mesquite.lib.duties
Class FileCoordinator

java.lang.Object
  mesquite.lib.MenuOwner
      mesquite.lib.EmployerEmployee
          mesquite.lib.MesquiteModule
              mesquite.lib.duties.FileCoordinator

All Implemented Interfaces:

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

public abstract class FileCoordinator
extends MesquiteModule

The defining superclass for file coordinating modules. A module of this class is the fundamental module second only to the MesquiteTrunk module itself. MesquiteTrunk hires a file coordinating module for each MesquiteProject. Example module: Basic File Coordinator

Field Summary

static int	totalCreated
static int	totalFinalized

Fields inherited from class mesquite.lib.MesquiteModule

author, browserString, checkMethodsAtStartup, hiredAsDefaultInScripting, lastResult, lastResultString, logWindow, mesquiteDirectory, mesquiteDirectoryPath, mesquiteTrunk, moduleInfo, prefsDirectory, proj, textEdgeCompensationHeight, textEdgeCompensationWidth, userDirectory

Fields inherited from class mesquite.lib.EmployerEmployee

employees, employer, startupBailOut, stringPos, suppressHireQueries, 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

FileCoordinator()

Method Summary

abstract boolean	closeFile(MesquiteFile file) closes the given file; returns false if cancelled by user.
abstract MesquiteFile	createBlankProject() make a new blank MesquiteProject without user input.
abstract MesquiteFile	createProject(java.lang.String pathname, boolean createTaxaBlockIfNew) make a new blank MesquiteProject with user input.
abstract TextDisplayer	displayFile(MesquiteFile file, int maxCharacters) Displays a given text file, local or not;
abstract TextDisplayer	displayFile(java.lang.String pathName, int maxCharacters) Displays a given local text file;
abstract TextDisplayer	displayText(java.lang.String text, java.lang.String windowTitle) Displays a given text string;
abstract void	elementAdded(FileElement e)
abstract void	elementDisposed(FileElement e)
abstract void	export(FileInterpreterI exporter, MesquiteFile file, java.lang.String arguments) exports the given file;
void	finalize()
abstract FileInterpreter	findImporter(MesquiteFile f, int fileType, java.lang.String arguments)
abstract FileInterpreter	findImporter(java.lang.String fileContents, java.lang.String fileName, int fileType, java.lang.String arguments, boolean mustReadFromString, java.lang.Class stateClass)
abstract ElementManager	findManager(MesquiteModule m, java.lang.Class fileElementClass) Finds the first employee in the m's clade of employees that manages a particular subclass of file element
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.
abstract Snapshot	getIDSnapshot(MesquiteFile file)
abstract MesquiteFile	getNEXUSFileForReading(java.lang.String arguments, java.lang.String message)
boolean	getSearchableAsModule()
abstract MesquiteProject	initiateProject(java.lang.String pathName, MesquiteFile homeFile)
boolean	isSubstantive() returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module
abstract MesquiteFile	readProject(boolean local, java.lang.String pathname, java.lang.String arguments) make a MesquiteProject, reading the information from the given path of a file (if local, interprets as file on disk; if not, as URL specification).
abstract MesquiteFile	readProjectGeneral(java.lang.String arguments) make a MesquiteProject, using a module.
abstract void	refreshProjectWindow()
abstract void	saveAllFiles() Saves all files in the project.
abstract void	saveFile(MesquiteFile file) Saves file.
abstract void	writeFile(MesquiteFile file) write the given file;

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, findNEXUSBlock, getAppletInfo, getAuthors, getAutoSaveMacros, getBrowserManualPath, getBrowserPanel, getBuildDate, getBuildVersion, getCitation, getCommandPagePath, getCompatibilityTest, getDateReleased, getDefaultModule, 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, 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

Field Detail

totalCreated

public static int totalCreated

totalFinalized

public static int totalFinalized

Constructor Detail

FileCoordinator

public FileCoordinator()

Method Detail

getSearchableAsModule

public boolean getSearchableAsModule()

Overrides:

getSearchableAsModule in class EmployerEmployee

finalize

public void finalize()
              throws java.lang.Throwable

Overrides:

finalize in class MesquiteModule

Throws:

java.lang.Throwable

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

Specified by:

getDutyClass in class MesquiteModule

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 MesquiteModule

elementAdded

public abstract void elementAdded(FileElement e)

elementDisposed

public abstract void elementDisposed(FileElement e)

createProject

public abstract MesquiteFile createProject(java.lang.String pathname,
                                           boolean createTaxaBlockIfNew)

make a new blank MesquiteProject with user input.

createBlankProject

public abstract MesquiteFile createBlankProject()

make a new blank MesquiteProject without user input.

refreshProjectWindow

public abstract void refreshProjectWindow()

readProject

public abstract MesquiteFile readProject(boolean local,
                                         java.lang.String pathname,
                                         java.lang.String arguments)

make a MesquiteProject, reading the information from the given path of a file (if local, interprets as file on disk; if not, as URL specification).

readProjectGeneral

public abstract MesquiteFile readProjectGeneral(java.lang.String arguments)

make a MesquiteProject, using a module.

getNEXUSFileForReading

public abstract MesquiteFile getNEXUSFileForReading(java.lang.String arguments,
                                                    java.lang.String message)

findImporter

public abstract FileInterpreter findImporter(MesquiteFile f,
                                             int fileType,
                                             java.lang.String arguments)

findImporter

public abstract FileInterpreter findImporter(java.lang.String fileContents,
                                             java.lang.String fileName,
                                             int fileType,
                                             java.lang.String arguments,
                                             boolean mustReadFromString,
                                             java.lang.Class stateClass)

initiateProject

public abstract MesquiteProject initiateProject(java.lang.String pathName,
                                                MesquiteFile homeFile)

writeFile

public abstract void writeFile(MesquiteFile file)

write the given file;

export

public abstract void export(FileInterpreterI exporter,
                            MesquiteFile file,
                            java.lang.String arguments)

exports the given file;

closeFile

public abstract boolean closeFile(MesquiteFile file)

closes the given file; returns false if cancelled by user.

saveFile

public abstract void saveFile(MesquiteFile file)

Saves file.

saveAllFiles

public abstract void saveAllFiles()

Saves all files in the project.

findManager

public abstract ElementManager findManager(MesquiteModule m,
                                           java.lang.Class fileElementClass)

Finds the first employee in the m's clade of employees that manages a particular subclass of file element

displayFile

public abstract TextDisplayer displayFile(java.lang.String pathName,
                                          int maxCharacters)

Displays a given local text file;

displayFile

public abstract TextDisplayer displayFile(MesquiteFile file,
                                          int maxCharacters)

Displays a given text file, local or not;

displayText

public abstract TextDisplayer displayText(java.lang.String text,
                                          java.lang.String windowTitle)

Displays a given text string;

isSubstantive

public boolean isSubstantive()

Description copied from class: MesquiteModule

returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module

Overrides:

isSubstantive in class MesquiteModule

getIDSnapshot

public abstract Snapshot getIDSnapshot(MesquiteFile file)