org.jmol.io2

Class ZipUtil

java.lang.Object

org.jmol.io2.ZipUtil

All Implemented Interfaces:

JmolZipUtility

public class ZipUtil
extends Object
implements JmolZipUtility

Constructor Summary

Constructors

Constructor and Description
ZipUtil()

Method Summary

Modifier and Type	Method and Description
void	addZipEntry(Object zos, String fileName)
boolean	cachePngjFile(FileManager fm, String[] data)
String	cacheZipContents(BufferedInputStream bis, String fileName, Map<String,byte[]> cache) caches an entire pngj file's contents into a Map
private static javajs.util.SB	checkSpecialData(InputStream is, 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 String[]	checkSpecialInZip(String[] zipDirectory) called by SmarterJmolAdapter to see if we can automatically assign a file from the zip file.
void	closeZipEntry(Object zos)
void	getAllZipData(InputStream is, String[] subfileList, String name0, String binaryFileList, Map<String,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(InputStream is, String[] subfileList, String name0, String binaryFileList, Map<String,String> fileData)
Object	getAtomSetCollectionOrBufferedReaderFromZip(JmolAdapter adapter, InputStream is, String fileName, String[] zipDirectory, Map<String,Object> htParams, int subFilePtr, boolean asBufferedReader)
private static String	getBinaryStringForBytes(byte[] bytes)
byte[]	getCachedPngjBytes(FileManager fm, String pathName)
int	getCrcValue(byte[] bytes)
private static String[]	getSpartanDirs(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 String[]	getSpartanFileList(String name, String[] dirNums) returns the list of files to read for every Spartan spardir.
(package private) static String	getStreamAsString(InputStream is)
(package private) static BufferedInputStream	getUnGzippedInputStream(byte[] bytes)
String[]	getZipDirectoryAndClose(BufferedInputStream bis, boolean addManifest)
String	getZipDirectoryAsStringAndClose(BufferedInputStream bis)
private String[]	getZipDirectoryOrErrorAndClose(BufferedInputStream bis, boolean addManifest)
Object	getZipFileContents(BufferedInputStream bis, String[] list, int listPtr, boolean asBufferedInputStream) iteratively drills into zip files of zip files to extract file content or zip file directory.
byte[]	getZipFileContentsAsBytes(BufferedInputStream bis, String[] list, int listPtr)
Object	getZipOutputStream(Object bos)
private static boolean	isJmolManifest(String thisEntry)
InputStream	newGZIPInputStream(InputStream is)
javajs.api.ZInputStream	newZipInputStream(InputStream is)
private static javajs.api.ZInputStream	newZIS(InputStream is)
private static String	shortSceneFilename(String pathName)
String[]	spartanFileList(String name, String type) Special loading for file directories.

Methods inherited from class java.lang.Object

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

Constructor Detail

ZipUtil

public ZipUtil()

Method Detail

newZipInputStream

public javajs.api.ZInputStream newZipInputStream(InputStream is)

Specified by:

newZipInputStream in interface JmolZipUtility

newZIS

private static javajs.api.ZInputStream newZIS(InputStream is)

getAllZipData

public void getAllZipData(InputStream is,
                          String[] subfileList,
                          String name0,
                          String binaryFileList,
                          Map<String,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(InputStream is,
                                        String[] subfileList,
                                        String name0,
                                        String binaryFileList,
                                        Map<String,String> fileData)

getBinaryStringForBytes

private static String getBinaryStringForBytes(byte[] bytes)

getZipFileContents

public Object getZipFileContents(BufferedInputStream bis,
                                 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(BufferedInputStream bis,
                                        String[] list,
                                        int listPtr)

Specified by:

getZipFileContentsAsBytes in interface JmolZipUtility

getZipDirectoryAsStringAndClose

public String getZipDirectoryAsStringAndClose(BufferedInputStream bis)

Specified by:

getZipDirectoryAsStringAndClose in interface JmolZipUtility

getZipDirectoryAndClose

public String[] getZipDirectoryAndClose(BufferedInputStream bis,
                                        boolean addManifest)

Specified by:

getZipDirectoryAndClose in interface JmolZipUtility

getZipDirectoryOrErrorAndClose

private String[] getZipDirectoryOrErrorAndClose(BufferedInputStream bis,
                                                boolean addManifest)
                                         throws IOException

Throws:

IOException

getStreamAsString

static String getStreamAsString(InputStream is)
                         throws IOException

Throws:

IOException

isJmolManifest

private static boolean isJmolManifest(String thisEntry)

cacheZipContents

public String cacheZipContents(BufferedInputStream bis,
                               String fileName,
                               Map<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

getUnGzippedInputStream

static BufferedInputStream getUnGzippedInputStream(byte[] bytes)

newGZIPInputStream

public InputStream newGZIPInputStream(InputStream is)
                               throws IOException

Specified by:

newGZIPInputStream in interface JmolZipUtility

Throws:

IOException

getAtomSetCollectionOrBufferedReaderFromZip

public Object getAtomSetCollectionOrBufferedReaderFromZip(JmolAdapter adapter,
                                                          InputStream is,
                                                          String fileName,
                                                          String[] zipDirectory,
                                                          Map<String,Object> htParams,
                                                          int subFilePtr,
                                                          boolean asBufferedReader)

Specified by:

getAtomSetCollectionOrBufferedReaderFromZip in interface JmolZipUtility

checkSpecialData

private static javajs.util.SB checkSpecialData(InputStream is,
                                               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 String[] spartanFileList(String name,
                                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 String[] getSpartanDirs(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 String[] getSpartanFileList(String name,
                                           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 String[] checkSpecialInZip(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,
                                 String pathName)

Specified by:

getCachedPngjBytes in interface JmolZipUtility

cachePngjFile

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

Specified by:

cachePngjFile in interface JmolZipUtility

shortSceneFilename

private static String shortSceneFilename(String pathName)

addZipEntry

public void addZipEntry(Object zos,
                        String fileName)
                 throws IOException

Specified by:

addZipEntry in interface JmolZipUtility

Throws:

IOException

closeZipEntry

public void closeZipEntry(Object zos)
                   throws IOException

Specified by:

closeZipEntry in interface JmolZipUtility

Throws:

IOException

getZipOutputStream

public Object getZipOutputStream(Object bos)

Specified by:

getZipOutputStream in interface JmolZipUtility

getCrcValue

public int getCrcValue(byte[] bytes)

Specified by:

getCrcValue in interface JmolZipUtility