String name, java.lang.Class stateClass)

Method Summary

boolean	checkValidityCharRates()
java.lang.String	getCapitalizedTypeName() Returns nexus command introducing this model.
java.lang.String	getExplanation() return an explanation of the model.
java.lang.String	getModelTypeName()
java.lang.String	getParadigm() returns the paradigm (e.g.
java.lang.String	getParameters() returns parameters of the model.
double	getRate()
double	getRate(int ic)
abstract void	initForNextCharacter()
void	initialize()
void	setRate(double newRate)
void	taxaSet()

Methods inherited from class mesquite.genesis.lib.ProbSubModel

addModelOptions, addOptions, checkOptions, checkOptionsReport, cloneModelWithMotherLink, getCharacterDistribution, getDefaultNumChars, getMCharactersStatesHolder, isFullySpecified, isLineageSpecific, needsEmpirical, recalcAfterSetMCharactersStatesHolder, recoverModelOptions, recoverOptions, setCharacterDistribution, setCompositProbCategModel, setDefaultNumChars, setMCharactersStatesHolder, setOptions, setSeed, toString

Methods inherited from class mesquite.lib.characters.CharacterModel

allowUseOnDataSubclasses, changed, chooseExistingCharacterModel, chooseExistingCharacterModel, chooseNewCharacterModel, completeDaughterClone, copyToClone, dispose, disposing, findCurators, fromString, getEditCancel, getMother, getName, getNEXUSClassName, getNEXUSCommand, getNEXUSName, getNexusSpecification, getSettingsString, getSnapshot, getStateClass, getStateClassName, getTypeName, isBuiltIn, isCompatible, isDisposed, isReversible, okToDispose, originalChanged, setBuiltIn, setEditCancel, setName

Methods inherited from class mesquite.lib.FileElement

addToBrowserPopup, addToFile, deleteMe, doCommand, doom, fileDirtiedByCommand, finalize, getAssignedID, getAssignedIDNumber, getCIPResIDString, getFile, getFileName, getHColor, getHDaughters, getHImage, getHMother, getHShow, getID, getLastModifiedAuthor, getManager, getNexusBlock, getNumSupplements, getProject, getSupplementName, hNodeAction, hSupplementTouched, isDoomed, okToClose, searchData, setAssignedIDNumber, setCIPResIDString, setFile, setManager, setProject, show, showMe, stampLastModifiedAuthor

Methods inherited from class mesquite.lib.AssociableWithSpecs

addParts, deleteParts, equalizeParts, getCurrentSpecsSet, getNumSpecsSets, getSpecSetsVector, getSpecSetsVectorVector, getSpecsSet, getSpecsSet, listAssociates, moveParts, prepareSpecsSetVector, removeSpecsSet, setCurrentSpecsSet, storeSpecsSet, swapParts, toHTMLStringDescription

Methods inherited from class mesquite.lib.Associable

anyAssociatedObject, anySelected, clearAllAssociatedBits, contiguousSelection, contiguousSelectionOld, copyCurrentToPreviousOrder, deassignAllAssociatedLongs, deassignAssociated, deassignAssociated, deleteJustAdded, deselectAll, equalizeParts, exchangeAssociated, firstSelected, getAnnotation, getAnnotation, getAssociatedBit, getAssociatedBits, getAssociatedDouble, getAssociatedDoubles, getAssociatedLong, getAssociatedLongs, getAssociatedObject, getAssociatedObjects, getDefaultPosition, getDirty, getJustAdded, getNumberAssociatedBits, getNumberAssociatedDoubles, getNumberAssociatedLongs, getNumberAssociatedObjects, getNumberOfParts, getNumberOfSelectableParts, getSelected, getSelectedBits, getVersionNumber, getWhichAssociatedBits, getWhichAssociatedDouble, getWhichAssociatedLong, getWhichAssociatedObject, inBounds, lastSelected, makeAssociatedBits, makeAssociatedDoubles, makeAssociatedLongs, makeAssociatedObjects, numberSelected, numberSelected, readAssociated, recordCurrentOrder, recordDefaultOrder, recordPreviousOrder, removeAssociatedBits, removeAssociatedDoubles, removeAssociatedLongs, removeAssociatedObjects, resetDefaultOrderToCurrent, resetJustAdded, restoreToPreviousOrder, selectAll, setAnnotation, setAnnotation, setAssociatedBit, setAssociatedDouble, setAssociatedLong, setAssociatedObject, setAssociateds, setDefaultPosition, setDirty, setJustAdded, setNumberOfParts, setSelected, transferAssociated, writeAssociated, zeroAllAssociatedDoubles, zeroAllAssociatedLongs, zeroAllAssociatedObjects

Methods inherited from class mesquite.lib.Attachable

anyAttachments, attach, attachIfUniqueName, detach, getAttachment, getAttachment, getAttachments, listAttachments, readAttachments, setAttachments, writeAttachments

Methods inherited from class mesquite.lib.Listened

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, doAfterNotify, getRemainingListeners, incrementNotifySuppress, listListeners, notifyDisposing, notifyListeners, notifyListeners, removeListener, reportListeners, setDumpNotified

Methods inherited from class java.lang.Object

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

Methods inherited from interface mesquite.lib.Annotatable

getAnnotation, setAnnotation

Methods inherited from interface mesquite.lib.Listenable

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, incrementNotifySuppress, listListeners, notifyListeners, removeListener

Constructor Detail

CharRatesModel

public CharRatesModel(java.lang.String name,
                      java.lang.Class stateClass)

CharRatesModel

public CharRatesModel()

Method Detail

getCapitalizedTypeName

public java.lang.String getCapitalizedTypeName()

Returns nexus command introducing this model.

initialize

public void initialize()

Specified by:

initialize in class ProbSubModel

taxaSet

public void taxaSet()

Specified by:

taxaSet in class ProbSubModel

checkValidityCharRates

public boolean checkValidityCharRates()

getRate

public double getRate(int ic)

getRate

public double getRate()

setRate

public void setRate(double newRate)

initForNextCharacter

public abstract void initForNextCharacter()

getExplanation

public java.lang.String getExplanation()

Description copied from class: CharacterModel

return an explanation of the model.

Specified by:

getExplanation in interface Explainable

Specified by:

getExplanation in class CharacterModel

getParadigm

public java.lang.String getParadigm()

Description copied from class: CharacterModel

returns the paradigm (e.g. "parsimony") of the model. Mostly used for user's information

Specified by:

getParadigm in class CharacterModel

getParameters

public java.lang.String getParameters()

returns parameters of the model.

getModelTypeName

public java.lang.String getModelTypeName()

Specified by:

getModelTypeName in class CharacterModel