mesquite.align.lib
Class BlockMover

java.lang.Object
  mesquite.lib.MenuOwner
      mesquite.lib.EmployerEmployee
          mesquite.lib.MesquiteModule
              mesquite.lib.duties.DataWindowAssistant
                  mesquite.lib.duties.DataWindowAssistantI
                      mesquite.align.lib.BlockMover

All Implemented Interfaces:

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

public abstract class BlockMover
extends DataWindowAssistantI

Field Summary

protected AlignTool

moveTool

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

BlockMover()

Method Summary

void	addPopUpMenuItems()
boolean	allowSplits()
boolean	canMoveLeft()
boolean	canMoveRight()
java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandChecker checker) A request for the MesquiteModule to perform a command.
abstract java.awt.Point	getCellToolHotSpot()
abstract java.lang.String	getCellToolImageFileName()
CompatibilityTest	getCompatibilityTest() Returns CompatibilityTest so other modules know if this is compatible with some object.
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.String	getExplanation() returns an explanation of what the module does.
abstract java.lang.String	getExplanationForTool()
abstract java.lang.String	getFullDescriptionForTool()
java.lang.String	getName() Returns the name of the module
boolean	getOptionDown()
Snapshot	getSnapshot(MesquiteFile file) Return Mesquite commands that will put the module (approximately) back into its current state.
abstract java.awt.Point	getSplitToolHotSpot()
abstract java.lang.String	getSplitToolImageFileName()
abstract java.lang.String	getToolName()
boolean	isPrerelease() returns whether this module is a prerelease version.
boolean	isSubstantive() returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module
void	setOptionTools()
void	setTableAndData(MesquiteTable table, CharacterData data) method called by data window to inform assistant that data have changed
boolean	startJob(java.lang.String arguments, java.lang.Object condition, boolean hiredByName) startJob is called automatically when an employee is hired.
boolean	wholeSelectedBlock()
boolean	wholeSequenceToLeft()
boolean	wholeSequenceToRight()

Methods inherited from class mesquite.lib.duties.DataWindowAssistantI

getDefaultModule

Methods inherited from class mesquite.lib.duties.DataWindowAssistant

colorsLegendGoAway, focusInCell, getCellExplanation, getCellString, getDisplayModString, getFunctionIconPath, hasDisplayModifications, isActive, setActive, tableSelectionChanged

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, echoStringToFile, employeeOutputInvalid, employeeParametersChanged, employeeQuit, employerWithWindow, endJob, fileAboutToBeWritten, fileDirtiedByCommand, fileElementAdded, fileReadIn, finalize, findNEXUSBlock, getAppletInfo, getAuthors, getAutoSaveMacros, getBrowserManualPath, getBrowserPanel, getBuildDate, getBuildVersion, getCitation, getCommandPagePath, getDateReleased, getDocsPath, getExpectedPath, getHireSubchoice, getHTMLExplanation, getID, getIfLastEmployee, getKeywords, getManualPath, getMesquiteVersion, getModuleInfo, getNameAndParameters, getNameForMenuItem, getNexusBlockTest, getNexusCommands, getNexusCommandTest, getPackageImagesPath, getPackageIntroModule, getPackagePath, getParameters, getParametersChangedNotifier, getPath, getPermanentIDString, getProject, getRootImageDirectoryPath, getRootPath, getShortClassName, getShortClassName, getSizedRootImageFilePath, getSubfunctions, getSubfunctionsVector, getURLString, getUserChooseable, getVersion, getVersionInt, getVersionOfFirstRelease, getVeryShortName, getXMLPrefsVersion, iQuit, iQuit, isCorrectRootTag, 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, 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.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

moveTool

protected AlignTool moveTool

Constructor Detail

BlockMover

public BlockMover()

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 DataWindowAssistantI

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 DataWindowAssistantI

startJob

public boolean startJob(java.lang.String arguments,
                        java.lang.Object condition,
                        boolean hiredByName)

Description copied from class: MesquiteModule

startJob is called automatically when an employee is hired. The parameter scripting indicates if the hiring occurs in the context of automated scripting (e.g., on reading a Mesquite block of a NEXUS file). The module can limit user interface calls (e.g. dialog boxes) when scripting occurs.

The MesquiteModule should override this method, to add code to initialize things it needs, and to hire relevant necessary employees. startJob must return true if the module was successfully started; false otherwise. Thus, if the module needs a data matrix but the file has none, it returns false and the hiring process is undone.

Most modules will ignore the arguments and condition.

Specified by:

startJob in class MesquiteModule

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

isPrerelease

public boolean isPrerelease()

Description copied from class: MesquiteModule

returns whether this module is a prerelease version. This returns "TRUE" here, forcing modules to override to claim they are not prerelease

Overrides:

isPrerelease in class MesquiteModule

getToolName

public abstract java.lang.String getToolName()

getCellToolImageFileName

public abstract java.lang.String getCellToolImageFileName()

getCellToolHotSpot

public abstract java.awt.Point getCellToolHotSpot()

getSplitToolImageFileName

public abstract java.lang.String getSplitToolImageFileName()

getSplitToolHotSpot

public abstract java.awt.Point getSplitToolHotSpot()

getExplanationForTool

public abstract java.lang.String getExplanationForTool()

getFullDescriptionForTool

public abstract java.lang.String getFullDescriptionForTool()

addPopUpMenuItems

public void addPopUpMenuItems()

setOptionTools

public void setOptionTools()

allowSplits

public boolean allowSplits()

canMoveLeft

public boolean canMoveLeft()

canMoveRight

public boolean canMoveRight()

wholeSelectedBlock

public boolean wholeSelectedBlock()

wholeSequenceToLeft

public boolean wholeSequenceToLeft()

wholeSequenceToRight

public boolean wholeSequenceToRight()

getOptionDown

public boolean getOptionDown()

getCompatibilityTest

public CompatibilityTest getCompatibilityTest()

Returns CompatibilityTest so other modules know if this is compatible with some object.

Overrides:

getCompatibilityTest in class DataWindowAssistantI

setTableAndData

public void setTableAndData(MesquiteTable table,
                            CharacterData data)

Description copied from class: DataWindowAssistant

method called by data window to inform assistant that data have changed

Specified by:

setTableAndData in class DataWindowAssistant

getSnapshot

public Snapshot getSnapshot(MesquiteFile file)

Description copied from class: MesquiteModule

Return Mesquite commands that will put the module (approximately) back into its current state. Used so that on file save, a Mesquite block can be saved that will return the user more or less to previous state.

Overrides:

getSnapshot in class MesquiteModule

doCommand

public java.lang.Object doCommand(java.lang.String commandName,
                                  java.lang.String arguments,
                                  CommandChecker checker)

Description copied from class: MesquiteModule

A request for the MesquiteModule to perform a command. It is passed two strings, the name of the command and the arguments. This should be overridden by any module that wants to respond to a command.

Specified by:

doCommand in interface Commandable

Overrides:

doCommand in class MesquiteModule

getName

public java.lang.String getName()

Description copied from class: MesquiteModule

Returns the name of the module

Specified by:

getName in interface HNode

Specified by:

getName in interface Listable

Specified by:

getName in class MesquiteModule

getExplanation

public java.lang.String getExplanation()

returns an explanation of what the module does.

Specified by:

getExplanation in interface Explainable

Overrides:

getExplanation in class MesquiteModule