mesquite.lib.duties
Class FileInterpreter

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

All Implemented Interfaces:

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

Direct Known Subclasses:

FileInterpreterI, NexusFileInterpreter

public abstract class FileInterpreter
extends MesquiteModule

Superclass of file interpreting modules (e.g., NEXUS file reader/writer). Different subclasses are expected to read different data file formats. Example module: "Interpret NEXUS files" (class InterpretNexus). Example of use: see BasicFileCoordinator.

Field Summary

static int	CURRENTDELIMITER
int	lineDelimiter
static int	MACOSDELIMITER
static int	UNIXDELIMITER
static int	WINDOWSDELIMITER
boolean	writeOnlySelectedData
boolean	writeOnlySelectedTaxa

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

FileInterpreter()

Method Summary

boolean	canExport() This is deprecated and should not be overridden.
boolean	canExportData(java.lang.Class dataClass) returns whether module can export a character data matrix of the given type.
boolean	canExportEver() returns whether module is able ever to export.
boolean	canExportProject(MesquiteProject project) returns whether module has something it can export in the project.
boolean	canImport() Returns whether the module can read (import) files
boolean	canImport(java.lang.Class dataClass) Returns whether the module can read (import) files with data of class dataClass
boolean	canImport(java.lang.String arguments) Returns whether the module can read (import) files considering the passed argument string (e.g., fuse)
boolean	canImport(java.lang.String arguments, java.lang.Class dataClass) Returns whether the module can read (import) files considering the passed argument string (e.g., fuse)
void	finishImport(ProgressIndicator progIndicator, MesquiteFile file, boolean abort)
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	getFunctionIconPath() returns an icon to accompany the explanation of what the module does.
java.lang.String	getLineEnding()
java.lang.String	getPathForExport(java.lang.String arguments, java.lang.String suggestedFileName, MesquiteString dir, MesquiteString fn)
boolean	isSubstantive() returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module
java.lang.String	preferredDataFileExtension()
abstract void	readFile(MesquiteProject mf, MesquiteFile mNF, java.lang.String arguments) reads a file using the methods of MesquiteFile and places its data into the given MesquiteProject which will already have been instantiated.
boolean	requestPrimaryChoice() returns whether this module is requesting to appear as a primary choice
void	saveExportedFile(java.lang.String output, java.lang.String arguments, java.lang.String suggestedFileName)
void	saveExportedFileWithExtension(java.lang.StringBuffer outputBuffer, java.lang.String arguments, java.lang.String suggestedFileEnding)
void	setLineDelimiter(int newDelimiter)
protected java.lang.String	stripNex(java.lang.String name)

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, getDefaultModule, getDocsPath, getExpectedPath, getExplanation, 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, 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.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

CURRENTDELIMITER

public static final int CURRENTDELIMITER

See Also:

Constant Field Values

MACOSDELIMITER

public static final int MACOSDELIMITER

See Also:

Constant Field Values

WINDOWSDELIMITER

public static final int WINDOWSDELIMITER

See Also:

Constant Field Values

UNIXDELIMITER

public static final int UNIXDELIMITER

See Also:

Constant Field Values

lineDelimiter

public int lineDelimiter

writeOnlySelectedData

public boolean writeOnlySelectedData

writeOnlySelectedTaxa

public boolean writeOnlySelectedTaxa

Constructor Detail

FileInterpreter

public FileInterpreter()

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

Specified by:

getDutyClass in class MesquiteModule

getFunctionIconPath

public java.lang.String getFunctionIconPath()

Description copied from class: MesquiteModule

returns an icon to accompany the explanation of what the module does.

Specified by:

getFunctionIconPath in interface FunctionExplainable

Overrides:

getFunctionIconPath in class MesquiteModule

requestPrimaryChoice

public boolean requestPrimaryChoice()

returns whether this module is requesting to appear as a primary choice

Overrides:

requestPrimaryChoice in class MesquiteModule

canExport

public boolean canExport()

This is deprecated and should not be overridden. The subsequent methods should be used instead.

canExportEver

public boolean canExportEver()

returns whether module is able ever to export.

canExportProject

public boolean canExportProject(MesquiteProject project)

returns whether module has something it can export in the project. Should be overridden

canExportData

public boolean canExportData(java.lang.Class dataClass)

returns whether module can export a character data matrix of the given type. Should be overridden

canImport

public boolean canImport(java.lang.Class dataClass)

Returns whether the module can read (import) files with data of class dataClass

canImport

public boolean canImport()

Returns whether the module can read (import) files

canImport

public boolean canImport(java.lang.String arguments,
                         java.lang.Class dataClass)

Returns whether the module can read (import) files considering the passed argument string (e.g., fuse)

canImport

public boolean canImport(java.lang.String arguments)

Returns whether the module can read (import) files considering the passed argument string (e.g., fuse)

readFile

public abstract void readFile(MesquiteProject mf,
                              MesquiteFile mNF,
                              java.lang.String arguments)

reads a file using the methods of MesquiteFile and places its data into the given MesquiteProject which will already have been instantiated. Recall that a MesquiteProject is not the external file on disk or server, but is rather the collection of taxa, data, trees, etc. that together typically make up the information in a NEXUS file. The external file is referred to by the MesquiteFile.

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

getLineEnding

public java.lang.String getLineEnding()

preferredDataFileExtension

public java.lang.String preferredDataFileExtension()

stripNex

protected java.lang.String stripNex(java.lang.String name)

setLineDelimiter

public void setLineDelimiter(int newDelimiter)

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

finishImport

public void finishImport(ProgressIndicator progIndicator,
                         MesquiteFile file,
                         boolean abort)

saveExportedFileWithExtension

public void saveExportedFileWithExtension(java.lang.StringBuffer outputBuffer,
                                          java.lang.String arguments,
                                          java.lang.String suggestedFileEnding)

getPathForExport

public java.lang.String getPathForExport(java.lang.String arguments,
                                         java.lang.String suggestedFileName,
                                         MesquiteString dir,
                                         MesquiteString fn)

saveExportedFile

public void saveExportedFile(java.lang.String output,
                             java.lang.String arguments,
                             java.lang.String suggestedFileName)