org.jmol.io2

Class ZipUtil

java.lang.Object

org.jmol.io2.ZipUtil

All Implemented Interfaces:

JmolZipUtility

public class ZipUtil
extends java.lang.Object
implements JmolZipUtility

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	SCENE_TAG

Constructor Summary

Constructors

Constructor and Description
ZipUtil()

Method Summary

Methods

Modifier and Type	Method and Description
private java.lang.String	addPngFileBytes(java.lang.String name, byte[] ret, int iFile, java.util.Hashtable<java.lang.Object,java.lang.String> crcMap, boolean isSparDir, java.lang.String newName, int ptSlash, JmolList<java.lang.Object> v)
boolean	cachePngjFile(FileManager fm, java.lang.String[] data)
java.lang.String	cacheZipContents(java.io.BufferedInputStream bis, java.lang.String fileName, java.util.Map<java.lang.String,byte[]> cache) caches an entire pngj file's contents into a Map
private static SB	checkSpecialData(java.io.InputStream is, java.lang.String[] zipDirectory) called by SmarterJmolAdapter to see if we have a Spartan directory and, if so, open it and get all the data into the correct order.
(package private) static java.lang.String[]	checkSpecialInZip(java.lang.String[] zipDirectory) called by SmarterJmolAdapter to see if we can automatically assign a file from the zip file.
java.lang.Object	createZipSet(FileManager fm, Viewer viewer, java.lang.String fileName, java.lang.String script, java.lang.String[] scripts, boolean includeRemoteFiles)
void	getAllZipData(java.io.InputStream is, java.lang.String[] subfileList, java.lang.String name0, java.lang.String binaryFileList, java.util.Map<java.lang.String,java.lang.String> fileData) reads a ZIP file and saves all data in a Hashtable so that the files may be organized later in a different order.
private static void	getAllZipDataStatic(java.io.InputStream is, java.lang.String[] subfileList, java.lang.String name0, java.lang.String binaryFileList, java.util.Map<java.lang.String,java.lang.String> fileData)
java.lang.Object	getAtomSetCollectionOrBufferedReaderFromZip(JmolAdapter adapter, java.io.InputStream is, java.lang.String fileName, java.lang.String[] zipDirectory, java.util.Map<java.lang.String,java.lang.Object> htParams, int subFilePtr, boolean asBufferedReader, boolean asBufferedInputStream)
private static java.lang.String	getBinaryStringForBytes(byte[] bytes)
byte[]	getCachedPngjBytes(FileManager fm, java.lang.String pathName)
java.lang.String	getGzippedBytesAsString(byte[] bytes)
java.io.InputStream	getGzippedInputStream(byte[] bytes)
java.lang.String	getSceneScript(java.lang.String[] scenes, java.util.Map<java.lang.String,java.lang.String> htScenes, JmolList<java.lang.Integer> list)
private static java.lang.String[]	getSpartanDirs(java.lang.String outputFileData) read the output file from the Spartan directory and decide from that what files need to be read and in what order - usually M0001 or a set of Profiles.
private static java.lang.String[]	getSpartanFileList(java.lang.String name, java.lang.String[] dirNums) returns the list of files to read for every Spartan spardir.
java.lang.String[]	getZipDirectoryAndClose(java.io.BufferedInputStream bis, boolean addManifest)
java.lang.String	getZipDirectoryAsStringAndClose(java.io.BufferedInputStream bis)
private java.lang.String[]	getZipDirectoryOrErrorAndClose(java.io.BufferedInputStream bis, boolean addManifest)
private static java.lang.String	getZipEntryAsString(java.io.InputStream is)
java.lang.Object	getZipFileContents(java.io.BufferedInputStream bis, java.lang.String[] list, int listPtr, boolean asBufferedInputStream) iteratively drills into zip files of zip files to extract file content or zip file directory.
byte[]	getZipFileContentsAsBytes(java.io.BufferedInputStream bis, java.lang.String[] list, int listPtr)
private static boolean	isJmolManifest(java.lang.String thisEntry)
java.io.InputStream	newGZIPInputStream(java.io.BufferedInputStream bis)
ZInputStream	newZipInputStream(java.io.InputStream is)
private static ZInputStream	newZIS(java.io.InputStream is)
private static java.lang.String	shortSceneFilename(java.lang.String pathName)
java.lang.String[]	spartanFileList(java.lang.String name, java.lang.String type) Special loading for file directories.
(package private) static java.lang.String	staticGetGzippedBytesAsString(byte[] bytes)
private static java.lang.String	wrapPathForAllFiles(java.lang.String cmd, java.lang.String strCatch)
java.lang.Object	writeZipFile(FileManager fm, Viewer viewer, java.lang.String outFileName, JmolList<java.lang.Object> fileNamesAndByteArrays, java.lang.String msg)

Methods inherited from class java.lang.Object

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

Field Detail

SCENE_TAG

private static final java.lang.String SCENE_TAG

See Also:

Constant Field Values

Constructor Detail

ZipUtil

public ZipUtil()

Method Detail

newZipInputStream

public ZInputStream newZipInputStream(java.io.InputStream is)

Specified by:

newZipInputStream in interface JmolZipUtility

newZIS

private static ZInputStream newZIS(java.io.InputStream is)

getAllZipData

public void getAllZipData(java.io.InputStream is,
                 java.lang.String[] subfileList,
                 java.lang.String name0,
                 java.lang.String binaryFileList,
                 java.util.Map<java.lang.String,java.lang.String> fileData)

reads a ZIP file and saves all data in a Hashtable so that the files may be organized later in a different order. Also adds a #Directory_Listing entry. Files are bracketed by BEGIN Directory Entry and END Directory Entry lines, similar to CompoundDocument.getAllData.

Specified by:

getAllZipData in interface JmolZipUtility

Parameters:

is -

subfileList -

name0 - prefix for entry listing

binaryFileList - |-separated list of files that should be saved as xx xx xx hex byte strings. The directory listing is appended with ":asBinaryString"

fileData -

getAllZipDataStatic

private static void getAllZipDataStatic(java.io.InputStream is,
                       java.lang.String[] subfileList,
                       java.lang.String name0,
                       java.lang.String binaryFileList,
                       java.util.Map<java.lang.String,java.lang.String> fileData)

getBinaryStringForBytes

private static java.lang.String getBinaryStringForBytes(byte[] bytes)

getZipFileContents

public java.lang.Object getZipFileContents(java.io.BufferedInputStream bis,
                                  java.lang.String[] list,
                                  int listPtr,
                                  boolean asBufferedInputStream)

iteratively drills into zip files of zip files to extract file content or zip file directory. Also works with JAR files. Does not return "__MACOS" paths

Specified by:

getZipFileContents in interface JmolZipUtility

Parameters:

bis -

list -

listPtr -

asBufferedInputStream - for Pmesh

Returns:

directory listing or subfile contents

getZipFileContentsAsBytes

public byte[] getZipFileContentsAsBytes(java.io.BufferedInputStream bis,
                               java.lang.String[] list,
                               int listPtr)

Specified by:

getZipFileContentsAsBytes in interface JmolZipUtility

getZipDirectoryAsStringAndClose

public java.lang.String getZipDirectoryAsStringAndClose(java.io.BufferedInputStream bis)

Specified by:

getZipDirectoryAsStringAndClose in interface JmolZipUtility

getZipDirectoryAndClose

public java.lang.String[] getZipDirectoryAndClose(java.io.BufferedInputStream bis,
                                         boolean addManifest)

Specified by:

getZipDirectoryAndClose in interface JmolZipUtility

getZipDirectoryOrErrorAndClose

private java.lang.String[] getZipDirectoryOrErrorAndClose(java.io.BufferedInputStream bis,
                                                boolean addManifest)
                                                   throws java.io.IOException

Throws:

java.io.IOException

getZipEntryAsString

private static java.lang.String getZipEntryAsString(java.io.InputStream is)
                                             throws java.io.IOException

Throws:

java.io.IOException

isJmolManifest

private static boolean isJmolManifest(java.lang.String thisEntry)

cacheZipContents

public java.lang.String cacheZipContents(java.io.BufferedInputStream bis,
                                java.lang.String fileName,
                                java.util.Map<java.lang.String,byte[]> cache)

caches an entire pngj file's contents into a Map

Specified by:

cacheZipContents in interface JmolZipUtility

Parameters:

bis -

fileName -

cache -

Returns:

file listing, separated by \n

getGzippedBytesAsString

public java.lang.String getGzippedBytesAsString(byte[] bytes)

Specified by:

getGzippedBytesAsString in interface JmolZipUtility

staticGetGzippedBytesAsString

static java.lang.String staticGetGzippedBytesAsString(byte[] bytes)

getGzippedInputStream

public java.io.InputStream getGzippedInputStream(byte[] bytes)

newGZIPInputStream

public java.io.InputStream newGZIPInputStream(java.io.BufferedInputStream bis)
                                       throws java.io.IOException

Specified by:

newGZIPInputStream in interface JmolZipUtility

Throws:

java.io.IOException

addPngFileBytes

private java.lang.String addPngFileBytes(java.lang.String name,
                               byte[] ret,
                               int iFile,
                               java.util.Hashtable<java.lang.Object,java.lang.String> crcMap,
                               boolean isSparDir,
                               java.lang.String newName,
                               int ptSlash,
                               JmolList<java.lang.Object> v)

writeZipFile

public java.lang.Object writeZipFile(FileManager fm,
                            Viewer viewer,
                            java.lang.String outFileName,
                            JmolList<java.lang.Object> fileNamesAndByteArrays,
                            java.lang.String msg)

Specified by:

writeZipFile in interface JmolZipUtility

getSceneScript

public java.lang.String getSceneScript(java.lang.String[] scenes,
                              java.util.Map<java.lang.String,java.lang.String> htScenes,
                              JmolList<java.lang.Integer> list)

Specified by:

getSceneScript in interface JmolZipUtility

wrapPathForAllFiles

private static java.lang.String wrapPathForAllFiles(java.lang.String cmd,
                                   java.lang.String strCatch)

createZipSet

public java.lang.Object createZipSet(FileManager fm,
                            Viewer viewer,
                            java.lang.String fileName,
                            java.lang.String script,
                            java.lang.String[] scripts,
                            boolean includeRemoteFiles)

Specified by:

createZipSet in interface JmolZipUtility

getAtomSetCollectionOrBufferedReaderFromZip

public java.lang.Object getAtomSetCollectionOrBufferedReaderFromZip(JmolAdapter adapter,
                                                           java.io.InputStream is,
                                                           java.lang.String fileName,
                                                           java.lang.String[] zipDirectory,
                                                           java.util.Map<java.lang.String,java.lang.Object> htParams,
                                                           int subFilePtr,
                                                           boolean asBufferedReader,
                                                           boolean asBufferedInputStream)

Specified by:

getAtomSetCollectionOrBufferedReaderFromZip in interface JmolZipUtility

checkSpecialData

private static SB checkSpecialData(java.io.InputStream is,
                  java.lang.String[] zipDirectory)

called by SmarterJmolAdapter to see if we have a Spartan directory and, if so, open it and get all the data into the correct order.

Parameters:

is -

zipDirectory -

Returns:

String data for processing

spartanFileList

public java.lang.String[] spartanFileList(java.lang.String name,
                                 java.lang.String type)

Special loading for file directories. This method is called from the FileManager via SmarterJmolAdapter. It's here because Resolver is the place where all distinctions are made. In the case of spt files, no need to load them; here we are just checking for type. In the case of .spardir directories, we need to provide a list of the critical files that need loading and concatenation for the SpartanSmolReader. we return an array for which: [0] file type (class prefix) or null for SPT file [1] header to add for each BEGIN/END block (ignored) [2...] files to load and concatenate

Specified by:

spartanFileList in interface JmolZipUtility

Parameters:

name -

type -

Returns:

array detailing action for this set of files

getSpartanDirs

private static java.lang.String[] getSpartanDirs(java.lang.String outputFileData)

read the output file from the Spartan directory and decide from that what files need to be read and in what order - usually M0001 or a set of Profiles. But Spartan saves the Profiles in alphabetical order, not numerical. So we fix that here.

Parameters:

outputFileData -

Returns:

String[] list of files to read

getSpartanFileList

private static java.lang.String[] getSpartanFileList(java.lang.String name,
                                    java.lang.String[] dirNums)

returns the list of files to read for every Spartan spardir. Simple numbers are assumed to be Profiles; others are models.

Parameters:

name -

dirNums -

Returns:

String[] list of files to read given a list of directory names

checkSpecialInZip

static java.lang.String[] checkSpecialInZip(java.lang.String[] zipDirectory)

called by SmarterJmolAdapter to see if we can automatically assign a file from the zip file. If so, return a subfile list for this file. The first element of the list is left empty -- it would be the zipfile name. Assignment can be made if (1) there is only one file in the collection or (2) if the first file is xxxx.spardir/ Note that __MACOS? files are ignored by the ZIP file reader.

Parameters:

zipDirectory -

Returns:

subFileList

getCachedPngjBytes

public byte[] getCachedPngjBytes(FileManager fm,
                        java.lang.String pathName)

Specified by:

getCachedPngjBytes in interface JmolZipUtility

cachePngjFile

public boolean cachePngjFile(FileManager fm,
                    java.lang.String[] data)

Specified by:

cachePngjFile in interface JmolZipUtility

shortSceneFilename

private static java.lang.String shortSceneFilename(java.lang.String pathName)