mesquite.genesis.lib
Class CharRatesEqual

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
                                      mesquite.genesis.lib.CharRatesEqual

All Implemented Interfaces:

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

public class CharRatesEqual
extends CharRatesModel

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

CharRatesEqual()

Method Summary

void	addOptions(ExtensibleDialog dialog)
boolean	checkOptions()
java.lang.String	checkOptionsReport()
CharacterModel	cloneModelWithMotherLink(CharacterModel formerClone)
java.lang.String	getName() returns name of model
java.lang.String	getNEXUSName() returns name of model
java.lang.String	getNexusSpecification() return the NEXUS-format string describing the model.
java.lang.String	getParameters() returns parameters of the model.
double	getRate(int ic)
void	initForNextCharacter()
boolean	isBuiltIn() returns whether model is built in
boolean	isFullySpecified() Returns whether parameters of model are fully specified.
boolean	recoverOptions()
void	setOptions()

Methods inherited from class mesquite.genesis.lib.CharRatesModel

checkValidityCharRates, getCapitalizedTypeName, getExplanation, getModelTypeName, getParadigm, getRate, initialize, setRate, taxaSet

Methods inherited from class mesquite.genesis.lib.ProbSubModel

addModelOptions, getCharacterDistribution, getDefaultNumChars, getMCharactersStatesHolder, isLineageSpecific, needsEmpirical, recalcAfterSetMCharactersStatesHolder, recoverModelOptions, setCharacterDistribution, setCompositProbCategModel, setDefaultNumChars, setMCharactersStatesHolder, setSeed, toString

Methods inherited from class mesquite.lib.characters.CharacterModel

allowUseOnDataSubclasses, changed, chooseExistingCharacterModel, chooseExistingCharacterModel, chooseNewCharacterModel, completeDaughterClone, copyToClone, dispose, disposing, findCurators, fromString, getEditCancel, getMother, getNEXUSClassName, getNEXUSCommand, getSettingsString, getSnapshot, getStateClass, getStateClassName, getTypeName, 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

CharRatesEqual

public CharRatesEqual()

Method Detail

getRate

public double getRate(int ic)

Overrides:

getRate in class CharRatesModel

getNexusSpecification

public java.lang.String getNexusSpecification()

Description copied from class: CharacterModel

return the NEXUS-format string describing the model. The string begins at the point of the modelSpecification in "USERTYPE modelName (modelClassName) = modelSpecification;"

Overrides:

getNexusSpecification in class CharacterModel

cloneModelWithMotherLink

public CharacterModel cloneModelWithMotherLink(CharacterModel formerClone)

Specified by:

cloneModelWithMotherLink in class ProbSubModel

initForNextCharacter

public void initForNextCharacter()

Specified by:

initForNextCharacter in class CharRatesModel

isFullySpecified

public boolean isFullySpecified()

Description copied from class: ProbSubModel

Returns whether parameters of model are fully specified. If so, it can be used for evolving states.

Specified by:

isFullySpecified in class ProbSubModel

isBuiltIn

public boolean isBuiltIn()

returns whether model is built in

Overrides:

isBuiltIn in class CharacterModel

addOptions

public void addOptions(ExtensibleDialog dialog)

Specified by:

addOptions in class ProbSubModel

recoverOptions

public boolean recoverOptions()

Specified by:

recoverOptions in class ProbSubModel

checkOptions

public boolean checkOptions()

Specified by:

checkOptions in class ProbSubModel

checkOptionsReport

public java.lang.String checkOptionsReport()

Specified by:

checkOptionsReport in class ProbSubModel

setOptions

public void setOptions()

Specified by:

setOptions in class ProbSubModel

getName

public java.lang.String getName()

returns name of model

Specified by:

getName in interface HNode

Specified by:

getName in interface Listable

Overrides:

getName in class CharacterModel

getNEXUSName

public java.lang.String getNEXUSName()

returns name of model

Overrides:

getNEXUSName in class CharacterModel

getParameters

public java.lang.String getParameters()

returns parameters of the model.

Overrides:

getParameters in class CharRatesModel