org.jmol.viewer
Class FileManager

java.lang.Object
  extended by org.jmol.viewer.FileManager

public class FileManager
extends java.lang.Object


Nested Class Summary
(package private)  class FileManager.DOMReaderThread
           
(package private)  class FileManager.FileReaderThread
           
(package private)  class FileManager.FilesReaderThread
           
 
Field Summary
private  FileManager.DOMReaderThread aDOMReaderThread
           
private  java.net.URL appletCodeBase
           
private  java.net.URL appletDocumentBase
           
private  java.lang.String appletProxy
           
private  java.lang.String fileName
           
(package private)  FileManager.FileReaderThread fileReaderThread
           
(package private)  FileManager.FilesReaderThread filesReaderThread
           
private  java.lang.String fileType
           
private  java.lang.String fullPathName
           
private  java.lang.String inlineData
           
private  java.lang.String loadScript
           
private  java.lang.String nameAsGiven
           
private  java.lang.String openErrorMessage
           
private static int URL_LOCAL
           
private static java.lang.String[] urlPrefixes
           
private static java.lang.String[] urlPrefixPairs
           
protected  Viewer viewer
           
 
Constructor Summary
FileManager(Viewer viewer)
           
 
Method Summary
private static java.lang.String addDirectory(java.lang.String defaultDirectory, java.lang.String name)
           
(package private)  void addLoadScript(java.lang.String script)
           
private  java.lang.String[] classifyName(java.lang.String name, boolean isFullLoad)
           
(package private)  void clear()
           
(package private)  void createAtomSeCollectionFromStrings(java.lang.String[] arrayModels, java.util.Hashtable htParams, boolean isAppend)
           
(package private)  void createAtomSetCollectionFromDOM(java.lang.Object DOMNode)
           
(package private)  void createAtomSetCollectionFromFile(java.lang.String name, java.util.Hashtable htParams, java.lang.String loadScript, boolean isAppend)
           
(package private)  void createAtomSetCollectionFromFiles(java.lang.String modelName, java.lang.String[] fileNames, java.lang.String loadScript, boolean isAppend, java.util.Hashtable htParams)
           
(package private)  void createAtomSetCollectionFromReader(java.lang.String fullPathName, java.lang.String name, java.io.Reader reader)
          not used in Jmol project -- will close reader
(package private)  void createAtomSetCollectionFromString(java.lang.String strModel, java.util.Hashtable htParams, boolean isAppend)
           
(package private)  void deallocateReaderThreads()
           
private  java.lang.String fixPath(java.lang.String path)
           
(package private)  java.lang.String getAppletDocumentBase()
           
(package private)  java.lang.Object getAtomSetCollectionOrError()
          after a file or other object has been opened and the atom set collection has been created, this method returns that atom set collection or an error message and closes the file.
static java.io.BufferedReader getBufferedReaderForString(java.lang.String string)
           
(package private)  java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name, java.lang.String[] fullPathNameReturn, boolean isBinary, boolean doSpecialLoad)
           
(package private)  java.lang.String getDefaultDirectory(java.lang.String name)
           
 java.lang.Object getFileAsBytes(java.lang.String name)
           
(package private)  java.lang.Object getFileAsImage(java.lang.String name, java.util.Hashtable htParams)
           
private  java.lang.String getFileDataAsSections(java.lang.String[] info, java.util.Hashtable fileData)
           
private  java.lang.String getFileDataAsSections(java.lang.String name, java.lang.String header, java.util.Hashtable fileData)
          delivers file contents and directory listing for a ZIP/JAR file into sb
(package private)  boolean getFileDataOrErrorAsString(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
           
(package private)  java.lang.String[] getFileInfo()
           
(package private)  java.lang.String getFileName()
           
(package private)  java.lang.String getFileTypeName(java.lang.String fileName)
           
 java.lang.String getFullPath(java.lang.String name, boolean addUrlPrefix)
           
(package private)  java.lang.String getFullPathName()
           
(package private)  java.lang.String getInlineData(int iData)
           
static java.lang.Object getInputStream(java.lang.String name, boolean showMsg, java.net.URL appletDocumentBase, java.lang.String appletProxy)
           
(package private)  java.lang.Object getInputStreamOrErrorMessageFromName(java.lang.String name, boolean showMsg)
           
(package private)  java.lang.String getLoadScript()
           
static java.io.File getLocalDirectory(JmolViewer viewer, boolean forDialog)
           
static java.lang.String getLocalUrl(java.io.File file)
           
(package private)  java.lang.String getState(java.lang.StringBuffer sfunc)
           
(package private)  java.lang.Object getUnzippedBufferedReaderOrErrorMessageFromName(java.lang.String name, boolean allowZipStream, boolean asInputStream, boolean isTypeCheckOnly, boolean doSpecialLoad)
           
(package private)  java.lang.String[] getZipDirectory(java.lang.String fileName, boolean addManifest)
           
(package private)  java.lang.String getZipDirectoryAsString(java.lang.String fileName)
           
(package private) static boolean isGzip(java.io.InputStream is)
           
(package private)  void setAppletContext(java.net.URL documentBase, java.net.URL codeBase, java.lang.String jmolAppletProxy)
           
(package private)  void setAppletProxy(java.lang.String appletProxy)
           
(package private)  void setFileInfo(java.lang.String[] fileInfo)
           
private  void setLoadScript(java.lang.String script, boolean isAppend)
           
static void setLocalPath(JmolViewer viewer, java.lang.String path, boolean forDialog)
           
static java.lang.String setLocalPathForWritingFile(JmolViewer viewer, java.lang.String file)
           
private  void setNames(java.lang.String[] names)
           
(package private) static java.lang.String shortNameOf(java.lang.String name)
           
private static int urlTypeIndex(java.lang.String name)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

viewer

protected Viewer viewer

openErrorMessage

private java.lang.String openErrorMessage

appletDocumentBase

private java.net.URL appletDocumentBase

appletCodeBase

private java.net.URL appletCodeBase

appletProxy

private java.lang.String appletProxy

nameAsGiven

private java.lang.String nameAsGiven

fullPathName

private java.lang.String fullPathName

fileName

private java.lang.String fileName

fileType

private java.lang.String fileType

inlineData

private java.lang.String inlineData

loadScript

private java.lang.String loadScript

fileReaderThread

FileManager.FileReaderThread fileReaderThread

filesReaderThread

FileManager.FilesReaderThread filesReaderThread

aDOMReaderThread

private FileManager.DOMReaderThread aDOMReaderThread

URL_LOCAL

private static final int URL_LOCAL
See Also:
Constant Field Values

urlPrefixes

private static final java.lang.String[] urlPrefixes

urlPrefixPairs

private static final java.lang.String[] urlPrefixPairs
Constructor Detail

FileManager

FileManager(Viewer viewer)
Method Detail

getInlineData

java.lang.String getInlineData(int iData)

getState

java.lang.String getState(java.lang.StringBuffer sfunc)

getFileTypeName

java.lang.String getFileTypeName(java.lang.String fileName)

clear

void clear()

getLoadScript

java.lang.String getLoadScript()

setLoadScript

private void setLoadScript(java.lang.String script,
                           boolean isAppend)

addLoadScript

void addLoadScript(java.lang.String script)

createAtomSetCollectionFromFile

void createAtomSetCollectionFromFile(java.lang.String name,
                                     java.util.Hashtable htParams,
                                     java.lang.String loadScript,
                                     boolean isAppend)

createAtomSetCollectionFromFiles

void createAtomSetCollectionFromFiles(java.lang.String modelName,
                                      java.lang.String[] fileNames,
                                      java.lang.String loadScript,
                                      boolean isAppend,
                                      java.util.Hashtable htParams)

createAtomSetCollectionFromString

void createAtomSetCollectionFromString(java.lang.String strModel,
                                       java.util.Hashtable htParams,
                                       boolean isAppend)

createAtomSeCollectionFromStrings

void createAtomSeCollectionFromStrings(java.lang.String[] arrayModels,
                                       java.util.Hashtable htParams,
                                       boolean isAppend)

createAtomSetCollectionFromDOM

void createAtomSetCollectionFromDOM(java.lang.Object DOMNode)

createAtomSetCollectionFromReader

void createAtomSetCollectionFromReader(java.lang.String fullPathName,
                                       java.lang.String name,
                                       java.io.Reader reader)
not used in Jmol project -- will close reader

Parameters:
fullPathName -
name -
reader -

isGzip

static boolean isGzip(java.io.InputStream is)
               throws java.lang.Exception
Throws:
java.lang.Exception

getFileAsBytes

public java.lang.Object getFileAsBytes(java.lang.String name)

getFileDataOrErrorAsString

boolean getFileDataOrErrorAsString(java.lang.String[] data,
                                   int nBytesMax,
                                   boolean doSpecialLoad)
Parameters:
data - [0] initially path name, but returned as full path name; [1]file contents (directory listing for a ZIP/JAR file) or error string
nBytesMax -
doSpecialLoad -
Returns:
true if successful; false on error

getFileAsImage

java.lang.Object getFileAsImage(java.lang.String name,
                                java.util.Hashtable htParams)

getFileDataAsSections

private java.lang.String getFileDataAsSections(java.lang.String[] info,
                                               java.util.Hashtable fileData)

getFileDataAsSections

private java.lang.String getFileDataAsSections(java.lang.String name,
                                               java.lang.String header,
                                               java.util.Hashtable fileData)
delivers file contents and directory listing for a ZIP/JAR file into sb

Parameters:
name -
header -
fileData -
Returns:
name of entry

getAtomSetCollectionOrError

java.lang.Object getAtomSetCollectionOrError()
after a file or other object has been opened and the atom set collection has been created, this method returns that atom set collection or an error message and closes the file.

Returns:
string error or an AtomSetCollection

deallocateReaderThreads

void deallocateReaderThreads()

getFullPathName

java.lang.String getFullPathName()

setFileInfo

void setFileInfo(java.lang.String[] fileInfo)

getFileInfo

java.lang.String[] getFileInfo()

getFileName

java.lang.String getFileName()

getAppletDocumentBase

java.lang.String getAppletDocumentBase()

setAppletContext

void setAppletContext(java.net.URL documentBase,
                      java.net.URL codeBase,
                      java.lang.String jmolAppletProxy)

setAppletProxy

void setAppletProxy(java.lang.String appletProxy)

urlTypeIndex

private static int urlTypeIndex(java.lang.String name)

setNames

private void setNames(java.lang.String[] names)

shortNameOf

static java.lang.String shortNameOf(java.lang.String name)

classifyName

private java.lang.String[] classifyName(java.lang.String name,
                                        boolean isFullLoad)
Parameters:
name -
isFullLoad -
Returns:
[0] full path name, [1] file name without path, [2] full URL

getDefaultDirectory

java.lang.String getDefaultDirectory(java.lang.String name)

fixPath

private java.lang.String fixPath(java.lang.String path)

getFullPath

public java.lang.String getFullPath(java.lang.String name,
                                    boolean addUrlPrefix)

getLocalUrl

public static java.lang.String getLocalUrl(java.io.File file)

getLocalDirectory

public static java.io.File getLocalDirectory(JmolViewer viewer,
                                             boolean forDialog)

setLocalPath

public static void setLocalPath(JmolViewer viewer,
                                java.lang.String path,
                                boolean forDialog)

setLocalPathForWritingFile

public static java.lang.String setLocalPathForWritingFile(JmolViewer viewer,
                                                          java.lang.String file)

addDirectory

private static java.lang.String addDirectory(java.lang.String defaultDirectory,
                                             java.lang.String name)

getInputStreamOrErrorMessageFromName

java.lang.Object getInputStreamOrErrorMessageFromName(java.lang.String name,
                                                      boolean showMsg)

getInputStream

public static java.lang.Object getInputStream(java.lang.String name,
                                              boolean showMsg,
                                              java.net.URL appletDocumentBase,
                                              java.lang.String appletProxy)

getBufferedReaderForString

public static java.io.BufferedReader getBufferedReaderForString(java.lang.String string)

getBufferedReaderOrErrorMessageFromName

java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name,
                                                         java.lang.String[] fullPathNameReturn,
                                                         boolean isBinary,
                                                         boolean doSpecialLoad)

getUnzippedBufferedReaderOrErrorMessageFromName

java.lang.Object getUnzippedBufferedReaderOrErrorMessageFromName(java.lang.String name,
                                                                 boolean allowZipStream,
                                                                 boolean asInputStream,
                                                                 boolean isTypeCheckOnly,
                                                                 boolean doSpecialLoad)

getZipDirectory

java.lang.String[] getZipDirectory(java.lang.String fileName,
                                   boolean addManifest)

getZipDirectoryAsString

java.lang.String getZipDirectoryAsString(java.lang.String fileName)