X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Fjavajs%2Futil%2FZipTools.java;fp=srcjar%2Fjavajs%2Futil%2FZipTools.java;h=0000000000000000000000000000000000000000;hb=5152dafd5d71c877156621def8463d437c9c5453;hp=5c6e4ec6195ffaeb12bf5907c8d49b95f898b7c9;hpb=c4cf7aa546ede43930f9a17fec5060119984da41;p=jalview.git

diff --git a/srcjar/javajs/util/ZipTools.java b/srcjar/javajs/util/ZipTools.java
deleted file mode 100644
index 5c6e4ec..0000000
--- a/srcjar/javajs/util/ZipTools.java
+++ /dev/null
@@ -1,462 +0,0 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- *
- * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
- * for use in SwingJS via transpilation into JavaScript using Java2Script.
- *
- * Copyright (C) 2006  The Jmol Development Team
- *
- * Contact: jmol-developers@lists.sf.net
- *
- *  This library is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public
- *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License, or (at your option) any later version.
- *
- *  This library is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
- *  02110-1301, USA.
- */
-
-package javajs.util;
-
-import java.io.BufferedInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.util.Map;
-import java.util.zip.CRC32;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-import java.util.zip.ZipOutputStream;
-
-import javajs.api.GenericZipInputStream;
-import javajs.api.GenericZipTools;
-import javajs.api.Interface;
-import javajs.api.ZInputStream;
-
-import org.apache.tools.bzip2.CBZip2InputStreamFactory;
-
-
-/**
- * Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
- * 
- */
-public class ZipTools implements GenericZipTools {
-
-  public ZipTools() {
-    // for reflection
-  }
-  
-  @Override
-  public ZInputStream newZipInputStream(InputStream is) {
-    return newZIS(is);
-  }
-
-  @SuppressWarnings("resource")
-  private static ZInputStream newZIS(InputStream is) {
-    return (is instanceof ZInputStream ? (ZInputStream) is
-        : is instanceof BufferedInputStream ? new GenericZipInputStream(is)
-            : new GenericZipInputStream(new BufferedInputStream(is)));
-  }
-
-  /**
-   * 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.
-   * 
-   * @param is
-   * @param subfileList
-   * @param name0
-   *        prefix for entry listing
-   * @param binaryFileList
-   *        |-separated list of files that should be saved as xx xx xx hex byte
-   *        strings. The directory listing is appended with ":asBinaryString"
-   * @param fileData
-   */
-  @Override
-  public void getAllZipData(InputStream is, String[] subfileList,
-                                          String name0, String binaryFileList, String exclude,
-                                          Map<String, String> fileData) {
-    ZipInputStream zis = (ZipInputStream) newZIS(is);
-    ZipEntry ze;
-    SB listing = new SB();
-    binaryFileList = "|" + binaryFileList + "|";
-    String prefix = PT.join(subfileList, '/', 1);
-    String prefixd = null;
-    if (prefix != null) {
-      prefixd = prefix.substring(0, prefix.indexOf("/") + 1);
-      if (prefixd.length() == 0)
-        prefixd = null;
-    }
-    try {
-      while ((ze = zis.getNextEntry()) != null) {
-        String name = ze.getName();
-        if (prefix != null && prefixd != null
-            && !(name.equals(prefix) || name.startsWith(prefixd))
-            || exclude != null && name.contains(exclude))
-          continue;
-        //System.out.println("ziputil: " + name);
-        listing.append(name).appendC('\n');
-        String sname = "|" + name.substring(name.lastIndexOf("/") + 1) + "|";
-        boolean asBinaryString = (binaryFileList.indexOf(sname) >= 0);
-        byte[] bytes = Rdr.getLimitedStreamBytes(zis, ze.getSize());
-        String str;
-        if (asBinaryString) {
-          str = getBinaryStringForBytes(bytes);
-          name += ":asBinaryString";
-        } else {
-          str = Rdr.fixUTF(bytes);
-        }
-        str = "BEGIN Directory Entry " + name + "\n" + str
-            + "\nEND Directory Entry " + name + "\n";
-        String key = name0 + "|" + name;
-        fileData.put(key, str);
-      }
-    } catch (Exception e) {
-    }
-    fileData.put("#Directory_Listing", listing.toString());
-  }
-
-  private String getBinaryStringForBytes(byte[] bytes) {
-    SB ret = new SB();
-    for (int i = 0; i < bytes.length; i++)
-      ret.append(Integer.toHexString(bytes[i] & 0xFF)).appendC(' ');
-    return ret.toString();
-  }
-
-  /**
-   * 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
-   * 
-   * @param bis
-   * @param list
-   * @param listPtr
-   * @param asBufferedInputStream
-   *        for Pmesh
-   * @return directory listing or subfile contents
-   */
-  @Override
-  public Object getZipFileDirectory(BufferedInputStream bis, String[] list,
-                                    int listPtr, boolean asBufferedInputStream) {
-    SB ret;
-    if (list == null || listPtr >= list.length)
-      return getZipDirectoryAsStringAndClose(bis);
-    bis = Rdr.getPngZipStream(bis, true);
-    String fileName = list[listPtr];
-    ZipInputStream zis = new ZipInputStream(bis);
-    ZipEntry ze;
-    //System.out.println("fname=" + fileName);
-    try {
-      boolean isAll = (fileName.equals("."));
-      if (isAll || fileName.lastIndexOf("/") == fileName.length() - 1) {
-        ret = new SB();
-        while ((ze = zis.getNextEntry()) != null) {
-          String name = ze.getName();
-          if (isAll || name.startsWith(fileName))
-            ret.append(name).appendC('\n');
-        }
-        String str = ret.toString();
-        return (asBufferedInputStream ? Rdr.getBIS(str.getBytes()) : str);
-      }
-      int pt = fileName.indexOf(":asBinaryString");
-      boolean asBinaryString = (pt > 0);
-      if (asBinaryString)
-        fileName = fileName.substring(0, pt);
-      fileName = fileName.replace('\\', '/');
-      while ((ze = zis.getNextEntry()) != null
-          && !fileName.equals(ze.getName())) {
-      }
-      byte[] bytes = (ze == null ? null : Rdr.getLimitedStreamBytes(zis,
-          ze.getSize()));
-      ze = null;
-      zis.close();
-      if (bytes == null)
-        return "";
-      if (Rdr.isZipB(bytes) || Rdr.isPngZipB(bytes))
-        return getZipFileDirectory(Rdr.getBIS(bytes), list, ++listPtr,
-            asBufferedInputStream);
-      if (asBufferedInputStream)
-        return Rdr.getBIS(bytes);
-      if (asBinaryString) {
-        ret = new SB();
-        for (int i = 0; i < bytes.length; i++)
-          ret.append(Integer.toHexString(bytes[i] & 0xFF)).appendC(' ');
-        return ret.toString();
-      }
-      if (Rdr.isGzipB(bytes))
-        bytes = Rdr.getLimitedStreamBytes(getUnGzippedInputStream(bytes), -1);
-      return Rdr.fixUTF(bytes);
-    } catch (Exception e) {
-      return "";
-    }
-  }
-
-  @Override
-  public byte[] getZipFileContentsAsBytes(BufferedInputStream bis,
-                                          String[] list, int listPtr) {
-    byte[] ret = new byte[0];
-    String fileName = list[listPtr];
-    if (fileName.lastIndexOf("/") == fileName.length() - 1)
-      return ret;
-    try {
-      bis = Rdr.getPngZipStream(bis, true);
-      ZipInputStream zis = new ZipInputStream(bis);
-      ZipEntry ze;
-      while ((ze = zis.getNextEntry()) != null) {
-        if (!fileName.equals(ze.getName()))
-          continue;
-        byte[] bytes = Rdr.getLimitedStreamBytes(zis, ze.getSize());
-        return ((Rdr.isZipB(bytes) || Rdr.isPngZipB(bytes)) && ++listPtr < list.length ? getZipFileContentsAsBytes(
-            Rdr.getBIS(bytes), list, listPtr) : bytes);
-      }
-    } catch (Exception e) {
-    }
-    return ret;
-  }
-  
-  @Override
-  public String getZipDirectoryAsStringAndClose(BufferedInputStream bis) {
-    SB sb = new SB();
-    String[] s = new String[0];
-    try {
-      s = getZipDirectoryOrErrorAndClose(bis, null);
-      bis.close();
-    } catch (Exception e) {
-      System.out.println(e.toString());
-    }
-    for (int i = 0; i < s.length; i++)
-      sb.append(s[i]).appendC('\n');
-    return sb.toString();
-  }
-
-  @Override
-  public String[] getZipDirectoryAndClose(BufferedInputStream bis,
-                                                 String manifestID) {
-    String[] s = new String[0];
-    try {
-      s = getZipDirectoryOrErrorAndClose(bis, manifestID);
-      bis.close();
-    } catch (Exception e) {
-      System.out.println(e.toString());
-    }
-    return s;
-  }
-
-  private String[] getZipDirectoryOrErrorAndClose(BufferedInputStream bis,
-                                                  String manifestID)
-      throws IOException {
-    bis = Rdr.getPngZipStream(bis, true);
-    Lst<String> v = new Lst<String>();
-    ZipInputStream zis = new ZipInputStream(bis);
-    ZipEntry ze;
-    String manifest = null;
-    while ((ze = zis.getNextEntry()) != null) {
-      String fileName = ze.getName();
-      if (manifestID != null && fileName.startsWith(manifestID))
-        manifest = getStreamAsString(zis);
-      else if (!fileName.startsWith("__MACOS")) // resource fork not nec.
-        v.addLast(fileName);
-    }
-    zis.close();
-    if (manifestID != null)
-      v.add(0, manifest == null ? "" : manifest + "\n############\n");
-    return v.toArray(new String[v.size()]);
-  }
-
-  public static String getStreamAsString(InputStream is) throws IOException {
-    return Rdr.fixUTF(Rdr.getLimitedStreamBytes(is, -1));
-  }
-
-  @Override
-  public InputStream newGZIPInputStream(InputStream is) throws IOException {
-    return new BufferedInputStream(new GZIPInputStream(is, 512));
-  }
-
-  @Override
-  public InputStream newBZip2InputStream(InputStream is) throws IOException {
-    return new BufferedInputStream(((CBZip2InputStreamFactory) Interface.getInterface("org.apache.tools.bzip2.CBZip2InputStreamFactory")).getStream(is));
-  }
-
-  @Override
-  public BufferedInputStream getUnGzippedInputStream(byte[] bytes) {
-    try {
-      return Rdr.getUnzippedInputStream(this, Rdr.getBIS(bytes));
-    } catch (Exception e) {
-      return null;
-    }
-  }
-
-  @Override
-  public void addZipEntry(Object zos, String fileName) throws IOException {
-    ((ZipOutputStream) zos).putNextEntry(new ZipEntry(fileName));
-  }
-
-  @Override
-  public void closeZipEntry(Object zos) throws IOException {
-    ((ZipOutputStream) zos).closeEntry();
-  }
-
-  @Override
-  public Object getZipOutputStream(Object bos) {
-//    /**
-//     * xxxxj2sNative
-//     * 
-//     *            return javajs.api.Interface.getInterface(
-//     *            "java.util.zip.ZipOutputStream").setZOS(bos);
-//     * 
-//     */
-//    {
-      return new ZipOutputStream((OutputStream) bos);
-//    }
-  }
-
-  @Override
-  public int getCrcValue(byte[] bytes) {
-    CRC32 crc = new CRC32();
-    crc.update(bytes, 0, bytes.length);
-    return (int) crc.getValue();
-  }
-
-  @Override
-  public void readFileAsMap(BufferedInputStream bis, Map<String, Object> bdata, String name) {
-  	readFileAsMapStatic(bis, bdata, name);
-  }
-
-  public static void readFileAsMapStatic(BufferedInputStream bis,
-			Map<String, Object> bdata, String name) {
-    int pt = (name == null ? -1 : name.indexOf("|"));
-    name = (pt >= 0 ? name.substring(pt + 1) : null);
-    try {
-      if (Rdr.isPngZipStream(bis)) {
-        boolean isImage = "_IMAGE_".equals(name);
-        if (name == null || isImage)
-          bdata.put((isImage ? "_DATA_" : "_IMAGE_"), new BArray(getPngImageBytes(bis)));
-        if (!isImage)
-          cacheZipContentsStatic(bis, name, bdata, true);
-      } else if (Rdr.isZipS(bis)) {
-        cacheZipContentsStatic(bis, name, bdata, true);
-      } else if (name == null){
-        bdata.put("_DATA_", new BArray(Rdr.getLimitedStreamBytes(bis, -1)));
-      } else {
-        throw new IOException("ZIP file " + name + " not found");
-      }
-      bdata.put("$_BINARY_$", Boolean.TRUE);
-    } catch (IOException e) {
-      bdata.clear();
-      bdata.put("_ERROR_", e.getMessage());
-    }
-  }
-
-  @Override
-  public String cacheZipContents(BufferedInputStream bis,
-                                        String fileName,
-                                        Map<String, Object> cache, 
-                                        boolean asByteArray) {
-		return cacheZipContentsStatic(bis, fileName, cache, asByteArray);
-  }
-
-	/**
-	 * 
-	 * @param bis
-	 * @param fileName may end with "/" for a prefix or contain "|xxxx.xxx" for a specific file or be null
-	 * @param cache
-	 * @param asByteArray
-	 * @return
-	 */
-  public static String cacheZipContentsStatic(BufferedInputStream bis,
-			String fileName, Map<String, Object> cache, boolean asByteArray) {
-    ZipInputStream zis = (ZipInputStream) newZIS(bis);
-    ZipEntry ze;
-    SB listing = new SB();
-    long n = 0;
-    boolean isPath = (fileName != null && fileName.endsWith("/"));
-    boolean oneFile = (asByteArray && !isPath && fileName != null);
-    int pt = (oneFile ? fileName.indexOf("|") : -1);
-    String file0 = (pt >= 0 ? fileName : null);
-    if (pt >= 0)
-      fileName = fileName.substring(0,  pt);
-    String prefix = (fileName == null ? "" : isPath ? fileName : fileName + "|");
-    try {
-      while ((ze = zis.getNextEntry()) != null) {
-        String name = ze.getName();
-        if (fileName != null) {
-          if (oneFile) {
-            if (!name.equalsIgnoreCase(fileName))
-              continue;
-          } else {
-            listing.append(name).appendC('\n');
-          }
-        }
-        long nBytes = ze.getSize();
-        byte[] bytes = Rdr.getLimitedStreamBytes(zis, nBytes);
-        if (file0 != null) {
-          readFileAsMapStatic(Rdr.getBIS(bytes), cache, file0);
-          return null;
-        }
-        n += bytes.length;
-        Object o = (asByteArray ? new BArray(bytes) : bytes);        
-        cache.put((oneFile ? "_DATA_" : prefix + name), o);
-        if (oneFile)
-          break;
-      }
-      zis.close();
-    } catch (Exception e) {
-      try {
-        zis.close();
-      } catch (IOException e1) {
-      }
-      return null;
-    }
-    if (n == 0 || fileName == null)
-      return null;
-    System.out.println("ZipTools cached " + n + " bytes from " + fileName);
-    return listing.toString();
-  }
-
-  private static byte[] getPngImageBytes(BufferedInputStream bis) {
-    try {
-      if (Rdr.isPngZipStream(bis)) {
-        int pt_count[] = new int[2];
-        Rdr.getPngZipPointAndCount(bis, pt_count);
-        if (pt_count[1] != 0)
-          return deActivatePngZipB(Rdr.getLimitedStreamBytes(bis, pt_count[0]));
-      }
-      return Rdr.getLimitedStreamBytes(bis, -1);
-    } catch (IOException e) {
-      return null;
-    }
-  }
-
-  /**
-   * Once a PNGJ image has been extracted, we want to red-line its
-   * iTXt "Jmol Type PNGJ" tag, since it is no longer associated with
-   * ZIP data.
-   *  
-   * @param bytes
-   * @return disfigured bytes
-   * 
-   */
-  private static byte[] deActivatePngZipB(byte[] bytes) {
-    // \0PNGJ starting at byte 50 changed to \0 NGJ
-    if (Rdr.isPngZipB(bytes))
-      bytes[51] = 32;
-    return bytes;
-  }
-
-
-
-}