示例#1
0
 Object createAtomSetCollectionFromString(
     String strModel, Map<String, Object> htParams, boolean isAppend) {
   setLoadState(htParams);
   boolean isAddH = (strModel.indexOf(JC.ADD_HYDROGEN_TITLE) >= 0);
   String[] fnames = (isAddH ? getFileInfo() : null);
   FileReader fileReader =
       new FileReader(
           this,
           viewer,
           "string",
           "string",
           "string",
           null,
           JmolBinary.getBR(strModel),
           htParams,
           isAppend);
   fileReader.run();
   if (fnames != null) setFileInfo(fnames);
   if (!isAppend && !(fileReader.getAtomSetCollection() instanceof String)) {
     viewer.zap(false, true, false);
     setFileInfo(
         new String[] {strModel == JC.MODELKIT_ZAP_STRING ? JC.MODELKIT_ZAP_TITLE : "string"});
   }
   return fileReader.getAtomSetCollection();
 }
示例#2
0
 Object getBufferedReaderOrErrorMessageFromName(
     String name, String[] fullPathNameReturn, boolean isBinary, boolean doSpecialLoad) {
   Object data = cacheGet(name, false);
   boolean isBytes = PT.isAB(data);
   byte[] bytes = (isBytes ? (byte[]) data : null);
   if (name.startsWith("cache://")) {
     if (data == null) return "cannot read " + name;
     if (isBytes) {
       bytes = (byte[]) data;
     } else {
       return JmolBinary.getBR((String) data);
     }
   }
   String[] names = classifyName(name, true);
   if (names == null) return "cannot read file name: " + name;
   if (fullPathNameReturn != null) fullPathNameReturn[0] = names[0].replace('\\', '/');
   return getUnzippedReaderOrStreamFromName(
       names[0], bytes, false, isBinary, false, doSpecialLoad, null);
 }
示例#3
0
  public Object getUnzippedReaderOrStreamFromName(
      String name,
      byte[] bytes,
      boolean allowZipStream,
      boolean forceInputStream,
      boolean isTypeCheckOnly,
      boolean doSpecialLoad,
      Map<String, Object> htParams) {
    String[] subFileList = null;
    String[] info = (bytes == null && doSpecialLoad ? getSpartanFileList(name) : null);
    String name00 = name;
    if (info != null) {
      if (isTypeCheckOnly) return info;
      if (info[2] != null) {
        String header = info[1];
        Map<String, String> fileData = new Hashtable<String, String>();
        if (info.length == 3) {
          // we need information from the output file, info[2]
          String name0 = getObjectAsSections(info[2], header, fileData);
          fileData.put("OUTPUT", name0);
          info = JmolBinary.spartanFileList(name, fileData.get(name0));
          if (info.length == 3) {
            // might have a second option
            name0 = getObjectAsSections(info[2], header, fileData);
            fileData.put("OUTPUT", name0);
            info = JmolBinary.spartanFileList(info[1], fileData.get(name0));
          }
        }
        // load each file individually, but return files IN ORDER
        SB sb = new SB();
        if (fileData.get("OUTPUT") != null) sb.append(fileData.get(fileData.get("OUTPUT")));
        String s;
        for (int i = 2; i < info.length; i++) {
          name = info[i];
          name = getObjectAsSections(name, header, fileData);
          Logger.info("reading " + name);
          s = fileData.get(name);
          sb.append(s);
        }
        s = sb.toString();
        if (spardirCache == null) spardirCache = new Hashtable<String, byte[]>();
        spardirCache.put(name00.replace('\\', '/'), s.getBytes());
        return JmolBinary.getBR(s);
      }
      // continuing...
      // here, for example, for an SPT file load that is not just a type check
      // (type check is only for application file opening and drag-drop to
      // determine if
      // script or load command should be used)
    }

    if (bytes == null && pngjCache != null) {
      bytes = JmolBinary.getCachedPngjBytes(this, name);
      if (bytes != null && htParams != null) htParams.put("sourcePNGJ", Boolean.TRUE);
    }
    String fullName = name;
    if (name.indexOf("|") >= 0) {
      subFileList = PT.split(name, "|");
      if (bytes == null) Logger.info("FileManager opening 3 " + name);
      name = subFileList[0];
    }
    Object t =
        (bytes == null
            ? getBufferedInputStreamOrErrorMessageFromName(
                name, fullName, true, false, null, !forceInputStream)
            : JmolBinary.getBIS(bytes));
    try {
      if (t instanceof String) return t;
      if (t instanceof BufferedReader) return t;
      BufferedInputStream bis = JmolBinary.getUnzippedInputStream((BufferedInputStream) t);
      if (JmolBinary.isCompoundDocumentS(bis)) {
        JmolDocument doc = (JmolDocument) Interface.getOptionInterface("io2.CompoundDocument");
        doc.setStream(bis, true);
        return JmolBinary.getBR(doc.getAllDataFiles("Molecule", "Input").toString());
      }
      if (JmolBinary.isPickleS(bis)) return bis;
      bis = JmolBinary.checkPngZipStream(bis);
      if (JmolBinary.isZipS(bis)) {
        if (allowZipStream) return JmolBinary.newZipInputStream(bis);
        Object o = JmolBinary.getZipFileContents(bis, subFileList, 1, forceInputStream);
        return (o instanceof String ? JmolBinary.getBR((String) o) : o);
      }
      return (forceInputStream ? bis : JmolBinary.getBufferedReader(bis, null));
    } catch (Exception ioe) {
      return ioe.toString();
    }
  }
示例#4
0
 public Object getBufferedInputStreamOrErrorMessageFromName(
     String name,
     String fullName,
     boolean showMsg,
     boolean checkOnly,
     byte[] outputBytes,
     boolean allowReader) {
   byte[] cacheBytes = null;
   if (outputBytes == null) {
     cacheBytes =
         (fullName == null || pngjCache == null
             ? null
             : JmolBinary.getCachedPngjBytes(this, fullName));
     if (cacheBytes == null) cacheBytes = (byte[]) cacheGet(name, true);
   }
   BufferedInputStream bis = null;
   Object ret = null;
   String errorMessage = null;
   try {
     if (cacheBytes == null) {
       boolean isPngjBinaryPost = (name.indexOf("?POST?_PNGJBIN_") >= 0);
       boolean isPngjPost = (isPngjBinaryPost || name.indexOf("?POST?_PNGJ_") >= 0);
       if (name.indexOf("?POST?_PNG_") > 0 || isPngjPost) {
         String[] errMsg = new String[1];
         byte[] bytes = viewer.getImageAsBytes(isPngjPost ? "PNGJ" : "PNG", 0, 0, -1, errMsg);
         if (errMsg[0] != null) return errMsg[0];
         if (isPngjBinaryPost) {
           outputBytes = bytes;
           name = PT.simpleReplace(name, "?_", "=_");
         } else {
           name = new SB().append(name).append("=").appendSB(Base64.getBase64(bytes)).toString();
         }
       }
       int iurl = urlTypeIndex(name);
       boolean isURL = (iurl >= 0);
       String post = null;
       if (isURL && (iurl = name.indexOf("?POST?")) >= 0) {
         post = name.substring(iurl + 6);
         name = name.substring(0, iurl);
       }
       boolean isApplet = (appletDocumentBaseURL != null);
       if (name.indexOf(".png") >= 0 && pngjCache == null && viewer.cachePngFiles())
         JmolBinary.cachePngjFile(this, null);
       if (isApplet || isURL) {
         if (isApplet && isURL && appletProxy != null)
           name = appletProxy + "?url=" + urlEncode(name);
         URL url =
             (isApplet
                 ? new URL(appletDocumentBaseURL, name, null)
                 : new URL((URL) null, name, null));
         if (checkOnly) return null;
         name = url.toString();
         if (showMsg && name.toLowerCase().indexOf("password") < 0)
           Logger.info("FileManager opening 1 " + name);
         ret = viewer.apiPlatform.getBufferedURLInputStream(url, outputBytes, post);
         byte[] bytes = null;
         if (ret instanceof SB) {
           SB sb = (SB) ret;
           if (allowReader && !JmolBinary.isBase64(sb)) return JmolBinary.getBR(sb.toString());
           bytes = JmolBinary.getBytesFromSB(sb);
         } else if (PT.isAB(ret)) {
           bytes = (byte[]) ret;
         }
         if (bytes != null) ret = JmolBinary.getBIS(bytes);
       } else if ((cacheBytes = (byte[]) cacheGet(name, true)) == null) {
         if (showMsg) Logger.info("FileManager opening 2 " + name);
         ret = viewer.apiPlatform.getBufferedFileInputStream(name);
       }
       if (ret instanceof String) return ret;
     }
     bis = (cacheBytes == null ? (BufferedInputStream) ret : JmolBinary.getBIS(cacheBytes));
     if (checkOnly) {
       bis.close();
       bis = null;
     }
     return bis;
   } catch (Exception e) {
     try {
       if (bis != null) bis.close();
     } catch (IOException e1) {
     }
     errorMessage = "" + e;
   }
   return errorMessage;
 }