Field Detail

• SIMULATION_PROTOCOL

  public static java.lang.String SIMULATION_PROTOCOL

• vwr

  public Viewer vwr

• spartanDoc

  private SpartanUtil spartanDoc

• jzu

  JmolUtil jzu

• pathForAllFiles

  private java.lang.String pathForAllFiles

• nameAsGiven

  private java.lang.String nameAsGiven

• fullPathName

  private java.lang.String fullPathName

• lastFullPathName

  private java.lang.String lastFullPathName

• lastNameAsGiven

  private java.lang.String lastNameAsGiven

• fileName

  private java.lang.String fileName

• appletDocumentBaseURL

  private java.net.URL appletDocumentBaseURL

• appletProxy

  private java.lang.String appletProxy

• DELPHI_BINARY_MAGIC_NUMBER

  private static final java.lang.String DELPHI_BINARY_MAGIC_NUMBER

  See Also:

  Constant Field Values

• PMESH_BINARY_MAGIC_NUMBER

  public static final java.lang.String PMESH_BINARY_MAGIC_NUMBER

  See Also:

  Constant Field Values

• JPEG_CONTINUE_STRING

  public static final java.lang.String JPEG_CONTINUE_STRING

  See Also:

  Constant Field Values

• scriptFilePrefixes

  private static java.lang.String[] scriptFilePrefixes

• cache

  private java.util.Map<java.lang.String,​java.lang.Object> cache

• pngjCache

  public java.util.Map<java.lang.String,​java.lang.Object> pngjCache

• spardirCache

  public java.util.Map<java.lang.String,​byte[]> spardirCache

Constructor Detail

• FileManager

  FileManager​(Viewer vwr)

Method Detail

• spartanUtil

  public SpartanUtil spartanUtil()

  An isolated class to retrieve Spartan file data from compound documents, zip files, and directories

  Returns:

  a SpartanUtil

• getJzu

  public JmolUtil getJzu()

• clear

  void clear()

• setLoadState

  private void setLoadState​(java.util.Map<java.lang.String,​java.lang.Object> htParams)

• getPathForAllFiles

  public java.lang.String getPathForAllFiles()

• setPathForAllFiles

  java.lang.String setPathForAllFiles​(java.lang.String value)

• setFileInfo

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

  Set fullPathName, fileName, and nameAsGiven

  Parameters:

  fileInfo - if null, replace fullPathName and nameAsGiven with last version of such

• getFileInfo

  public java.lang.String[] getFileInfo()

• getFullPathName

  public java.lang.String getFullPathName​(boolean orPrevious)

• getFileName

  public java.lang.String getFileName()

• getAppletDocumentBase

  java.lang.String getAppletDocumentBase()

• setAppletContext

  void setAppletContext​(java.lang.String documentBase)

• setAppletProxy

  void setAppletProxy​(java.lang.String appletProxy)

• createAtomSetCollectionFromFile

  java.lang.Object createAtomSetCollectionFromFile​(java.lang.String name,
                                                   java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                   boolean isAppend)

• createAtomSetCollectionFromFiles

  java.lang.Object createAtomSetCollectionFromFiles​(java.lang.String[] fileNames,
                                                    java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                    boolean isAppend)

• createAtomSetCollectionFromString

  java.lang.Object createAtomSetCollectionFromString​(java.lang.String strModel,
                                                     java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                     boolean isAppend)

• createAtomSeCollectionFromStrings

  java.lang.Object createAtomSeCollectionFromStrings​(java.lang.String[] arrayModels,
                                                     javajs.util.SB loadScript,
                                                     java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                     boolean isAppend)

• createAtomSeCollectionFromArrayData

  java.lang.Object createAtomSeCollectionFromArrayData​(javajs.util.Lst<java.lang.Object> arrayData,
                                                       java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                       boolean isAppend)

• newDataReader

  static javajs.util.DataReader newDataReader​(Viewer vwr,
                                              java.lang.Object data)

• newFilesReader

  private JmolFilesReaderInterface newFilesReader​(java.lang.String[] fullPathNames,
                                                  java.lang.String[] namesAsGiven,
                                                  java.lang.String[] fileTypes,
                                                  javajs.util.DataReader[] readers,
                                                  java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                  boolean isAppend)

• createAtomSetCollectionFromDOM

  java.lang.Object createAtomSetCollectionFromDOM​(java.lang.Object DOMNode,
                                                  java.util.Map<java.lang.String,​java.lang.Object> htParams)

• createAtomSetCollectionFromReader

  java.lang.Object createAtomSetCollectionFromReader​(java.lang.String fullPathName,
                                                     java.lang.String name,
                                                     java.lang.Object reader,
                                                     java.util.Map<java.lang.String,​java.lang.Object> htParams)

  not used in Jmol project -- will close reader

  Parameters:

  fullPathName -

  name -

  reader - could be a Reader, or a BufferedInputStream or byte[]

  htParams -

  Returns:

  fileData

• getBufferedInputStream

  java.io.BufferedInputStream getBufferedInputStream​(java.lang.String fullPathName)

• getBufferedInputStreamOrErrorMessageFromName

  public java.lang.Object getBufferedInputStreamOrErrorMessageFromName​(java.lang.String name,
                                                                       java.lang.String fullName,
                                                                       boolean showMsg,
                                                                       boolean checkOnly,
                                                                       byte[] outputBytes,
                                                                       boolean allowReader,
                                                                       boolean allowCached)

• getBufferedReaderForResource

  public static java.io.BufferedReader getBufferedReaderForResource​(Viewer vwr,
                                                                    java.lang.Object resourceClass,
                                                                    java.lang.String classPath,
                                                                    java.lang.String resourceName)
                                                             throws java.io.IOException

  Throws:

  java.io.IOException

• urlEncode

  private java.lang.String urlEncode​(java.lang.String name)

• getEmbeddedFileState

  public java.lang.String getEmbeddedFileState​(java.lang.String fileName,
                                               boolean allowCached)

• getFullPathNameOrError

  java.lang.Object getFullPathNameOrError​(java.lang.String filename,
                                          boolean getStream,
                                          java.lang.String[] ret)

  just check for a file as being readable. Do not go into a zip file

  Parameters:

  filename -

  getStream -

  ret -

  Returns:

  String[2] where [0] is fullpathname and [1] is error message or null

• getBufferedReaderOrErrorMessageFromName

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

• getUnzippedReaderOrStreamFromName

  public java.lang.Object getUnzippedReaderOrStreamFromName​(java.lang.String name,
                                                            java.lang.Object bytesOrStream,
                                                            boolean allowZipStream,
                                                            boolean forceInputStream,
                                                            boolean isTypeCheckOnly,
                                                            boolean doSpecialLoad,
                                                            java.util.Map<java.lang.String,​java.lang.Object> htParams)

  Parameters:

  name -

  bytesOrStream - cached bytes or a BufferedInputStream

  allowZipStream - if the file is a zip file, allow a return that is a ZipInputStream

  forceInputStream - always return a raw BufferedInputStream, not a BufferedReader, and do not process PNGJ files

  isTypeCheckOnly - when possibly reading a spartan file for content (doSpecialLoad == true), just return the compound document's file list

  doSpecialLoad - check for a Spartan file

  htParams -

  Returns:

  String if error or String[] if a type check or BufferedReader or BufferedInputStream

• getZipDirectory

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

  Parameters:

  fileName -

  addManifest -

  allowCached -

  Returns:

  [] if not a zip file;

• getFileAsBytes

  public java.lang.Object getFileAsBytes​(java.lang.String name,
                                         javajs.util.OC out)

• getFileAsMap

  public java.util.Map<java.lang.String,​java.lang.Object> getFileAsMap​(java.lang.String name)

• getFileDataAsString

  public boolean getFileDataAsString​(java.lang.String[] data,
                                     int nBytesMax,
                                     boolean doSpecialLoad,
                                     boolean allowBinary,
                                     boolean checkProtected)

  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 - or -1

  doSpecialLoad -

  allowBinary -

  checkProtected - TODO

  Returns:

  true if successful; false on error

• checkSecurity

  private boolean checkSecurity​(java.lang.String f)

• loadImage

  public boolean loadImage​(java.lang.Object nameOrBytes,
                           java.lang.String echoName,
                           boolean forceSync)

  Load an image

  Parameters:

  nameOrBytes -

  echoName -

  forceSync - TODO

  Returns:

  true if asynchronous

• getClassifiedName

  private java.lang.String[] getClassifiedName​(java.lang.String name,
                                               boolean isFullLoad)

  [0] and [2] may return same as [1] in the case of a local unsigned applet.

  Parameters:

  name -

  isFullLoad - false only when just checking path

  Returns:

  [0] full path name, [1] file name without path, [2] full URL

• addDirectory

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

• getDefaultDirectory

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

• fixPath

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

• getFilePath

  public java.lang.String getFilePath​(java.lang.String name,
                                      boolean addUrlPrefix,
                                      boolean asShortName)

• getLocalDirectory

  public static javajs.api.GenericFileInterface getLocalDirectory​(Viewer vwr,
                                                                  boolean forDialog)

• setLocalPath

  public static void setLocalPath​(Viewer vwr,
                                  java.lang.String path,
                                  boolean forDialog)

  called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog. In this way, saving a file from a dialog doesn't change the "CD" directory. Neither of these is saved in the state, but

  Parameters:

  vwr -

  path -

  forDialog -

• getLocalPathForWritingFile

  public static java.lang.String getLocalPathForWritingFile​(Viewer vwr,
                                                            java.lang.String file)

• fixDOSName

  public static java.lang.String fixDOSName​(java.lang.String fileName)

  Switch \ for / only for DOS names such as C:\temp\t.xyz, not names like http://cactus.nci.nih.gov/chemical/structure/CC/C=C\CC

  Parameters:

  fileName -

  Returns:

  fixed name

• stripPath

  public static java.lang.String stripPath​(java.lang.String name)

• determineSurfaceTypeIs

  public static java.lang.String determineSurfaceTypeIs​(java.io.InputStream is)

• isScriptType

  public static boolean isScriptType​(java.lang.String fname)

• isSurfaceType

  public static boolean isSurfaceType​(java.lang.String fname)

• determineSurfaceFileType

  public static java.lang.String determineSurfaceFileType​(java.io.BufferedReader bufferedReader)

• getManifestScriptPath

  public static java.lang.String getManifestScriptPath​(java.lang.String manifest)

  check a JmolManifest for a reference to a script file (.spt)

  Parameters:

  manifest -

  Returns:

  null, "", or a directory entry in the ZIP file

• getEmbeddedScript

  public static java.lang.String getEmbeddedScript​(java.lang.String script)

• getFileReferences

  public static void getFileReferences​(java.lang.String script,
                                       javajs.util.Lst<java.lang.String> fileList)

• setScriptFileReferences

  public static java.lang.String setScriptFileReferences​(java.lang.String script,
                                                         java.lang.String localPath,
                                                         java.lang.String remotePath,
                                                         java.lang.String scriptPath)

• setScriptFileRefs

  private static java.lang.String setScriptFileRefs​(java.lang.String script,
                                                    java.lang.String dataPath,
                                                    boolean isLocal)

  Sets all local file references in a script file to point to files within dataPath. If a file reference contains dataPath, then the file reference is left with that RELATIVE path. Otherwise, it is changed to a relative file name within that dataPath. Only file references starting with "file://" are changed.

  Parameters:

  script -

  dataPath -

  isLocal -

  Returns:

  revised script

• cachePut

  void cachePut​(java.lang.String key,
                java.lang.Object data)

• cacheGet

  public java.lang.Object cacheGet​(java.lang.String key,
                                   boolean bytesOnly)

• cacheClear

  void cacheClear()

• cacheFileByNameAdd

  public int cacheFileByNameAdd​(java.lang.String fileName,
                                boolean isAdd)

• cacheList

  public java.util.Map<java.lang.String,​java.lang.Integer> cacheList()

• getCanonicalName

  public java.lang.String getCanonicalName​(java.lang.String pathName)

• recachePngjBytes

  public void recachePngjBytes​(java.lang.String fileName,
                               byte[] bytes)

• getPngjOrDroppedBytes

  private byte[] getPngjOrDroppedBytes​(java.lang.String fullName,
                                       java.lang.String name)

• getCachedPngjBytes

  private byte[] getCachedPngjBytes​(java.lang.String pathName)

• postByteArray

  public java.lang.String postByteArray​(java.lang.String fileName,
                                        byte[] bytes)

  Specified by:

  postByteArray in interface javajs.api.BytePoster