mesquite.genesis.lib
Class CharRatesCodePos

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.CharRatesCodePos

All Implemented Interfaces:

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

public class CharRatesCodePos
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

CharRatesCodePos()

CharRatesCodePos(double[] codePosRates)

Method Summary

void	addOptions(ExtensibleDialog dialog)
boolean	checkOptions()
java.lang.String	checkOptionsReport()
boolean	checkValidityCharRates()
CharacterModel	cloneModelWithMotherLink(CharacterModel formerClone)
void	copyToClone(CharacterModel md)
void	fromString(java.lang.String description, MesquiteInteger stringPos, int format) reads parameters from string (same format as written by "toSTring"
double[]	getCodePosRates()
java.lang.String	getNEXUSClassName() returns name of model class (e.g.
java.lang.String	getNexusSpecification() returns speficiations
java.lang.String	getParameters() returns parameters of the model.
void	initForNextCharacter()
void	initialize()
boolean	isFullySpecified() Returns whether parameters of model are fully specified.
boolean	needsEmpirical() Should be overridden to return true if submodel needs an empirical matrix
boolean	recoverOptions()
void	setCodePosRates(double[] codePosRates)
void	setNewRate(int ic)
void	setOptions()
void	setSeed(long seed)

Methods inherited from class mesquite.genesis.lib.CharRatesModel

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

Methods inherited from class mesquite.genesis.lib.ProbSubModel

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

Methods inherited from class mesquite.lib.characters.CharacterModel

allowUseOnDataSubclasses, changed, chooseExistingCharacterModel, chooseExistingCharacterModel, chooseNewCharacterModel, completeDaughterClone, dispose, disposing, findCurators, getEditCancel, getMother, getName, getNEXUSCommand, getNEXUSName, 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

CharRatesCodePos

public CharRatesCodePos(double[] codePosRates)

CharRatesCodePos

public CharRatesCodePos()

Method Detail

needsEmpirical

public boolean needsEmpirical()

Should be overridden to return true if submodel needs an empirical matrix

Overrides:

needsEmpirical in class ProbSubModel

initialize

public void initialize()

Overrides:

initialize in class CharRatesModel

setSeed

public void setSeed(long seed)

Overrides:

setSeed in class ProbSubModel

cloneModelWithMotherLink

public CharacterModel cloneModelWithMotherLink(CharacterModel formerClone)

Specified by:

cloneModelWithMotherLink in class ProbSubModel

copyToClone

public void copyToClone(CharacterModel md)

Overrides:

copyToClone in class CharacterModel

setNewRate

public void setNewRate(int ic)

checkValidityCharRates

public boolean checkValidityCharRates()

Overrides:

checkValidityCharRates in class CharRatesModel

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

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

setCodePosRates

public void setCodePosRates(double[] codePosRates)

getCodePosRates

public double[] getCodePosRates()

initForNextCharacter

public void initForNextCharacter()

Specified by:

initForNextCharacter in class CharRatesModel

getNexusSpecification

public java.lang.String getNexusSpecification()

returns speficiations

Overrides:

getNexusSpecification in class CharacterModel

fromString

public void fromString(java.lang.String description,
                       MesquiteInteger stringPos,
                       int format)

reads parameters from string (same format as written by "toSTring"

Overrides:

fromString in class CharacterModel

getNEXUSClassName

public java.lang.String getNEXUSClassName()

returns name of model class (e.g. "stepmatrix")

Overrides:

getNEXUSClassName in class CharacterModel

getParameters

public java.lang.String getParameters()

returns parameters of the model.

Overrides:

getParameters in class CharRatesModel