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Class mesquite.lib.MesquiteModule 

mesquite.lib.MenuOwner
   |
   +----mesquite.lib.EmployerEmployee
           |
           +----mesquite.lib.MesquiteModule
public abstract class MesquiteModule
extends mesquite.lib.EmployerEmployee
implements mesquite.lib.Commandable, mesquite.lib.Showable, mesquite.lib.Logger, mesquite.lib.Explainable, mesquite.lib.Identifiable, mesquite.lib.FileDirtier, mesquite.lib.MesquiteListener
The Mesquite system operates around a tree of modules (subclasses of MesquiteModule), with the class containing the "main" method being the trunk module, and the other modules like branches that are attached to the trunk.

When Mesquite starts up, the trunk starts up and surveys the mesquite folder to acquire information about all of the available modules (i.e., all of the available subclasses of MesquiteModule). To be found, a module must be in a folder (directory) of the same name as itself; that is, a module whose class file is "MyModule.class" must be in a directory named "MyModule". Mesquite remembers the modules in a vector of MesquiteModuleInfo objects. Later, when modules need to be "hired" to perform certain tasks, this vector of information can be used to help choose which module to hire. To be hired, a module is instantiated and linked to its employer module. Thus, a new branch sprouts in the Mesquite bureacratic hierarchy.

Modules are chosen for hire by other modules according to their talents. What talents a module has is implicit in its superclass. For instance, a module that subclasses the NumberForTree class (itself a subclass of MesquiteModule) calculates a number for a tree. Any module that wants numbers calculated for trees can therefore hire a module that is an instance of the NumberForTree class. The basic talent-defining classes are part of the Mesquite Class LIbrary, in the subpackage duties. There is in addition a system to determine whether a module is compatible with a particular condition (e.g. operating on continuous-valued data.)

The only types of module that the trunk knows of directly are the FileCoordinator and FileInterpreter classes. Each instance of the File Coordinator is associated with one file, and it is responsible for using employee modules to read and write the file, and to hire tree windows and data windows. The trunk is a specific subclass of MesquiteModule, a MesquiteTrunk

Because menus are composed hierarchically along the employee tree, menu composition is most easily done where there is easy access to employee-employer relations. For this reason, it is most convenient to have the menu composition embedded within the module code. In order not to burden the MesquiteModule class with numerous methods to handle employee-employer relations, the MesquiteModule class was split into three: its superclass, EmployeeEmployer (which handles employee-employer relations), MenuOwner (which handles all menu issues) and MesquiteModule itself, which handles its basic functions. EmployeeEmployer and MenuOwner are intended to be used ONLY as superclasses to MesquiteModule

The MesquiteModule class is more or less equivalent to the MacClade proto4 ModuleRecord, while its instantiated objects are more or less equivalent to the MacClade proto4 Tasks. Hence, "task" is sometimes used in names for MesquiteModule objects.

Variable Index

o browserString
the file path to the web browser for showing web pages
o checkMethodsAtStartup
true if does extra check for module compatibility at startup.
o hiredAsDefaultInScripting
This module was hired as a default choice in scripting
o logWindow
The window, created by mesquiteTrunk, that displays the log.
o mesquiteDirectory
The root of the mesquite classpath.
o mesquiteDirectoryPath
The root of the mesquite classpath.
o mesquiteTrunk
Static storage so that everyone can find the trunk MesquiteModule object
o moduleInfo
the MesquiteModuleInfo that refers to the module
o prefsDirectory
The directory that includes all the preference files.
o proj
The project that the module was hired under.
o textEdgeCompensationHeight
o textEdgeCompensationWidth
o totalFinalized
o userDirectory
The user's directory.

Constructor Index

o MesquiteModule()
The constructor in general is to be avoided, because modules are instantiated momentarily on startup to gather information.

Method Index

o accumulateParameters(String)
o addNEXUSBlock(NexusBlock)
Adds NEXUS block to the file.
o alert(String)
Displays an alert in log; also in dialog if flag is set.
o alert(String, String, String)
Displays an alert in log; also in dialog if flag is set.
o anySubstantivePrereleases()
returns whether this or employee modules are substantive and prerelease
o broadCastAssignedID(MesquiteModule, String, CommandRecord)
Broadcasts that an id has been assigned to a module.
o changed(Object, Object, Notification, CommandRecord)
passes which object changed, along with optional integer (e.g.
o classFieldChanged(Class, String, CommandRecord)
Notifies all employees that a class field has changed.
o compatibleWithSystem()
returns whether the module is compatible with the current OS, Mesquite system, Java VM, and so on.
o containerOfModule()
Returns the window of the MesquiteModule, or if none, the window of the nearest employer with a window.
o discreetAlert(boolean, String)
If scripting, puts alert in log; otherwise puts up alert dialog.
o discreetAlert(CommandRecord, String)
If scripting, puts alert in log; otherwise puts up alert dialog.
o dispose()
dispose is called automatically when an employee is fired.
o disposing(Object)
passes which object is being disposed (from MesquiteListener interface)
o doCommand(String, String, CommandRecord, CommandChecker)
A request for the MesquiteModule to perform a command.
o employeeOutputInvalid(MesquiteModule, MesquiteModule, CommandRecord)
Generated by an employee calling its outputInvalide method.
o employeeParametersChanged(MesquiteModule, MesquiteModule, Notification, CommandRecord)
Generated by an employee calling its parametersChanged method.
o employeeQuit(MesquiteModule)
Generated by an employee who quit.
o employerWithWindow()
Returns the employer with a window
o endJob()
endJob is called as a module is quitting; modules should put their clean up code here.
o fileAboutToBeWritten(MesquiteFile)
A method called immediately before a file is to be saved.
o fileDirtiedByCommand(MesquiteCommand)
for FileDirtier interface
o fileElementAdded(FileElement)
A method called when a FileElement added to the project; module can respond as needed (e.g., InitializeParsimony can add default model set to a CharacterData.
o fileReadIn(MesquiteFile)
A method called immediately after the file has been read in or completely set up (if a new file).
o finalize()
o findNEXUSBlock(FileElement)
Finds the NEXUS block containing the given FileElement.
o getAppletInfo()
o getAuthors()
Returns the authors of the module.
o getAutoSaveMacros()
Returns whether module has requested to enable auto-save of macros.
o getBrowserManualPath()
returns path to manual.
o getBrowserPanel()
Asks for hierarchy browser panel (File coordinator or trunk should override to return.
o getBuildVersion()
returns build number of the Mesquite system ("e58")
o getCitation()
Returns the citation of the module.
o getCommandPagePath()
returns path to page showing the commands.
o getCompatibilityTest()
Returns CompatibilityTest so other modules know if this is compatible with some object.
o getDateReleased()
returns the year released, as a string.
o getDefaultModule()
Returns name of default module for superclass.
o getDocsPath()
returns path to the root directory of the documentation of Mesquite
o getDutyClass()
Returns duty Class the module belongs to; should be defined not by module itself but by abstract class representing duty
o getDutyName()
Returns the name of the duty; set by the duty-defining library classes.
o getExpectedPath()
returns a local file path expected by the module.
o getExplanation()
returns an explanation of what the module does.
o getHireSubchoice()
Returns duty Class that module would like to hire immediately upon hiring.
o getID()
instantiations of modules are numbered sequentially so they can be referred to by number
o getIfLastEmployee()
Returns whether this module is to remain one of the last employees of its employers.
o getManualPath()
returns path to manual.
o getMesquiteVersion()
returns version of the Mesquite system
o getModuleInfo()
Returns module info for module
o getName()
Returns the name of the module
o getNameAndParameters()
returns name plus current parameters, for logging etc..
o getNameForMenuItem()
Returns the name of the module for menu items.
o getNexusBlockTest()
Returns NexusBlockTest so interpreter knows if this module can interpret a block.
o getNexusCommands(MesquiteFile, String)
Return any nexus commands belonging to block in file.
o getNexusCommandTest()
Returns NexusCommandTest so interpreter knows if this module can interpret a command.
o getPackageIntroModule()
Returns the name of the module introducing package of modules (e.g., "#aParsimonyIntro")
o getParameters()
returns current parameters, for logging etc..
o getPath()
returns path to this module's directory
o getPermanentIDString()
A string that uniquely refers to this module (unique even across runs of Mesquite)
o getProject()
Returns the project of the MesquiteModule
o getRootImageDirectoryPath()
returns path to the root directory of Mesquite images
o getRootPath()
returns path to the root directory of Mesquite (i.e., above mesquite, images, etc.)
o getShortClassName()
returns short (not full package) name of class
o getShortClassName(Class)
returns short (not full package) name of class
o getSizedRootImageFilePath(int, String)
o getSnapshot(MesquiteFile)
Return Mesquite commands that will put the module (approximately) back into its current state.
o getUserChooseable()
Returns true if the module is to appear in menus and other places in which users can choose, and if can be selected in any way other than by direct request
o getVersion()
returns the version number string of the module.
o getVeryShortName()
Returns the name of the module in very short form.
o iQuit()
To be called by a module to close down on its own (as opposed to being fired).
o isPrerelease()
returns whether this module is a prerelease version
o isSubstantive()
returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module
o listEmployeeParameters(String)
Lists the parameters of all employees of this MesquiteModule.
o loadPreferences()
This causes the file "prefs" in the module's directory to be read, and the contents are then sent to "processPreferencesFromFile".
o log(String)
Places string in log AND in System.out.println.
o logln(String)
Places string and newline character in log AND in System.out.println.
o loglnNoEcho(String)
Places string and newline character in log.
o logNoEcho(String)
Places string in log.
o makeCommand(String, Commandable)
Commands are created here.
o mesquiteStartup()
Called during Mesquite startup when the list of available modules is being constructed.
o nameIsInstanceOf(String, Class)
returns whether the passed class, or a superclass or interface of it, has the passed name
o nameMatches(String)
returns whether name of Module matches passed String.
o offHold()
Called typically by employer to turn off hold, therefore don't update graphics.
o okToDispose(Object, int)
passes which object is being disposed (from MesquiteListener interface)
o onHold()
Called typically by employer to indicate that will be called soon, therefore don't update graphics.
o outputInvalid(CommandRecord)
This passes an employeeOutputInvalid call to the employer, and so on, until some employer overrides it to do something about it.
o pageModule(MesquiteModule, boolean)
for the paging system (may be defunct)
o parametersChanged(CommandRecord)
o parametersChanged(Notification, CommandRecord)
A generic call to tell employer that the module's parameters have changed sufficiently that its basic calculations are no longer valid, and a recalculation should be requested.
o permanentIDExists(String)
o preparePreferencesForFile()
This is called following a "storePreferences" call by a module.
o processPreferencesFromFile(String[])
This is called following a "loadPreferences" call by a module.
o projectEstablished()
A method called immediately after the file has been established but not yet read in.
o quittingConditions()
Query module as to whether conditions are such that it will have to quit soon -- e.g.
o readNexusBlock(MesquiteFile, String, FileBlock, StringBuffer, String, CommandRecord)
Read the nexus block passed (passed only to modules claiming they can read it).
o readNexusCommand(MesquiteFile, String, String, MesquiteString)
Read the nexus command in the given block (passed only to modules claiming they can read it).
o readUnrecognizedCommand(MesquiteFile, NexusBlock, String, FileBlock, String, String, StringBuffer, MesquiteString)
Read the unrecognized command, first by looking for a module reading it, second by storing it as unrecognized within the nexus block.
o removeNEXUSBlock(NexusBlock)
Remove NEXUS block from the file.
o removePaging(MesquiteModule)
for the paging system (may be defunct)
o reportProfiling()
Requests modules to report profiling.
o requestPrimaryChoice()
returns whether this module is requesting to appear as a primary choice
o respondToPaging()
for the paging system (may be defunct)
o returningPage(MesquiteModule)
for the paging system (may be defunct)
o setAutoSaveMacros(boolean)
Sets whether module has requested to enable auto-save of macros.
o setProject(MesquiteProject)
sets the file of the MesquiteModule
o setToLastEmployee(boolean)
Sets this module to remain one of the last employees of its employers.
o showCitation()
Returns whether or not the module does substantive calculations and thus should be cited.
o showLogWindow()
Shows the log window.
o showLogWindow(boolean)
Shows the log window.
o showManual()
shows manual for module
o showMe()
In some way shows the module, either by showing its window or its place in hierarchy
o showWebPage(String, boolean)
requests browser to show page.
o sorry(CommandRecord, String)
Displays a message and returns false.
o startJob(String, Object, CommandRecord, boolean)
startJob is called automatically when an employee is hired.
o startProfiling()
Requests modules to start profiling.
o storePreferences()
This causes the file "prefs" in the module's directory to be written, using contents returned by the module via "preparePreferencesForFile"
o superStartJob(String, Object, CommandRecord, boolean)
superStartJob is called automatically when an employee is hired.
o toString()
o windowGoAway(MesquiteWindow)
Requests a window to close.

Variables

o mesquiteTrunk 
 public static mesquite.lib.MesquiteTrunk mesquiteTrunk
Static storage so that everyone can find the trunk MesquiteModule object

o mesquiteDirectory 
 public static java.io.File mesquiteDirectory
The root of the mesquite classpath.

o mesquiteDirectoryPath 
 public static java.lang.String mesquiteDirectoryPath
The root of the mesquite classpath.

o prefsDirectory 
 public static java.io.File prefsDirectory
The directory that includes all the preference files.

o userDirectory 
 public static java.io.File userDirectory
The user's directory.

o logWindow 
 public static mesquite.lib.LogWindow logWindow
The window, created by mesquiteTrunk, that displays the log.

o browserString 
 protected static java.lang.String browserString
the file path to the web browser for showing web pages

o checkMethodsAtStartup 
 public static boolean checkMethodsAtStartup
true if does extra check for module compatibility at startup.

o hiredAsDefaultInScripting 
 public boolean hiredAsDefaultInScripting
This module was hired as a default choice in scripting

o totalFinalized 
 public static int totalFinalized
o moduleInfo 
 protected mesquite.lib.MesquiteModuleInfo moduleInfo
the MesquiteModuleInfo that refers to the module

o proj 
 protected mesquite.lib.MesquiteProject proj
The project that the module was hired under. Almost all modules are descendant from a file coordinating module that belongs to a specific project

o textEdgeCompensationHeight 
 public static int textEdgeCompensationHeight
o textEdgeCompensationWidth 
 public static int textEdgeCompensationWidth

Constructors

o MesquiteModule 
 public MesquiteModule()
The constructor in general is to be avoided, because modules are instantiated momentarily on startup to gather information. The usual functions of a constructor are performed by startJob

Methods

o getID 
 public long getID()
instantiations of modules are numbered sequentially so they can be referred to by number

o getPermanentIDString 
 public java.lang.String getPermanentIDString()
A string that uniquely refers to this module (unique even across runs of Mesquite)

o broadCastAssignedID 
 public void broadCastAssignedID(mesquite.lib.MesquiteModule module,
                                 java.lang.String assignedID,
                                 mesquite.lib.CommandRecord commandRec)
Broadcasts that an id has been assigned to a module. This is used for scripting, in which a module assigns itself an id string in a snapshot (e.g., a TreeContext) that an interested module can clue in to (e.g., TreeOfContext). This allows the interested module to hook up to the assigning module even if the former was script-created before the latter (see interaction between BasicTreeWindow and TreeOfContext)

o superStartJob 
 public boolean superStartJob(java.lang.String arguments,
                              java.lang.Object condition,
                              mesquite.lib.CommandRecord commandRec,
                              boolean hiredByName)
superStartJob is called automatically when an employee is hired. This is intended for use by superclasses of modules that need their own constructor-like call, without relying on the subclass to be polite enough to call super.startJob().

o startJob 
 public abstract boolean startJob(java.lang.String arguments,
                                  java.lang.Object condition,
                                  mesquite.lib.CommandRecord commandRec,
                                  boolean hiredByName)
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.

o endJob 
 public void endJob()
endJob is called as a module is quitting; modules should put their clean up code here.

o finalize 
 public void finalize() throws java.lang.Throwable
o dispose 
 protected void dispose()
dispose is called automatically when an employee is fired. It fires all employees and their subemployees etc. The MesquiteModule should call endJob to finalize things it needs.. NOTE: if a module wants to quit on its own accord, it should call "iQuit" so that the replacement hiring system can take effect.

o iQuit 
 public final void iQuit()
To be called by a module to close down on its own (as opposed to being fired). This might happen, for example, if conditions change so that the module can no longer function (e.g. all stored matrices are deleted from a file, and so StoredMatrices can no longer supply matrices). A module could also call its own endJob() method, but iQuit is to be preferred because it evokes the automatic replacement hiring system if available. (See setHiringCommand of EmployerEmployee)

o quittingConditions 
 public boolean quittingConditions()
Query module as to whether conditions are such that it will have to quit soon -- e.g. if its taxa block has been doomed. The tree window, data window, etc. override this to return true if their object is doomed. This is useful in case MesquiteListener disposing method is not called for an employer before one of its employees discovers that it needs to quit. If the employer is going to quit anyway,there is no use to use auto rehire for the quit employee.

o projectEstablished 
 public void projectEstablished()
A method called immediately after the file has been established but not yet read in.

o fileReadIn 
 public void fileReadIn(mesquite.lib.MesquiteFile f)
A method called immediately after the file has been read in or completely set up (if a new file).

o fileAboutToBeWritten 
 public void fileAboutToBeWritten(mesquite.lib.MesquiteFile f)
A method called immediately before a file is to be saved.

o fileElementAdded 
 public void fileElementAdded(mesquite.lib.FileElement element)
A method called when a FileElement added to the project; module can respond as needed (e.g., InitializeParsimony can add default model set to a CharacterData. (currently only called for Taxa and CharacterData additions).

o getDutyClass 
 public abstract java.lang.Class getDutyClass()
Returns duty Class the module belongs to; should be defined not by module itself but by abstract class representing duty

o getModuleInfo 
 public mesquite.lib.MesquiteModuleInfo getModuleInfo()
Returns module info for module

o classFieldChanged 
 public void classFieldChanged(java.lang.Class c,
                               java.lang.String fieldName,
                               mesquite.lib.CommandRecord commandRec)
Notifies all employees that a class field has changed.

o parametersChanged 
 public final void parametersChanged(mesquite.lib.Notification notification,
                                     mesquite.lib.CommandRecord commandRec)
A generic call to tell employer that the module's parameters have changed sufficiently that its basic calculations are no longer valid, and a recalculation should be requested. The employer receives the message as a call to its employeeParametersChanged. (Typically, this might follow an outputInvalid call, which

o parametersChanged 
 public final void parametersChanged(mesquite.lib.CommandRecord commandRec)
o employeeParametersChanged 
 public void employeeParametersChanged(mesquite.lib.MesquiteModule employee,
                                       mesquite.lib.MesquiteModule source,
                                       mesquite.lib.Notification notification,
                                       mesquite.lib.CommandRecord commandRec)
Generated by an employee calling its parametersChanged method. The MesquiteModule should act accordingly, for instance, asking the employee to do a recalculation.

o outputInvalid 
 public final void outputInvalid(mesquite.lib.CommandRecord commandRec)
This passes an employeeOutputInvalid call to the employer, and so on, until some employer overrides it to do something about it. The purpose of this is not to call for recalculations, but primarily to allow the output to be turned blank while long recalculations are done. To force recalculation, parametersChanged should be called after outputInvalid is called

o employeeOutputInvalid 
 public void employeeOutputInvalid(mesquite.lib.MesquiteModule employee,
                                   mesquite.lib.MesquiteModule source,
                                   mesquite.lib.CommandRecord commandRec)
Generated by an employee calling its outputInvalide method. The MesquiteModule should blank any output.

o employeeQuit 
 public void employeeQuit(mesquite.lib.MesquiteModule employee)
Generated by an employee who quit. The MesquiteModule should act accordingly.

o setToLastEmployee 
 public void setToLastEmployee(boolean last)
Sets this module to remain one of the last employees of its employers.

o getIfLastEmployee 
 public boolean getIfLastEmployee()
Returns whether this module is to remain one of the last employees of its employers.

o setAutoSaveMacros 
 public void setAutoSaveMacros(boolean aut)
Sets whether module has requested to enable auto-save of macros.

o getAutoSaveMacros 
 public boolean getAutoSaveMacros()
Returns whether module has requested to enable auto-save of macros.

o onHold 
 public void onHold()
Called typically by employer to indicate that will be called soon, therefore don't update graphics.

o offHold 
 public void offHold()
Called typically by employer to turn off hold, therefore don't update graphics.

o loadPreferences 
 public final void loadPreferences()
This causes the file "prefs" in the module's directory to be read, and the contents are then sent to "processPreferencesFromFile".

o processPreferencesFromFile 
 public void processPreferencesFromFile(java.lang.String prefs[])
This is called following a "loadPreferences" call by a module. A module can override it to process the preferences string

o storePreferences 
 public final void storePreferences()
This causes the file "prefs" in the module's directory to be written, using contents returned by the module via "preparePreferencesForFile"

o preparePreferencesForFile 
 public java.lang.String[] preparePreferencesForFile()
This is called following a "storePreferences" call by a module. A module should override it to indicate the strings to save to its preferences file.

o getPath 
 public java.lang.String getPath()
returns path to this module's directory

o getRootPath 
 public static java.lang.String getRootPath()
returns path to the root directory of Mesquite (i.e., above mesquite, images, etc.)

o getRootImageDirectoryPath 
 public static java.lang.String getRootImageDirectoryPath()
returns path to the root directory of Mesquite images

o getSizedRootImageFilePath 
 public static java.lang.String getSizedRootImageFilePath(int s,
                                                          java.lang.String imageFileName)
o getDocsPath 
 public static java.lang.String getDocsPath()
returns path to the root directory of the documentation of Mesquite

o getExpectedPath 
 public java.lang.String getExpectedPath()
returns a local file path expected by the module. This allows the module to say "I am going to need this". Mesquite check on startup and issues warning if not found .

o alert 
 public void alert(java.lang.String s,
                   java.lang.String windowTitle,
                   java.lang.String logTitle)
Displays an alert in log; also in dialog if flag is set.

o alert 
 public void alert(java.lang.String s)
Displays an alert in log; also in dialog if flag is set.

o discreetAlert 
 public void discreetAlert(mesquite.lib.CommandRecord commandRec,
                           java.lang.String s)
If scripting, puts alert in log; otherwise puts up alert dialog.

o discreetAlert 
 public void discreetAlert(boolean beDiscreet,
                           java.lang.String s)
If scripting, puts alert in log; otherwise puts up alert dialog.

o sorry 
 public boolean sorry(mesquite.lib.CommandRecord commandRec,
                      java.lang.String s)
Displays a message and returns false. For use when a method fails and is returning false to indicate this, and needs to present a notice to the user. (This method was made so as to change easily statements of "return false" so that they also gave a message, without having to split into two lines.)

o log 
 public void log(java.lang.String s)
Places string in log AND in System.out.println.

o logln 
 public void logln(java.lang.String s)
Places string and newline character in log AND in System.out.println.

o logNoEcho 
 public void logNoEcho(java.lang.String s)
Places string in log.

o loglnNoEcho 
 public void loglnNoEcho(java.lang.String s)
Places string and newline character in log.

o showLogWindow 
 public static void showLogWindow()
Shows the log window.

o showLogWindow 
 public static void showLogWindow(boolean bringToFront)
Shows the log window.

o disposing 
 public void disposing(java.lang.Object obj)
passes which object is being disposed (from MesquiteListener interface)

o okToDispose 
 public boolean okToDispose(java.lang.Object obj,
                            int queryUser)
passes which object is being disposed (from MesquiteListener interface)

o changed 
 public void changed(java.lang.Object caller,
                     java.lang.Object obj,
                     mesquite.lib.Notification notification,
                     mesquite.lib.CommandRecord commandRec)
passes which object changed, along with optional integer (e.g. for character) (from MesquiteListener interface)

o startProfiling 
 public void startProfiling()
Requests modules to start profiling.

o reportProfiling 
 public void reportProfiling()
Requests modules to report profiling.

o permanentIDExists 
 public boolean permanentIDExists(java.lang.String id)
o doCommand 
 public java.lang.Object doCommand(java.lang.String commandName,
                                   java.lang.String arguments,
                                   mesquite.lib.CommandRecord commandRec,
                                   mesquite.lib.CommandChecker checker)
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.

o containerOfModule 
 public java.awt.Frame containerOfModule()
Returns the window of the MesquiteModule, or if none, the window of the nearest employer with a window. NONEMBEDDED VERSION

o employerWithWindow 
 public mesquite.lib.MesquiteModule employerWithWindow()
Returns the employer with a window

o getProject 
 public mesquite.lib.MesquiteProject getProject()
Returns the project of the MesquiteModule

o setProject 
 public void setProject(mesquite.lib.MesquiteProject proj)
sets the file of the MesquiteModule

o windowGoAway 
 public void windowGoAway(mesquite.lib.MesquiteWindow whichWindow)
Requests a window to close. In the process, subclasses of MesquiteWindow might close down their owning MesquiteModules etc.

o makeCommand 
 public static final mesquite.lib.MesquiteCommand makeCommand(java.lang.String commandName,
                                                              mesquite.lib.Commandable ownerObject)
Commands are created here. This method is used in case Mesquite wants to catalogue available Commands (so far, this has not proved useful). The commands used to be stored within a single static vector, but this caused many otherwise defunct objects (the Commandables that are the object of the commands) to be referenced and thus not GC'd. In the future, commands might be more sophisticated, and passed here will be not only the commandName, but also the parameter types expected and how they are to be called. See the sublibrary for more information about Commands.

o addNEXUSBlock 
 public void addNEXUSBlock(mesquite.lib.NexusBlock nb)
Adds NEXUS block to the file.

o removeNEXUSBlock 
 public void removeNEXUSBlock(mesquite.lib.NexusBlock nb)
Remove NEXUS block from the file.

o findNEXUSBlock 
 public mesquite.lib.NexusBlock findNEXUSBlock(mesquite.lib.FileElement e)
Finds the NEXUS block containing the given FileElement.

o readNexusBlock 
 public mesquite.lib.NexusBlock readNexusBlock(mesquite.lib.MesquiteFile file,
                                               java.lang.String name,
                                               mesquite.lib.FileBlock block,
                                               java.lang.StringBuffer blockComments,
                                               java.lang.String fileReadingArguments,
                                               mesquite.lib.CommandRecord commandRec)
Read the nexus block passed (passed only to modules claiming they can read it).

o readNexusCommand 
 public boolean readNexusCommand(mesquite.lib.MesquiteFile file,
                                 java.lang.String blockName,
                                 java.lang.String command,
                                 mesquite.lib.MesquiteString comment)
Read the nexus command in the given block (passed only to modules claiming they can read it). Returns true if successful

o readUnrecognizedCommand 
 public void readUnrecognizedCommand(mesquite.lib.MesquiteFile file,
                                     mesquite.lib.NexusBlock nBlock,
                                     java.lang.String blockName,
                                     mesquite.lib.FileBlock block,
                                     java.lang.String commandName,
                                     java.lang.String command,
                                     java.lang.StringBuffer blockComments,
                                     mesquite.lib.MesquiteString comment)
Read the unrecognized command, first by looking for a module reading it, second by storing it as unrecognized within the nexus block.

o getNexusCommands 
 public java.lang.String getNexusCommands(mesquite.lib.MesquiteFile file,
                                          java.lang.String blockName)
Return any nexus commands belonging to block in file.

o getSnapshot 
 public mesquite.lib.Snapshot getSnapshot(mesquite.lib.MesquiteFile file)
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.

o pageModule 
 public void pageModule(mesquite.lib.MesquiteModule fromModule,
                        boolean persistent)
for the paging system (may be defunct)

o removePaging 
 public void removePaging(mesquite.lib.MesquiteModule fromModule)
for the paging system (may be defunct)

o returningPage 
 protected void returningPage(mesquite.lib.MesquiteModule pagedModule)
for the paging system (may be defunct)

o respondToPaging 
 protected void respondToPaging()
for the paging system (may be defunct)

o accumulateParameters 
 public java.lang.String accumulateParameters(java.lang.String spacer)
o getParameters 
 public java.lang.String getParameters()
returns current parameters, for logging etc..

o getNameAndParameters 
 public java.lang.String getNameAndParameters()
returns name plus current parameters, for logging etc..

o listEmployeeParameters 
 public java.lang.String listEmployeeParameters(java.lang.String spacer)
Lists the parameters of all employees of this MesquiteModule.

o getShortClassName 
 public static java.lang.String getShortClassName(java.lang.Class classToShow)
returns short (not full package) name of class

o getShortClassName 
 public java.lang.String getShortClassName()
returns short (not full package) name of class

o nameMatches 
 public boolean nameMatches(java.lang.String s)
returns whether name of Module matches passed String. First checks to see if name matches directly (e.g., "Tree Window"); then checks to see if matches at whole package path (e.g. mesquite.minimal.BasicTreeWindowMaker.BasicTreeWindowMaker); then checks to see if matches at immediate classname (e.g., BasicTreeWindowMaker)

o nameIsInstanceOf 
 public static boolean nameIsInstanceOf(java.lang.String n,
                                        java.lang.Class c)
returns whether the passed class, or a superclass or interface of it, has the passed name

o getManualPath 
 public java.lang.String getManualPath()
returns path to manual. Null if manual doesn't exist

o getCommandPagePath 
 public java.lang.String getCommandPagePath()
returns path to page showing the commands. Null if page doesn't exist

o getBrowserManualPath 
 public java.lang.String getBrowserManualPath()
returns path to manual. Null if manual doesn't exist

o showManual 
 public void showManual()
shows manual for module

o showWebPage 
 public static void showWebPage(java.lang.String path,
                                boolean autoCompose)
requests browser to show page. boolean indicates whether the standard auto-generated documentation pages for all the modules should be composed if they haven't been. * public static void TEMPshowWebPage(String path, boolean autoCompose) { if (path !=null) { if (MesquiteTrunk.isApplet()) { //TODO: FILL THIS IN } else { if (System.getProperty("os.name").startsWith("Mac OS X") && path.indexOf(":/")<0) { osXshowLocalWebPage(path, autoCompose); return; } if (path.indexOf(":/")<0) {//local file File testing = new File(path); if (!testing.exists()) { MesquiteTrunk.mesquiteTrunk.alert("The requested page could not be shown, because the file could not be found." ); return; } path = MesquiteFile.massageFilePathToURL(path); } try { BrowserLauncher.openURL(path); } catch (IOException e) { browserString = null; MesquiteTrunk.mesquiteTrunk.alert("The requested page could not be shown, because the web browser could not be used properly. There may be a problem with insufficient memory or the location of the web page or browser." ); } } } } /*.................................................................................................................

o getBrowserPanel 
 public mesquite.lib.HPanel getBrowserPanel()
Asks for hierarchy browser panel (File coordinator or trunk should override to return.

o showMe 
 public void showMe()
In some way shows the module, either by showing its window or its place in hierarchy

o getVeryShortName 
 public java.lang.String getVeryShortName()
Returns the name of the module in very short form. For use for column headings and other constrained places. Unless overridden returns getName()

o getNameForMenuItem 
 public java.lang.String getNameForMenuItem()
Returns the name of the module for menu items. Unless overridden returns getName()

o getName 
 public abstract java.lang.String getName()
Returns the name of the module

Overrides:
getName in class mesquite.lib.EmployerEmployee
o getAuthors 
 public java.lang.String getAuthors()
Returns the authors of the module.

o getVersion 
 public java.lang.String getVersion()
returns the version number string of the module.

o getDateReleased 
 public java.lang.String getDateReleased()
returns the year released, as a string. //TODO: SHOULD BE ABSTRACT TO FORCE INCLUSION

o showCitation 
 public boolean showCitation()
Returns whether or not the module does substantive calculations and thus should be cited. If true, its citation will appear in the citations panel of the windows

o getCitation 
 public java.lang.String getCitation()
Returns the citation of the module. By default this returns the citation of the package in which the module resides, and returns if only if "showCitation" returns true. The method may be overridden for module-specific citations.

o getPackageIntroModule 
 public mesquite.lib.MesquiteModuleInfo getPackageIntroModule()
Returns the name of the module introducing package of modules (e.g., "#aParsimonyIntro")

o getMesquiteVersion 
 public static final java.lang.String getMesquiteVersion()
returns version of the Mesquite system

o getBuildVersion 
 public static final java.lang.String getBuildVersion()
returns build number of the Mesquite system ("e58")

o requestPrimaryChoice 
 public boolean requestPrimaryChoice()
returns whether this module is requesting to appear as a primary choice

o isPrerelease 
 public boolean isPrerelease()
returns whether this module is a prerelease version

o isSubstantive 
 public boolean isSubstantive()
returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module

o anySubstantivePrereleases 
 public boolean anySubstantivePrereleases()
returns whether this or employee modules are substantive and prerelease

o compatibleWithSystem 
 public boolean compatibleWithSystem()
returns whether the module is compatible with the current OS, Mesquite system, Java VM, and so on. If false then the module will not be loaded as a possibility at startup

o getAppletInfo 
 public java.lang.String getAppletInfo()
o toString 
 public java.lang.String toString()
o getExplanation 
 public java.lang.String getExplanation()
returns an explanation of what the module does. //TODO: SHOULD BE ABSTRACT TO FORCE INCLUSION

o fileDirtiedByCommand 
 public void fileDirtiedByCommand(mesquite.lib.MesquiteCommand command)
for FileDirtier interface

o getDutyName 
 public java.lang.String getDutyName()
Returns the name of the duty; set by the duty-defining library classes.

o getDefaultModule 
 public java.lang.String[] getDefaultModule()
Returns name of default module for superclass.

o getCompatibilityTest 
 public mesquite.lib.CompatibilityTest getCompatibilityTest()
Returns CompatibilityTest so other modules know if this is compatible with some object.

o getNexusBlockTest 
 public mesquite.lib.NexusBlockTest getNexusBlockTest()
Returns NexusBlockTest so interpreter knows if this module can interpret a block.

o getNexusCommandTest 
 public mesquite.lib.NexusCommandTest getNexusCommandTest()
Returns NexusCommandTest so interpreter knows if this module can interpret a command.

o getUserChooseable 
 public boolean getUserChooseable()
Returns true if the module is to appear in menus and other places in which users can choose, and if can be selected in any way other than by direct request

o getHireSubchoice 
 public java.lang.Class getHireSubchoice()
Returns duty Class that module would like to hire immediately upon hiring. If a module wants to present a user with a choice of employees to hire, it can request a submenu listing these possible employees. However, if one of these employees would like to immediately (on startup) hire a user-specified subemployee (without having to go through a dialog box, etc.), this employee can indicate this by passing back through getHireSubchoice the duty class of the subemployee it would like to hire. Mesquite then lists a subsubmenu indicating possible subemployees. That way, the user not only chooses the employee, but specifies the subemployee. When the employee is started via startJob, the tokenized string of the name of the module that the user requested as subemployee is passed as an argument.

o mesquiteStartup 
 public void mesquiteStartup()
Called during Mesquite startup when the list of available modules is being constructed. 

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