mesquite.lib
Class MesquiteFile

java.lang.Object
  mesquite.lib.Listened
      mesquite.lib.MesquiteFile

All Implemented Interfaces:

Commandable, Explainable, HNode, Listable, Listenable

public class MesquiteFile
extends Listened
implements HNode, Commandable, Listable, Explainable

This MesquiteFile is the file on disk, not the project.

Field Summary

boolean	ambiguityToMissing
static boolean	appendToLog
int	exporting
static java.lang.String	fileSeparator
java.util.Vector	foreignElements
static int	HOME
static int	INCLUDED
boolean	interleaveAllowed
static int	LINKED
java.util.Vector	notesBugVector
boolean	notesBugWarn
static int	QUERY_CLOSE
static int	QUERY_DELETE
static int	QUERY_NONE
static int	QUERY_QUIT
boolean	simplifyNames
static int	totalCreated
static int	totalDisposed
static int	totalFinalized
boolean	useDataBlocks
boolean	useSimplifiedNexus
boolean	writeExcludedCharacters

Fields inherited from class mesquite.lib.Listened

allListeners, classes, classesNotified, listeners, listenersRemaining, notifications

Fields inherited from interface mesquite.lib.HNode

MOUSEDOWN, MOUSEEXIT, MOUSEMOVE

Constructor Summary

MesquiteFile()

Method Summary

void	addFileElement(FileElement element) Adds the passed FileElement to the file.
static void	appendFileContents(java.lang.String relativePath, java.lang.String contents, boolean ascii) Appends to a file the contents.
static boolean	canWrite(java.lang.String path) Checks to see if can write to a file
boolean	changeLocation(java.lang.String message) for use by save as; user puts file.
void	changeLocation(java.lang.String directoryName, java.lang.String fileName) redirects place at which file will be rewritten; for use by save as
static java.lang.String	checkFilePath(java.lang.String path, java.lang.String selectMessage) Checks to see if path leads to a file; if so, path returned; if not, user is asked to choose new file.
static java.lang.String	chooseDirectory(java.lang.String message) To choose a directory; returns path
static java.lang.String	chooseDirectory(java.lang.String message, java.lang.String suggestedDir) To choose a directory; returns path
boolean	close() Closes the file and removes from the project all file elements belonging to it.
boolean	closeAndDelete() Closes the file, removes from the project all file elements belonging to it, and deletes it.
static void	closeLog() Closes to the log file
void	closeReading() Closes the file for reading.
void	closeWriting() Close file for writing
void	closeWriting(int numBackups) Close file for writing
static java.lang.String	composePath(java.lang.String d, java.lang.String f) Return string for path, accommodating ../ at start of filename.
static void	copy(java.io.File src, java.io.File dst) A basic method for copying one File to another; if the destination file does not exist, it will be created
static java.lang.String	decomposePath(java.lang.String relativeTo, java.lang.String path) Converts absolute to relative string for path
static boolean	deleteDirectory(java.lang.String directoryPath)
static boolean	deleteFile(java.lang.String path) deletes file at path
java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandChecker checker) The method by which commands are sent to the file using text-based scripting.
static boolean	downloadFTPorHTTPFile(java.lang.String urlString, java.lang.String localSaveDirectoryPath) Downloads the file present at the ftp URL urlString, saves the file into the local directory at localSaveDirectoryPath, using the file name given in the URL.
static boolean	downloadFTPorHTTPFile(java.lang.String urlString, java.lang.String localSaveDirectoryPath, java.lang.String localSaveName) Downloads the file present at the ftp URL urlString, saves the file into the local directory at localSaveDirectoryPath, in the file localSaveName.
long	existingLength() Returns size of existing file on disk corresponding to this MesquiteFile
static boolean	fileExists(java.lang.String path) Checks to see if path leads to a file that is not a directory
void	finalize()
java.lang.String	firstToken(java.lang.StringBuffer commentBuffer) Returns next token from file.
java.lang.String	getAnnotation() Returns the annotation (e.g., footnote) of this element
boolean	getBeingSaved()
boolean	getCloseAfterReading()
CharacterData	getCurrentData()
Taxa	getCurrentTaxa()
java.lang.String	getDirectoryName() Get directory in which file resides (actually, entire path)
static java.lang.String	getDirectoryPathFromFilePath(java.lang.String path) Return string for directory path from full file path
java.lang.String	getExplanation() Returns the explanation (e.g., footnote plus additional information) of this file
boolean	getFileAborted() Returns true if user has requested file reading or writing stop.
java.lang.String	getFileContentsAsString(int maxCharacters) Returns the contents of the file, local or remote.
static java.lang.String	getFileContentsAsString(java.lang.String relativePath) Returns the contents of the file.
static java.lang.String	getFileContentsAsString(java.lang.String relativePath, int maxCharacters) Returns the contents of the file.
static java.lang.String	getFileContentsAsString(java.lang.String relativePath, int maxCharacters, int startBufferSize) Returns the contents of the file.
static java.lang.String	getFileContentsAsString(java.lang.String relativePath, int maxCharacters, int startBufferSize, boolean warnIfProblem) Returns the contents of the file.
static java.lang.String	getFileContentsAsStringOld(java.lang.String relativePath, int maxCharacters, int startBufferSize) Returns the contents of the file.
static java.lang.String[]	getFileContentsAsStrings(java.lang.String relativePath) Returns the contents of the file.
ListableVector	getFileElements() Gets list of file elements.
static java.lang.String	getFileFirstContents(java.lang.String relativePath) Returns the first line of the file.
java.lang.String	getFileName() Get name of file.
static java.lang.String	getFileNameFromFilePath(java.lang.String path) Return string for directory path from full file path
long	getFilePosition()
java.awt.Color	getHColor()
HNode[]	getHDaughters()
java.awt.Image	getHImage()
HNode	getHMother()
boolean	getHShow()
long	getID()
static java.io.PrintWriter	getLogWriter()
java.lang.String	getName()
FileBlock	getNextBlock(MesquiteString blockName, java.lang.StringBuffer fileComments, java.lang.StringBuffer blockComments) returns the next block; blockName is passed back via the MesquiteString object
FileBlock	getNextBlockOLD(MesquiteString blockName, java.lang.StringBuffer fileComments, java.lang.StringBuffer blockComments) returns the next block; blockName is passed back via the MesquiteString object
java.lang.String	getNextCommand(MesquiteInteger status, java.lang.StringBuffer commandComments) returns the next command in the file.
java.lang.String	getNextCommand(MesquiteInteger status, java.lang.StringBuffer commandComments, boolean includeEntireCommand) returns the next command in the file.
static int	getNumberOfFiles()
int	getNumSupplements()
java.lang.String	getOpenAsUntitled()
java.lang.String	getPath() Returns path to file on disk 19 Jan 02
Author	getPreviousSaver()
MesquiteProject	getProject() gets the project to which the MesquiteFile belongs.
int	getReadCategory()
java.lang.String	getSupplementName(int index)
static java.lang.String[][]	getTabDelimitedTextFile(java.lang.String relativePath) Returns the contents of the file.
java.lang.String	getTypeName()
java.net.URL	getURL() Get URL of file (null if a local file).
static java.lang.String	getURLContentsAsString(java.lang.String path, int maxCharacters) Returns the contents of the file at the url
static java.lang.String	getURLContentsAsString(java.lang.String path, int maxCharacters, boolean warnIfProblem) Returns the contents of the file at the url
static java.lang.String[]	getURLContentsAsStrings(java.lang.String path) Returns the contents of the file.
boolean	getWriteProtected()
void	goToFilePosition(long pos)
java.lang.String	goToNextBlockStart(MesquiteLong startPos) returns the file position of the start of the next block; returns blockName
void	hNodeAction(java.awt.Container c, int x, int y, int action) for HNode interface
void	hSupplementTouched(int index)
boolean	isClosed()
boolean	isDirty()
boolean	isLocal() returns true if file is local (on disk), false if remote (via URL).
boolean	isWriting()
void	linkProgressIndicator(ProgressIndicator pi) Links progress indicator
static java.lang.String	massageFilePathToURL(java.lang.String path) converts an existing local file path to a URL string.
static java.lang.String	massageStringToFilePathSafe(java.lang.String path) converts an existing local file path to a URL string.
static MesquiteFile	newFile(java.lang.String directoryName, java.lang.String fileName) if not applet, opens new file on disk with given name
java.lang.String	nextToken(java.lang.StringBuffer commentBuffer) Returns next token from file.
static MesquiteFile	open(boolean local, java.io.FilenameFilter fileFilter, java.lang.String message, java.lang.String suggestedDirectory) if not applet, allows user to choose, then opens existing file on disk
static MesquiteFile	open(boolean local, java.lang.String location) opens existing file on disk or URL
static MesquiteFile	open(boolean local, java.lang.String location, java.lang.String suggestedDirectory) opens existing file on disk or URL
static MesquiteFile	open(boolean local, java.lang.String location, java.lang.String message, java.lang.String suggestedDirectory) opens existing file on disk or URL
static MesquiteFile	open(java.lang.String directoryName, java.lang.String fileName) if not applet, opens existing file on disk with given name
static MesquiteFile	open(java.net.URL url) opens existing file at given URL
static java.lang.String	openFileDialog(java.lang.String message, MesquiteString directoryName, MesquiteString fileName) for use by open; chooses file.
boolean	openReading() Opens the file for reading.
boolean	openWriting(boolean ascii) Open file for writing.
static void	putFileContents(java.lang.String relativePath, java.lang.String[] contents, boolean ascii) Places to a file the contents.
static void	putFileContents(java.lang.String relativePath, java.lang.String contents, boolean ascii) Places to a file the contents.
static void	putFileContents(java.lang.String relativePath, java.util.Vector contents, boolean ascii) Places to a file the contents.
static void	putFileContentsQuery(java.lang.String message, java.lang.String output, boolean ascii)
java.lang.String	readLine() read next line from file, return as String.
static java.lang.String	readLine(java.io.InputStream inStream, java.lang.StringBuffer sBuff, MesquiteInteger remnantChar) read next line from file, return as String.
java.lang.String	readLine(java.lang.String endLine) read next line from file, return as String.
boolean	readLine(java.lang.StringBuffer buffer) read next line from file, return as String.
java.lang.String	readNextDarkLine() read next dark line from file, return as String.
void	removeFileElement(FileElement element) Removes the passed FileElement from the file.
void	reportTimes() for development purposes; to time file reading //TODO: get rid of this in final
static java.lang.String	saveFileAsDialog(java.lang.String message) for use by save as; user puts file.
static java.lang.String	saveFileAsDialog(java.lang.String message, java.lang.StringBuffer fileNameBuffer) for use by save as; user puts file.
void	setAnnotation(java.lang.String e, boolean notify) Sets the annotation (e.g., footnote) of this element
void	setBeingSaved(boolean s)
void	setCloseAfterReading(boolean c)
void	setCurrentData(CharacterData d)
void	setCurrentTaxa(Taxa d)
void	setDirtiedByCommand(boolean dirtied)
void	setFileName(java.lang.String fileName)
void	setIsNexus(boolean s)
void	setLocs(boolean local, java.net.URL url, java.lang.String f, java.lang.String d) A low-level call to change various location parameters.
void	setOpenAsUntitled(java.lang.String reason)
void	setPath(java.lang.String path) A low-level call to change fileName.
void	setPreviousSaver(Author a)
void	setProject(MesquiteProject proj) sets the project to which the MesquiteFile belongs.
void	setReadCategory(int r)
void	setWriteProtected(boolean prot)
void	skipNextCommand(MesquiteInteger status) skips the next command in the file.
static void	throwableToLog(java.lang.Object obj, java.lang.Throwable e)
java.lang.String	toString()
void	write(java.lang.String s) Write string to file
void	writeLine(java.lang.String s) Write string to file and add newline character.
static void	writeToLog(java.lang.String s) Writes to the log file

Methods inherited from class mesquite.lib.Listened

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, dispose, doAfterNotify, getRemainingListeners, incrementNotifySuppress, listListeners, notifyDisposing, notifyListeners, notifyListeners, removeListener, reportListeners, setDumpNotified

Methods inherited from class java.lang.Object

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

Field Detail

QUERY_NONE

public static final int QUERY_NONE

See Also:

Constant Field Values

QUERY_CLOSE

public static final int QUERY_CLOSE

See Also:

Constant Field Values

QUERY_DELETE

public static final int QUERY_DELETE

See Also:

Constant Field Values

QUERY_QUIT

public static final int QUERY_QUIT

See Also:

Constant Field Values

LINKED

public static final int LINKED

See Also:

Constant Field Values

INCLUDED

public static final int INCLUDED

See Also:

Constant Field Values

HOME

public static final int HOME

See Also:

Constant Field Values

totalCreated

public static int totalCreated

totalDisposed

public static int totalDisposed

totalFinalized

public static int totalFinalized

foreignElements

public java.util.Vector foreignElements

useDataBlocks

public boolean useDataBlocks

useSimplifiedNexus

public boolean useSimplifiedNexus

interleaveAllowed

public boolean interleaveAllowed

simplifyNames

public boolean simplifyNames

ambiguityToMissing

public boolean ambiguityToMissing

writeExcludedCharacters

public boolean writeExcludedCharacters

exporting

public int exporting

notesBugWarn

public boolean notesBugWarn

notesBugVector

public java.util.Vector notesBugVector

fileSeparator

public static java.lang.String fileSeparator

appendToLog

public static boolean appendToLog

Constructor Detail

MesquiteFile

public MesquiteFile()

Method Detail

getID

public long getID()

finalize

public void finalize()
              throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable

setReadCategory

public void setReadCategory(int r)

getReadCategory

public int getReadCategory()

setPreviousSaver

public void setPreviousSaver(Author a)

getPreviousSaver

public Author getPreviousSaver()

setCurrentData

public void setCurrentData(CharacterData d)

getCurrentData

public CharacterData getCurrentData()

setCurrentTaxa

public void setCurrentTaxa(Taxa d)

getCurrentTaxa

public Taxa getCurrentTaxa()

getNumberOfFiles

public static int getNumberOfFiles()

getOpenAsUntitled

public java.lang.String getOpenAsUntitled()

setOpenAsUntitled

public void setOpenAsUntitled(java.lang.String reason)

getCloseAfterReading

public boolean getCloseAfterReading()

setCloseAfterReading

public void setCloseAfterReading(boolean c)

setBeingSaved

public void setBeingSaved(boolean s)

getBeingSaved

public boolean getBeingSaved()

setIsNexus

public void setIsNexus(boolean s)

isClosed

public boolean isClosed()

reportTimes

public void reportTimes()

for development purposes; to time file reading //TODO: get rid of this in final

doCommand

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

The method by which commands are sent to the file using text-based scripting.

Specified by:

doCommand in interface Commandable

existingLength

public long existingLength()

Returns size of existing file on disk corresponding to this MesquiteFile

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

newFile

public static MesquiteFile newFile(java.lang.String directoryName,
                                   java.lang.String fileName)

if not applet, opens new file on disk with given name

copy

public static void copy(java.io.File src,
                        java.io.File dst)
                 throws java.io.IOException

A basic method for copying one File to another; if the destination file does not exist, it will be created

Throws:

java.io.IOException

open

public static MesquiteFile open(boolean local,
                                java.io.FilenameFilter fileFilter,
                                java.lang.String message,
                                java.lang.String suggestedDirectory)

if not applet, allows user to choose, then opens existing file on disk

open

public static MesquiteFile open(boolean local,
                                java.lang.String location)

opens existing file on disk or URL

open

public static MesquiteFile open(boolean local,
                                java.lang.String location,
                                java.lang.String suggestedDirectory)

opens existing file on disk or URL

open

public static MesquiteFile open(boolean local,
                                java.lang.String location,
                                java.lang.String message,
                                java.lang.String suggestedDirectory)

opens existing file on disk or URL

open

public static MesquiteFile open(java.lang.String directoryName,
                                java.lang.String fileName)

if not applet, opens existing file on disk with given name

open

public static MesquiteFile open(java.net.URL url)

opens existing file at given URL

isDirty

public boolean isDirty()

close

public boolean close()

Closes the file and removes from the project all file elements belonging to it.

setDirtiedByCommand

public void setDirtiedByCommand(boolean dirtied)

closeAndDelete

public boolean closeAndDelete()

Closes the file, removes from the project all file elements belonging to it, and deletes it.

downloadFTPorHTTPFile

public static boolean downloadFTPorHTTPFile(java.lang.String urlString,
                                            java.lang.String localSaveDirectoryPath,
                                            java.lang.String localSaveName)

Downloads the file present at the ftp URL urlString, saves the file into the local directory at localSaveDirectoryPath, in the file localSaveName. If localSaveName is blank, then it saves the file name given in the URL.

downloadFTPorHTTPFile

public static boolean downloadFTPorHTTPFile(java.lang.String urlString,
                                            java.lang.String localSaveDirectoryPath)

Downloads the file present at the ftp URL urlString, saves the file into the local directory at localSaveDirectoryPath, using the file name given in the URL.

setLocs

public void setLocs(boolean local,
                    java.net.URL url,
                    java.lang.String f,
                    java.lang.String d)

A low-level call to change various location parameters. Shouldn't be used too liberally; changeLocation does more housekeeping.

setPath

public void setPath(java.lang.String path)

A low-level call to change fileName. Shouldn't be used too liberally; changeLocation does more housekeeping.

getPath

public java.lang.String getPath()

Returns path to file on disk 19 Jan 02

setFileName

public void setFileName(java.lang.String fileName)

changeLocation

public void changeLocation(java.lang.String directoryName,
                           java.lang.String fileName)

redirects place at which file will be rewritten; for use by save as

changeLocation

public boolean changeLocation(java.lang.String message)

for use by save as; user puts file. Returns true if new location successfuly found

saveFileAsDialog

public static java.lang.String saveFileAsDialog(java.lang.String message)

for use by save as; user puts file. Returns new location

saveFileAsDialog

public static java.lang.String saveFileAsDialog(java.lang.String message,
                                                java.lang.StringBuffer fileNameBuffer)

for use by save as; user puts file. Returns new location

chooseDirectory

public static java.lang.String chooseDirectory(java.lang.String message)

To choose a directory; returns path

chooseDirectory

public static java.lang.String chooseDirectory(java.lang.String message,
                                               java.lang.String suggestedDir)

To choose a directory; returns path

openFileDialog

public static java.lang.String openFileDialog(java.lang.String message,
                                              MesquiteString directoryName,
                                              MesquiteString fileName)

for use by open; chooses file. Returns full path and also separate directory and file names in MesquiteStrings

isLocal

public boolean isLocal()

returns true if file is local (on disk), false if remote (via URL).

setProject

public void setProject(MesquiteProject proj)

sets the project to which the MesquiteFile belongs.

getProject

public MesquiteProject getProject()

gets the project to which the MesquiteFile belongs.

openReading

public boolean openReading()

Opens the file for reading.

closeReading

public void closeReading()

Closes the file for reading.

openWriting

public boolean openWriting(boolean ascii)

Open file for writing.

writeLine

public void writeLine(java.lang.String s)

Write string to file and add newline character.

write

public void write(java.lang.String s)

Write string to file

closeWriting

public void closeWriting()

Close file for writing

closeWriting

public void closeWriting(int numBackups)

Close file for writing

isWriting

public boolean isWriting()

getDirectoryName

public java.lang.String getDirectoryName()

Get directory in which file resides (actually, entire path)

getFileName

public java.lang.String getFileName()

Get name of file.

getURL

public java.net.URL getURL()

Get URL of file (null if a local file).

getDirectoryPathFromFilePath

public static java.lang.String getDirectoryPathFromFilePath(java.lang.String path)

Return string for directory path from full file path

getFileNameFromFilePath

public static java.lang.String getFileNameFromFilePath(java.lang.String path)

Return string for directory path from full file path

composePath

public static java.lang.String composePath(java.lang.String d,
                                           java.lang.String f)

Return string for path, accommodating ../ at start of filename. If second string passed begins with "/", this assumes that the string is an entire path to a local volume (e.g. "/HardDrive/MyDirectory/picture.gif") and ignores the first string. In some cases, d is directory; f is file

decomposePath

public static java.lang.String decomposePath(java.lang.String relativeTo,
                                             java.lang.String path)

Converts absolute to relative string for path

massageStringToFilePathSafe

public static java.lang.String massageStringToFilePathSafe(java.lang.String path)

converts an existing local file path to a URL string. See also StringUtil.encodeForURL

massageFilePathToURL

public static java.lang.String massageFilePathToURL(java.lang.String path)

converts an existing local file path to a URL string. See also StringUtil.encodeForURL

linkProgressIndicator

public void linkProgressIndicator(ProgressIndicator pi)

Links progress indicator

getFileAborted

public boolean getFileAborted()

Returns true if user has requested file reading or writing stop.

readLine

public java.lang.String readLine(java.lang.String endLine)

read next line from file, return as String.

readLine

public boolean readLine(java.lang.StringBuffer buffer)

read next line from file, return as String.

readLine

public java.lang.String readLine()

read next line from file, return as String.

readLine

public static java.lang.String readLine(java.io.InputStream inStream,
                                        java.lang.StringBuffer sBuff,
                                        MesquiteInteger remnantChar)

read next line from file, return as String.

readNextDarkLine

public java.lang.String readNextDarkLine()

read next dark line from file, return as String.

firstToken

public java.lang.String firstToken(java.lang.StringBuffer commentBuffer)

Returns next token from file. Used for first token of command, to preserves leading whitespace (used to preserve leading tabs/spaces for blocks such as the MesquiteBlock).

nextToken

public java.lang.String nextToken(java.lang.StringBuffer commentBuffer)

Returns next token from file. Note that firstToken is used for the first token in a command

getNextCommand

public java.lang.String getNextCommand(MesquiteInteger status,
                                       java.lang.StringBuffer commandComments,
                                       boolean includeEntireCommand)

returns the next command in the file. Extra information about the command is returned in the MesquiteInteger status. If the command is the "begin", 1 is returned; if "end;", 2 is returned. Otherwise 0 is returned. If includeEntireCommand is true, then the entire command is returned; if false, the only the first token (command name) is returned. (Returning only part of the command can save time if the commands are long (e.g., a TREE) and not needed.

getNextCommand

public java.lang.String getNextCommand(MesquiteInteger status,
                                       java.lang.StringBuffer commandComments)

returns the next command in the file. Extra information about the command is returned in the MesquiteInteger status. If the command is the "begin", 1 is returned; if "end;", 2 is returned. Otherwise 0 is returned.

skipNextCommand

public void skipNextCommand(MesquiteInteger status)

skips the next command in the file. Extra information is returned in the MesquiteInteger status. If the command is the "begin", 1 is returned; if "end;", 2 is returned. Otherwise 0 is returned.

getNextBlockOLD

public FileBlock getNextBlockOLD(MesquiteString blockName,
                                 java.lang.StringBuffer fileComments,
                                 java.lang.StringBuffer blockComments)

returns the next block; blockName is passed back via the MesquiteString object

getNextBlock

public FileBlock getNextBlock(MesquiteString blockName,
                              java.lang.StringBuffer fileComments,
                              java.lang.StringBuffer blockComments)

returns the next block; blockName is passed back via the MesquiteString object

getFilePosition

public long getFilePosition()

goToFilePosition

public void goToFilePosition(long pos)

goToNextBlockStart

public java.lang.String goToNextBlockStart(MesquiteLong startPos)

returns the file position of the start of the next block; returns blockName

addFileElement

public void addFileElement(FileElement element)

Adds the passed FileElement to the file.

removeFileElement

public void removeFileElement(FileElement element)

Removes the passed FileElement from the file.

getFileElements

public ListableVector getFileElements()

Gets list of file elements.

deleteFile

public static boolean deleteFile(java.lang.String path)

deletes file at path

deleteDirectory

public static boolean deleteDirectory(java.lang.String directoryPath)

fileExists

public static boolean fileExists(java.lang.String path)

Checks to see if path leads to a file that is not a directory

canWrite

public static boolean canWrite(java.lang.String path)

Checks to see if can write to a file

checkFilePath

public static java.lang.String checkFilePath(java.lang.String path,
                                             java.lang.String selectMessage)

Checks to see if path leads to a file; if so, path returned; if not, user is asked to choose new file.

getFileFirstContents

public static java.lang.String getFileFirstContents(java.lang.String relativePath)

Returns the first line of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

getFileContentsAsStrings

public static java.lang.String[] getFileContentsAsStrings(java.lang.String relativePath)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

getTabDelimitedTextFile

public static java.lang.String[][] getTabDelimitedTextFile(java.lang.String relativePath)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

getFileContentsAsString

public static java.lang.String getFileContentsAsString(java.lang.String relativePath)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName".

getFileContentsAsString

public java.lang.String getFileContentsAsString(int maxCharacters)

Returns the contents of the file, local or remote. The parameter "maxCharacters" sets an upper limit on how many characters are read (if <0, then all characters read in)

getFileContentsAsString

public static java.lang.String getFileContentsAsString(java.lang.String relativePath,
                                                       int maxCharacters)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName". The parameter "maxCharacters" sets an upper limit on how many characters are read (if <0, then all characters read in)

getFileContentsAsString

public static java.lang.String getFileContentsAsString(java.lang.String relativePath,
                                                       int maxCharacters,
                                                       int startBufferSize)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName". The parameter "maxCharacters" sets an upper limit on how many characters are read (if <0, then all characters read in)

getFileContentsAsString

public static java.lang.String getFileContentsAsString(java.lang.String relativePath,
                                                       int maxCharacters,
                                                       int startBufferSize,
                                                       boolean warnIfProblem)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName". The parameter "maxCharacters" sets an upper limit on how many characters are read (if <0, then all characters read in)

getFileContentsAsStringOld

public static java.lang.String getFileContentsAsStringOld(java.lang.String relativePath,
                                                          int maxCharacters,
                                                          int startBufferSize)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName". The parameter "maxCharacters" sets an upper limit on how many characters are read (if <0, then all characters read in)

getURLContentsAsString

public static java.lang.String getURLContentsAsString(java.lang.String path,
                                                      int maxCharacters)

Returns the contents of the file at the url

getURLContentsAsString

public static java.lang.String getURLContentsAsString(java.lang.String path,
                                                      int maxCharacters,
                                                      boolean warnIfProblem)

Returns the contents of the file at the url

getURLContentsAsStrings

public static java.lang.String[] getURLContentsAsStrings(java.lang.String path)

Returns the contents of the file. path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

putFileContentsQuery

public static void putFileContentsQuery(java.lang.String message,
                                        java.lang.String output,
                                        boolean ascii)

putFileContents

public static void putFileContents(java.lang.String relativePath,
                                   java.lang.String[] contents,
                                   boolean ascii)

Places to a file the contents. Path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

putFileContents

public static void putFileContents(java.lang.String relativePath,
                                   java.util.Vector contents,
                                   boolean ascii)

Places to a file the contents. Path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

putFileContents

public static void putFileContents(java.lang.String relativePath,
                                   java.lang.String contents,
                                   boolean ascii)

Places to a file the contents. Path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

appendFileContents

public static void appendFileContents(java.lang.String relativePath,
                                      java.lang.String contents,
                                      boolean ascii)

Appends to a file the contents. Path is relative to the root of the package heirarchy; i.e. for file in a module's folder, indicate "mesquite/modules/moduleFolderName/fileName"

writeToLog

public static void writeToLog(java.lang.String s)

Writes to the log file

getLogWriter

public static java.io.PrintWriter getLogWriter()

throwableToLog

public static void throwableToLog(java.lang.Object obj,
                                  java.lang.Throwable e)

closeLog

public static void closeLog()

Closes to the log file

getWriteProtected

public boolean getWriteProtected()

setWriteProtected

public void setWriteProtected(boolean prot)

setAnnotation

public void setAnnotation(java.lang.String e,
                          boolean notify)

Sets the annotation (e.g., footnote) of this element

getAnnotation

public java.lang.String getAnnotation()

Returns the annotation (e.g., footnote) of this element

getExplanation

public java.lang.String getExplanation()

Returns the explanation (e.g., footnote plus additional information) of this file

Specified by:

getExplanation in interface Explainable

getHDaughters

public HNode[] getHDaughters()

Specified by:

getHDaughters in interface HNode

getHMother

public HNode getHMother()

Specified by:

getHMother in interface HNode

getName

public java.lang.String getName()

Specified by:

getName in interface HNode

Specified by:

getName in interface Listable

getTypeName

public java.lang.String getTypeName()

Specified by:

getTypeName in interface HNode

getNumSupplements

public int getNumSupplements()

Specified by:

getNumSupplements in interface HNode

getSupplementName

public java.lang.String getSupplementName(int index)

Specified by:

getSupplementName in interface HNode

hNodeAction

public void hNodeAction(java.awt.Container c,
                        int x,
                        int y,
                        int action)

for HNode interface

Specified by:

hNodeAction in interface HNode

hSupplementTouched

public void hSupplementTouched(int index)

Specified by:

hSupplementTouched in interface HNode

getHImage

public java.awt.Image getHImage()

Specified by:

getHImage in interface HNode

getHColor

public java.awt.Color getHColor()

Specified by:

getHColor in interface HNode

getHShow

public boolean getHShow()

Specified by:

getHShow in interface HNode