Class FileManager

Method Details

• 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(Map<String,Object> htParams)

• getPathForAllFiles

  public String getPathForAllFiles()

• setPathForAllFiles

  String setPathForAllFiles(String value)

• setFileInfo

  public void setFileInfo(String[] fileInfo)

  Set fullPathName, fileName, and nameAsGiven

  Parameters:

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

• getFileInfo

  public String[] getFileInfo()

• getFullPathName

  public String getFullPathName(boolean orPrevious)

• getFileType

  public String getFileType()

• setFileType

  public void setFileType(String fileType)

• getFileName

  public String getFileName()

• getAppletDocumentBase

  String getAppletDocumentBase()

• setAppletContext

  void setAppletContext(String documentBase)

• setAppletProxy

  void setAppletProxy(String appletProxy)

• createAtomSetCollectionFromFile

  Object createAtomSetCollectionFromFile(String name, Map<String,Object> htParams, boolean isAppend)

• createAtomSetCollectionFromFiles

  Object createAtomSetCollectionFromFiles(String[] fileNames, Map<String,Object> htParams, boolean isAppend)

• createAtomSetCollectionFromString

  Object createAtomSetCollectionFromString(String strModel, Map<String,Object> htParams, boolean isAppend)

• createAtomSeCollectionFromStrings

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

• createAtomSeCollectionFromArrayData

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

• newDataReader

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

• newFilesReader

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

• createAtomSetCollectionFromReader

  Object createAtomSetCollectionFromReader(String fullPathName, String name, Object reader, Map<String,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

  BufferedInputStream getBufferedInputStream(String fullPathName)

• getBufferedInputStreamOrErrorMessageFromName

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

• getBufferedReaderForResource

  public static BufferedReader getBufferedReaderForResource(Viewer vwr, Object resourceClass, String classPath, String resourceName) throws IOException

  Throws:

  IOException

• urlEncode

  private String urlEncode(String name)

• getFullPathNameOrError

  Object getFullPathNameOrError(String filename, boolean getStream, 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 Object getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary, boolean doSpecialLoad)

• getUnzippedReaderOrStreamFromName

  public Object getUnzippedReaderOrStreamFromName(String name, Object bytesOrStream, boolean allowZipStream, boolean forceInputStream, boolean isTypeCheckOnly, boolean doSpecialLoad, Map<String,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 String[] getZipDirectory(String fileName, boolean addManifest, boolean allowCached)

  Parameters:

  fileName -

  addManifest -

  allowCached -

  Returns:

  [] if not a zip file;

• getFileAsBytes

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

• getFileAsMap

  public Object getFileAsMap(String name, String type, boolean asBytes)

  create a PNG or ZIP file and return it as a map or, optionally, as a byte[]

  Parameters:

  name -

  type -

  asBytes - true to return byte[] instead of a map

  Returns:

  Map or byte[]

• getFileDataAsString

  public boolean getFileDataAsString(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(String f)

• loadImage

  public boolean loadImage(Object nameOrBytes, String echoName, boolean forceSync)

  Load an image

  Parameters:

  nameOrBytes -

  echoName -

  forceSync - TODO

  Returns:

  true if asynchronous

• getImage

  public Object getImage(Object nameOrBytes, String echoName, boolean forceSync)

• getClassifiedName

  private String[] getClassifiedName(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 String addDirectory(String defaultDirectory, String name)

• getDefaultDirectory

  String getDefaultDirectory(String name)

• fixPath

  private static String fixPath(String path)

• getFilePath

  public String getFilePath(String name, boolean addUrlPrefix, boolean asShortName)

• getLocalDirectory

  public static GenericFileInterface getLocalDirectory(Viewer vwr, boolean forDialog)

• setLocalPath

  public static void setLocalPath(Viewer vwr, 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 String getLocalPathForWritingFile(Viewer vwr, String file)

• fixDOSName

  public static String fixDOSName(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 String stripPath(String name)

• isScriptType

  public static boolean isScriptType(String fname)

• determineSurfaceFileType

  public static String determineSurfaceFileType(BufferedReader bufferedReader)

  Try to determine a surface file type based on its header. Also identifies Menu files.

  Parameters:

  bufferedReader -

  Returns:

  file type

• getManifestScriptPath

  public static String getManifestScriptPath(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

• getFileReferences

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

• setScriptFileReferences

  public static String setScriptFileReferences(String script, String localPath, String remotePath, String scriptPath)

• setScriptFileRefs

  private static String setScriptFileRefs(String script, 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(String key, Object data)

• cacheGet

  public Object cacheGet(String key, boolean bytesOnly)

• cacheClear

  void cacheClear()

• cacheFileByNameAdd

  public int cacheFileByNameAdd(String fileName, boolean isAdd)

• cacheList

  public Map<String,Integer> cacheList()

• getCanonicalName

  public String getCanonicalName(String pathName)

• recachePngjBytes

  public void recachePngjBytes(String fileName, byte[] bytes)

• getPngjOrDroppedBytes

  private byte[] getPngjOrDroppedBytes(String fullName, String name)

• getCachedPngjBytes

  private byte[] getCachedPngjBytes(String pathName)

• postByteArray

  public String postByteArray(String fileName, byte[] bytes)

  Specified by:

  postByteArray in interface javajs.api.BytePoster

• isJmolType

  public static boolean isJmolType(String type)

  Check to see if this is a Jmol WRITE file type that might be or have attached a ZIP collection .

  Parameters:

  type - the

  Returns:

  true if PNG, PNGJ, JMOL, ZIP, or ZIPALL

• isEmbeddable

  public static boolean isEmbeddable(String type)

  Check to see if it is possible that this file has been embedded by Jmol using JC.EMBEDDED_SCRIPT_TAG. This includes all Jmol types, JPEG images, and export types POV, POVRAY, and IDTF

  Parameters:

  type - raw extension or file name

  Returns:

  true if this file might contain an embedded script

• getEmbeddedFileState

  public String getEmbeddedFileState(String fileName, boolean allowCached, String sptName)

  Get the specified SPT file of a Jmol zip collection or the embedded script for any other file that is embeddable.

  Parameters:

  fileName -

  allowCached -

  sptName - state.spt, movie.spt, or null

  Returns:

  embedded state.spt, movie.spt, or a script embedded using JC.EMBEDDED_SCRIPT_TAG, or "" if not found.

• stripTypePrefix

  public static String stripTypePrefix(String fileName)

  Stip PDB::file://... from a file name

  Parameters:

  fileName -

  Returns:

  stripped name

• getEmbeddedScript

  public static String getEmbeddedScript(String s)

  Extract a Jmol script embedded using JC.EMBEDDED_SCRIPT_TAG.

  Parameters:

  s -

  Returns:

  the embedded script or null

• isZipStream

  public boolean isZipStream(Object br)