mesquite.genesis.lib
Class CharRateMatrixModelSet

java.lang.Object
  mesquite.lib.Listened
      mesquite.lib.Attachable
          mesquite.lib.Associable
              mesquite.lib.AssociableWithSpecs
                  mesquite.lib.FileElement
                      mesquite.lib.SpecsSet
                          mesquite.lib.ObjectSpecsSet
                              mesquite.lib.characters.CharObjectSpecsSet
                                  mesquite.lib.characters.ModelSet
                                      mesquite.genesis.lib.CharRateMatrixModelSet

All Implemented Interfaces:

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

public class CharRateMatrixModelSet
extends ModelSet

a ModelSet for probability models.

Field Summary

Fields inherited from class mesquite.lib.characters.CharObjectSpecsSet

data

Fields inherited from class mesquite.lib.SpecsSet

totalCreated

Fields inherited from class mesquite.lib.FileElement

assignedIDNumber, assignedIDString, classesCreated, classesFinalized, countsOfClasses, countsOfClassesDisposed, DIRTY, disposed, doomed, IN_USE, name, OK, 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, listeners, listenersRemaining, notifications

Fields inherited from interface mesquite.lib.HNode

MOUSEDOWN, MOUSEEXIT, MOUSEMOVE

Fields inherited from interface mesquite.lib.HTMLDescribable

verbose

Constructor Summary

CharRateMatrixModelSet(java.lang.String name, int numChars, CharacterModel defaultModel, CharacterData data)

Method Summary

SpecsSet	cloneSpecsSet()
SpecsSet	makeSpecsSet(AssociableWithSpecs parent, int numParts)

Methods inherited from class mesquite.lib.characters.ModelSet

getDefaultModel, getDefaultModel, getModel, getModels, getNewPropertyStorage, getTypeName, setDefaultModel, setModel, toString

Methods inherited from class mesquite.lib.characters.CharObjectSpecsSet

getCharacterData, getNumChars

Methods inherited from class mesquite.lib.ObjectSpecsSet

addParts, deleteParts, disposing, equalizeSpecs, getDefaultProperty, getDefaultProperty, getProperties, getProperty, moveParts, setDefaultProperty, setProperty, swapParts, toString

Methods inherited from class mesquite.lib.SpecsSet

getNexusBlockStored, getNumberOfParts, getParent, setChangedFromCloned, setNexusBlockStored, setParent, toHTMLStringDescription

Methods inherited from class mesquite.lib.FileElement

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

Methods inherited from class mesquite.lib.AssociableWithSpecs

equalizeParts, getCurrentSpecsSet, getNumSpecsSets, getSpecSetsVector, getSpecSetsVectorVector, getSpecsSet, getSpecsSet, listAssociates, prepareSpecsSetVector, removeSpecsSet, setCurrentSpecsSet, storeSpecsSet

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, getNumberOfSelectableParts, getSelected, getSelectedBits, getSnapshot, 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.characters.CharSpecsSet

addParts, deleteParts, moveParts, swapParts

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Identifiable

getID

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

CharRateMatrixModelSet

public CharRateMatrixModelSet(java.lang.String name,
                              int numChars,
                              CharacterModel defaultModel,
                              CharacterData data)

Method Detail

cloneSpecsSet

public SpecsSet cloneSpecsSet()

Specified by:

cloneSpecsSet in class SpecsSet

makeSpecsSet

public SpecsSet makeSpecsSet(AssociableWithSpecs parent,
                             int numParts)

Specified by:

makeSpecsSet in class SpecsSet