mesquite.lib.duties
Class CharactersManager

java.lang.Object
  mesquite.lib.MenuOwner
      mesquite.lib.EmployerEmployee
          mesquite.lib.MesquiteModule
              mesquite.lib.duties.FileElementManager
                  mesquite.lib.duties.CharactersManager

All Implemented Interfaces:

Commandable, Doomable, ElementManager, Explainable, FileDirtier, FunctionExplainable, HNode, Identifiable, Listable, Logger, MesquiteListener, Showable

public abstract class CharactersManager
extends FileElementManager

Coordinates managers of character data matrices. Relies on CharMatrixManagers for the details of each data type. Example module: "Manage CHARACTERS blocks" (class ManageCharacters)

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

CharactersManager()

Method Summary

abstract java.lang.String[]	dataClassesAvailable()
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.
java.lang.Class	getElementClass()
abstract MesquiteModule	getListOfCharactersModule(CharacterData data, boolean showIfClosed)
abstract MesquiteSubmenuSpec	getListsSubmenu()
abstract CharMatrixManager	getMatrixManager(java.lang.Class dataClass) Returns the module that reads and writes matrices of a particular subclass
boolean	getSearchableAsModule()
abstract CharacterData	newCharacterData(Taxa taxa, int numChars, java.lang.String dataType) create new CharacterData object with data type indicated by passed string.
abstract CharacterData	processFormat(MesquiteFile file, Taxa taxa, java.lang.String formatCommand, int numChars, java.lang.String title, java.lang.String fileReadingArguments)

Methods inherited from class mesquite.lib.duties.FileElementManager

deleteElement, getIDSnapshot, showElement

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, 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 java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface mesquite.lib.duties.ElementManager

elementAdded, elementDisposed, elementsReordered

Constructor Detail

CharactersManager

public CharactersManager()

Method Detail

getDutyClass

public java.lang.Class getDutyClass()

Description copied from class: MesquiteModule

Returns duty Class the module belongs to; should be defined not by module itself but by abstract class representing duty

Overrides:

getDutyClass in class FileElementManager

getDutyName

public java.lang.String getDutyName()

Description copied from class: MesquiteModule

Returns the name of the duty; set by the duty-defining library classes.

Overrides:

getDutyName in class FileElementManager

getDefaultModule

public java.lang.String[] getDefaultModule()

Description copied from class: MesquiteModule

Returns name of default module for superclass.

Overrides:

getDefaultModule in class MesquiteModule

newCharacterData

public abstract CharacterData newCharacterData(Taxa taxa,
                                               int numChars,
                                               java.lang.String dataType)

create new CharacterData object with data type indicated by passed string. String is *not* NEXUS keyword for data type, but rather the descriptive phrase returned by the CharMatrixManagers' getDataClassName methods.

dataClassesAvailable

public abstract java.lang.String[] dataClassesAvailable()

processFormat

public abstract CharacterData processFormat(MesquiteFile file,
                                            Taxa taxa,
                                            java.lang.String formatCommand,
                                            int numChars,
                                            java.lang.String title,
                                            java.lang.String fileReadingArguments)

getMatrixManager

public abstract CharMatrixManager getMatrixManager(java.lang.Class dataClass)

Returns the module that reads and writes matrices of a particular subclass

getListOfCharactersModule

public abstract MesquiteModule getListOfCharactersModule(CharacterData data,
                                                         boolean showIfClosed)

getElementClass

public java.lang.Class getElementClass()

getListsSubmenu

public abstract MesquiteSubmenuSpec getListsSubmenu()

getSearchableAsModule

public boolean getSearchableAsModule()

Overrides:

getSearchableAsModule in class FileElementManager