mesquite.genesis.lib
Class CharRatesGamma

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.CharRatesGamma

All Implemented Interfaces:

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

public class CharRatesGamma
extends CharRatesModel

A class that provides for a site-to-site rate variation model using the gamma distribution.

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

CharRatesGamma()

CharRatesGamma(double shape, boolean isDiscrete, int numCategories)

Method Summary

void	addOptions(ExtensibleDialog dialog) adds items to extensible dialog box used for setting parameter values
void	calculateDiscreteRates()
boolean	checkOptions()
java.lang.String	checkOptionsReport()
CharacterModel	cloneModelWithMotherLink(CharacterModel formerClone)
void	copyToClone(CharacterModel pm)
void	fromString(java.lang.String description, MesquiteInteger stringPos, int format) reads parameters from string (same format as written by "toString")
java.lang.String	getNEXUSClassName() returns name of model class (e.g.
java.lang.String	getNexusSpecification() returns specifications
java.lang.String	getParameters() returns parameters of the model.
double	getShape()
void	initForNextCharacter()
boolean	isFullySpecified() Returns whether parameters of model are fully specified.
double	meanRate(double lowerBoundary, double upperBoundary, double increment) Calculates mean value for a section of a gamma distribution.
boolean	recoverOptions() recovers values from items in extensible dialog box used for setting parameter values
void	setOptions() moves parameter values from temporary storage (where they were put from dialog box) into permanent storage.
void	setSeed(long seed)
void	setShape(double shape)

Methods inherited from class mesquite.genesis.lib.CharRatesModel

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

Methods inherited from class mesquite.genesis.lib.ProbSubModel

addModelOptions, getCharacterDistribution, getDefaultNumChars, getMCharactersStatesHolder, isLineageSpecific, needsEmpirical, 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

CharRatesGamma

public CharRatesGamma(double shape,
                      boolean isDiscrete,
                      int numCategories)

CharRatesGamma

public CharRatesGamma()

Method Detail

cloneModelWithMotherLink

public CharacterModel cloneModelWithMotherLink(CharacterModel formerClone)

Specified by:

cloneModelWithMotherLink in class ProbSubModel

copyToClone

public void copyToClone(CharacterModel pm)

Overrides:

copyToClone in class CharacterModel

getNexusSpecification

public java.lang.String getNexusSpecification()

returns specifications

Overrides:

getNexusSpecification in class CharacterModel

setSeed

public void setSeed(long seed)

Overrides:

setSeed in class ProbSubModel

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

addOptions

public void addOptions(ExtensibleDialog dialog)

adds items to extensible dialog box used for setting parameter values

Specified by:

addOptions in class ProbSubModel

recoverOptions

public boolean recoverOptions()

recovers values from items in extensible dialog box used for setting parameter values

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()

moves parameter values from temporary storage (where they were put from dialog box) into permanent storage.

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

meanRate

public double meanRate(double lowerBoundary,
                       double upperBoundary,
                       double increment)

Calculates mean value for a section of a gamma distribution.

calculateDiscreteRates

public void calculateDiscreteRates()

setShape

public void setShape(double shape)

getShape

public double getShape()

initForNextCharacter

public void initForNextCharacter()

Specified by:

initForNextCharacter in class CharRatesModel

getParameters

public java.lang.String getParameters()

returns parameters of the model.

Overrides:

getParameters in class CharRatesModel