CharStatesForNodes

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mesquite.lib.duties
Class CharStatesForNodes

java.lang.Object
  mesquite.lib.MenuOwner
      mesquite.lib.EmployerEmployee
          mesquite.lib.MesquiteModule
              mesquite.lib.duties.CharMapper
                  mesquite.lib.duties.CharStatesForNodes

All Implemented Interfaces:: Commandable, Doomable, Explainable, FileDirtier, FunctionExplainable, HNode, Identifiable, Listable, Logger, MesquiteListener, Showable

public abstract class CharStatesForNodes
extends CharMapper
extends CharMapper

Assigns states to nodes of tree for a character. Example modules: ParsAncestralStates, MaxPosteriorJoint, MLEAncestralStates. In 1. 1 this was moved to be subclass of CharMapper. Employers using as before would call calculateStates and it should behave as before. Employers using as CharMapper have that one's abstract methods filled in to use the calcu

Field Summary

Fields inherited from class mesquite.lib.MesquiteModule
`author, browserString, checkMethodsAtStartup, hiredAsDefaultInScripting, lastResult, lastResultString, logWindow, mesquiteDirectory, mesquiteDirectoryPath, mesquiteTrunk, moduleInfo, prefsDirectory, proj, textEdgeCompensationHeight, textEdgeCompensationWidth, totalFinalized, userDirectory`

Fields inherited from class mesquite.lib.EmployerEmployee
`employees, employer, startupBailOut, stringPos, suppressHireQueries, totalCreated, totalDisposed, useOtherChoices`

Fields inherited from class mesquite.lib.MenuOwner
`considerPriorities, doomed, MAXPRIORITY, menuCompositionTime, menuCompositionTime1, menuCompositionTime2, menuCompositionTime2a, menuCompositionTime2b, menuCompositionTime2c, menuCompositionTime3, menuCompositionTime4, menuCompositionTime5, menuCompositionTime6, menuCompositionTime7, menuCompositionTime8, menuCompositionTime9, menuTracing, module, parser`

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`

Constructor Summary
`CharStatesForNodes()`

Method Summary
`abstract void`	`calculateStates(Tree tree, CharacterDistribution charStates, CharacterHistory resultStates, MesquiteString resultString)`
`java.lang.String[]`	`getDefaultModule()` Returns name of default module for superclass.
`java.lang.Class`	`getDutyClass()` Returns duty Class the module belongs to; should be defined not by module itself but by abstract class representing duty
`java.lang.String`	`getDutyName()` Returns the name of the duty; set by the duty-defining library classes.
`void`	`getMapping(int i, CharacterHistory resultStates, MesquiteString resultString)`
`int`	`getNumberOfMappings()`
`void`	`setObservedStates(Tree tree, CharacterDistribution observedStates)`

Methods inherited from class mesquite.lib.duties.CharMapper
`allowsStateWeightChoice, setOneCharacterAtATime`

Methods inherited from class mesquite.lib.MesquiteModule
accumulateParameters, addNEXUSBlock, alert, alert, anySubstantivePrereleases, broadCastAssignedID, changed, classFieldChanged, clearLastResult, clearResultAndLastResult, compatibleWithSystem, containerOfModule, createSupportDirectory, deleteSupportDirectory, discreetAlert, discreetAlert, dispose, disposing, doCommand, echoStringToFile, employeeOutputInvalid, employeeParametersChanged, employeeQuit, employerWithWindow, endJob, fileAboutToBeWritten, fileDirtiedByCommand, fileElementAdded, fileReadIn, finalize, findNEXUSBlock, getAppletInfo, getAuthors, getAutoSaveMacros, getBrowserManualPath, getBrowserPanel, getBuildDate, getBuildVersion, getCitation, getCommandPagePath, getCompatibilityTest, getDateReleased, getDocsPath, getExpectedPath, getExplanation, getFunctionIconPath, getHireSubchoice, getHTMLExplanation, getID, getIfLastEmployee, getKeywords, getManualPath, getMesquiteVersion, getModuleInfo, getName, getNameAndParameters, getNameForMenuItem, getNexusBlockTest, getNexusCommands, getNexusCommandTest, getPackageImagesPath, getPackageIntroModule, getPackagePath, getParameters, getParametersChangedNotifier, getPath, getPermanentIDString, getProject, getRootImageDirectoryPath, getRootPath, getShortClassName, getShortClassName, getSizedRootImageFilePath, getSnapshot, getSubfunctions, getSubfunctionsVector, getURLString, getUserChooseable, getVersion, getVersionInt, getVersionOfFirstRelease, getVeryShortName, getXMLPrefsVersion, iQuit, iQuit, isCorrectRootTag, isPrerelease, isSubstantive, listEmployeeParameters, listEmployees, loadPreferences, log, log, logln, logln, loglnNoEcho, logNoEcho, makeCommand, mesquiteStartup, nameIsInstanceOf, nameMatches, offHold, okToDispose, onHold, outputInvalid, pageModule, panelGoAway, parametersChanged, parametersChanged, parseFullXMLDocument, permanentIDExists, preparePreferencesForFile, preparePreferencesForXML, processPreferencesFromFile, processPreferencesFromXML, processSingleXMLPreference, projectEstablished, quittingConditions, readNexusBlock, readNexusCommand, readUnrecognizedCommand, registerSubfunction, removeNEXUSBlock, removePaging, reportProfiling, requestPrimaryChoice, respondToPaging, returningPage, saveLastResult, saveLastResult, saveLastResult, saveLastResult, saveLastResultString, saveLastResultString, setAutoSaveMacros, setProject, setToLastEmployee, showCitation, showHTMLSnippet, showLogWindow, showLogWindow, showManual, showMe, showWebPage, showWebPage, sorry, startJob, startProfiling, storePreferences, superStartJob, supportDirectoryPath, toString, URLinPackageIntro, windowGoAway, writeNexusCommands, xmlPrefsVersionMustMatch

Methods inherited from class mesquite.lib.MesquiteModule

accumulateParameters, addNEXUSBlock, alert, alert, anySubstantivePrereleases, broadCastAssignedID, changed, classFieldChanged, clearLastResult, clearResultAndLastResult, compatibleWithSystem, containerOfModule, createSupportDirectory, deleteSupportDirectory, discreetAlert, discreetAlert, dispose, disposing, doCommand, echoStringToFile, employeeOutputInvalid, employeeParametersChanged, employeeQuit, employerWithWindow, endJob, fileAboutToBeWritten, fileDirtiedByCommand, fileElementAdded, fileReadIn, finalize, findNEXUSBlock, getAppletInfo, getAuthors, getAutoSaveMacros, getBrowserManualPath, getBrowserPanel, getBuildDate, getBuildVersion, getCitation, getCommandPagePath, getCompatibilityTest, getDateReleased, getDocsPath, getExpectedPath, getExplanation, getFunctionIconPath, getHireSubchoice, getHTMLExplanation, getID, getIfLastEmployee, getKeywords, getManualPath, getMesquiteVersion, getModuleInfo, getName, getNameAndParameters, getNameForMenuItem, getNexusBlockTest, getNexusCommands, getNexusCommandTest, getPackageImagesPath, getPackageIntroModule, getPackagePath, getParameters, getParametersChangedNotifier, getPath, getPermanentIDString, getProject, getRootImageDirectoryPath, getRootPath, getShortClassName, getShortClassName, getSizedRootImageFilePath, getSnapshot, getSubfunctions, getSubfunctionsVector, getURLString, getUserChooseable, getVersion, getVersionInt, getVersionOfFirstRelease, getVeryShortName, getXMLPrefsVersion, iQuit, iQuit, isCorrectRootTag, isPrerelease, isSubstantive, listEmployeeParameters, listEmployees, loadPreferences, log, log, logln, logln, loglnNoEcho, logNoEcho, makeCommand, mesquiteStartup, nameIsInstanceOf, nameMatches, offHold, okToDispose, onHold, outputInvalid, pageModule, panelGoAway, parametersChanged, parametersChanged, parseFullXMLDocument, permanentIDExists, preparePreferencesForFile, preparePreferencesForXML, processPreferencesFromFile, processPreferencesFromXML, processSingleXMLPreference, projectEstablished, quittingConditions, readNexusBlock, readNexusCommand, readUnrecognizedCommand, registerSubfunction, removeNEXUSBlock, removePaging, reportProfiling, requestPrimaryChoice, respondToPaging, returningPage, saveLastResult, saveLastResult, saveLastResult, saveLastResult, saveLastResultString, saveLastResultString, setAutoSaveMacros, setProject, setToLastEmployee, showCitation, showHTMLSnippet, showLogWindow, showLogWindow, showManual, showMe, showWebPage, showWebPage, sorry, startJob, startProfiling, storePreferences, superStartJob, supportDirectoryPath, toString, URLinPackageIntro, windowGoAway, writeNexusCommands, xmlPrefsVersionMustMatch

Methods inherited from class mesquite.lib.EmployerEmployee
canHireMoreThanOnce, closeDownAllEmployees, decrementEmployeeBrowserRefreshSuppression, deferBranchPriority, employeeOfWhichEmployee, findCharacterDataEditor, findCharacterDataEditorRec, findElementManager, findEmployee, findEmployee, findEmployeeNeed, findEmployeeWithDuty, findEmployeeWithDuty, findEmployeeWithIDNumber, findEmployeeWithName, findEmployeeWithName, findEmployeeWithName, findEmployeeWithPermanentID, findEmployerWithDuty, findImmediateEmployeeWithDuty, findModelCurator, findModelCuratorRec, findModules, findModulesWithDuty, findNearestColleagueWithDuty, findNearestColleagueWithName, findNearestModuleWithDuty, findNextEmployeeWithDuty, fireEmployee, getClonableEmployeeCommand, getEmployeeNeeds, getEmployeeNeedsVector, getEmployeeReference, getEmployeeVector, getEmployer, getEmployerPath, getExplanationByWhichHired, getFileCoordinator, getHColor, getHDaughters, getHImage, getHiredAs, getHiringCommand, getHiringCondition, getHMother, getHShow, getImmediateEmployeesWithDuty, getNextEmployeeWithDuty, getNumberOfEmployees, getNumSupplements, getSearchableAsModule, getSupplementName, getTypeName, hireAllCompatibleEmployees, hireAllEmployees, hireAllOtherCompatibleEmployees, hireAllOtherEmployees, hireCompatibleEmployee, hireEmployee, hireEmployeeFromModuleInfo, hireNamedEmployee, hireNamedEmployee, hireNamedEmployee, hNodeAction, hSupplementTouched, incrementEmployeeBrowserRefreshSuppression, instantiateEmployee, instantiateModule, internalStartUp, isEmployerOf, isMacroAnchor, isPriorityFixed, listEmployees, listNeeds, makeEmployeeVector, moduleActiveWord, moveEmployeeToFront, numCompatibleModulesAvailable, numModulesAvailable, purposeOfEmployee, queryChooseModule, refreshBrowser, registerEmployeeNeed, registerEmployeeNeed, replaceCompatibleEmployee, replaceEmployee, replaceEmployeeWithNext, setHiringCommand, setPriorityFixed, setShowHiringPath, whatIsMyPurpose

Methods inherited from class mesquite.lib.EmployerEmployee

canHireMoreThanOnce, closeDownAllEmployees, decrementEmployeeBrowserRefreshSuppression, deferBranchPriority, employeeOfWhichEmployee, findCharacterDataEditor, findCharacterDataEditorRec, findElementManager, findEmployee, findEmployee, findEmployeeNeed, findEmployeeWithDuty, findEmployeeWithDuty, findEmployeeWithIDNumber, findEmployeeWithName, findEmployeeWithName, findEmployeeWithName, findEmployeeWithPermanentID, findEmployerWithDuty, findImmediateEmployeeWithDuty, findModelCurator, findModelCuratorRec, findModules, findModulesWithDuty, findNearestColleagueWithDuty, findNearestColleagueWithName, findNearestModuleWithDuty, findNextEmployeeWithDuty, fireEmployee, getClonableEmployeeCommand, getEmployeeNeeds, getEmployeeNeedsVector, getEmployeeReference, getEmployeeVector, getEmployer, getEmployerPath, getExplanationByWhichHired, getFileCoordinator, getHColor, getHDaughters, getHImage, getHiredAs, getHiringCommand, getHiringCondition, getHMother, getHShow, getImmediateEmployeesWithDuty, getNextEmployeeWithDuty, getNumberOfEmployees, getNumSupplements, getSearchableAsModule, getSupplementName, getTypeName, hireAllCompatibleEmployees, hireAllEmployees, hireAllOtherCompatibleEmployees, hireAllOtherEmployees, hireCompatibleEmployee, hireEmployee, hireEmployeeFromModuleInfo, hireNamedEmployee, hireNamedEmployee, hireNamedEmployee, hNodeAction, hSupplementTouched, incrementEmployeeBrowserRefreshSuppression, instantiateEmployee, instantiateModule, internalStartUp, isEmployerOf, isMacroAnchor, isPriorityFixed, listEmployees, listNeeds, makeEmployeeVector, moduleActiveWord, moveEmployeeToFront, numCompatibleModulesAvailable, numModulesAvailable, purposeOfEmployee, queryChooseModule, refreshBrowser, registerEmployeeNeed, registerEmployeeNeed, replaceCompatibleEmployee, replaceEmployee, replaceEmployeeWithNext, setHiringCommand, setPriorityFixed, setShowHiringPath, whatIsMyPurpose

Methods inherited from class mesquite.lib.MenuOwner
addAuxiliaryMenu, addCheckMenuItem, addCheckMenuItemToSubmenu, addItemToSubmenu, addItemToSubmenu, addLineToSubmenu, addMenuItem, addMenuItem, addMenuItem, addMenuLine, addModuleMenuItems, addSubmenu, addSubmenu, addSubmenu, addSubmenu, addSubmenu, checkMISVector, composeMenuBar, decrementMenuResetSuppression, defineMenus, deleteAllMenuItems, deleteMenuItem, destroyMenu, disposeMenuSpecifications, doom, findMenuAmongEmployers, getContainingMenuSpec, getMenu, getMenuItemSpecs, getMenuResetSuppression, getModuleWindow, getUseMenubar, incrementMenuResetSuppression, isDoomed, makeMenu, needsMenu, recomposeWindowsMenu, resetAllMenuBars, resetAllWindowsMenus, resetContainingMenuBar, setMenuResetSuppression, setMenuToUse, setModule, setModuleWindow, setUndoMenuItemEnabled, setUseMenubar, showPopUp, zeroMenuResetSuppression

Methods inherited from class mesquite.lib.MenuOwner

addAuxiliaryMenu, addCheckMenuItem, addCheckMenuItemToSubmenu, addItemToSubmenu, addItemToSubmenu, addLineToSubmenu, addMenuItem, addMenuItem, addMenuItem, addMenuLine, addModuleMenuItems, addSubmenu, addSubmenu, addSubmenu, addSubmenu, addSubmenu, checkMISVector, composeMenuBar, decrementMenuResetSuppression, defineMenus, deleteAllMenuItems, deleteMenuItem, destroyMenu, disposeMenuSpecifications, doom, findMenuAmongEmployers, getContainingMenuSpec, getMenu, getMenuItemSpecs, getMenuResetSuppression, getModuleWindow, getUseMenubar, incrementMenuResetSuppression, isDoomed, makeMenu, needsMenu, recomposeWindowsMenu, resetAllMenuBars, resetAllWindowsMenus, resetContainingMenuBar, setMenuResetSuppression, setMenuToUse, setModule, setModuleWindow, setUndoMenuItemEnabled, setUseMenubar, showPopUp, zeroMenuResetSuppression

Methods inherited from class java.lang.Object
`clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Constructor Detail