コード例 #1
0
 Object createAtomSeCollectionFromStrings(
     String[] arrayModels, SB loadScript, Map<String, Object> htParams, boolean isAppend) {
   if (!htParams.containsKey("isData")) {
     String oldSep = "\"" + viewer.getDataSeparator() + "\"";
     String tag = "\"" + (isAppend ? "append" : "model") + " inline\"";
     SB sb = new SB();
     sb.append("set dataSeparator \"~~~next file~~~\";\ndata ").append(tag);
     for (int i = 0; i < arrayModels.length; i++) {
       if (i > 0) sb.append("~~~next file~~~");
       sb.append(arrayModels[i]);
     }
     sb.append("end ").append(tag).append(";set dataSeparator ").append(oldSep);
     loadScript.appendSB(sb);
   }
   setLoadState(htParams);
   Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");
   String[] fullPathNames = new String[arrayModels.length];
   DataReader[] readers = new DataReader[arrayModels.length];
   for (int i = 0; i < arrayModels.length; i++) {
     fullPathNames[i] = "string[" + i + "]";
     readers[i] = newDataReader(arrayModels[i]);
   }
   JmolFilesReaderInterface filesReader =
       newFilesReader(fullPathNames, fullPathNames, null, readers, htParams, isAppend);
   filesReader.run();
   return filesReader.getAtomSetCollection();
 }
コード例 #2
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();
 }
コード例 #3
0
 /*
  * note -- createAtomSetCollectionFromXXX methods
  * were "openXXX" before refactoring 11/29/2008 -- BH
  *
  * The problem was that while they did open the file, they
  * (mostly) also closed them, and this was confusing.
  *
  * The term "clientFile" was replaced by "atomSetCollection"
  * here because that's what it is --- an AtomSetCollection,
  * not a file. The file is closed at this point. What is
  * returned is the atomSetCollection object.
  *
  * One could say this is just semantics, but there were
  * subtle bugs here, where readers were not always being
  * closed explicitly. In the process of identifying Out of
  * Memory Errors, I felt it was necessary to clarify all this.
  *
  * Apologies to those who feel the original clientFile notation
  * was more generalizable or understandable.
  *
  */
 Object createAtomSetCollectionFromFile(
     String name, Map<String, Object> htParams, boolean isAppend) {
   if (htParams.get("atomDataOnly") == null) {
     setLoadState(htParams);
   }
   name = viewer.resolveDatabaseFormat(name);
   int pt = name.indexOf("::");
   String nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
   String fileType = (pt >= 0 ? name.substring(0, pt) : null);
   Logger.info(
       "\nFileManager.getAtomSetCollectionFromFile("
           + nameAsGiven
           + ")"
           + (name.equals(nameAsGiven) ? "" : " //" + name));
   String[] names = classifyName(nameAsGiven, true);
   if (names.length == 1) return names[0];
   String fullPathName = names[0];
   String fileName = names[1];
   htParams.put(
       "fullPathName",
       (fileType == null ? "" : fileType + "::") + fullPathName.replace('\\', '/'));
   if (viewer.getBoolean(T.messagestylechime) && viewer.getBoolean(T.debugscript))
     viewer.scriptStatus("Requesting " + fullPathName);
   FileReader fileReader =
       new FileReader(
           this, viewer, fileName, fullPathName, nameAsGiven, fileType, null, htParams, isAppend);
   fileReader.run();
   return fileReader.getAtomSetCollection();
 }
コード例 #4
0
 Object createAtomSetCollectionFromFiles(
     String[] fileNames, Map<String, Object> htParams, boolean isAppend) {
   setLoadState(htParams);
   String[] fullPathNames = new String[fileNames.length];
   String[] namesAsGiven = new String[fileNames.length];
   String[] fileTypes = new String[fileNames.length];
   for (int i = 0; i < fileNames.length; i++) {
     int pt = fileNames[i].indexOf("::");
     String nameAsGiven = (pt >= 0 ? fileNames[i].substring(pt + 2) : fileNames[i]);
     String fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
     String[] names = classifyName(nameAsGiven, true);
     if (names.length == 1) return names[0];
     fullPathNames[i] = names[0];
     fileNames[i] = names[0].replace('\\', '/');
     fileTypes[i] = fileType;
     namesAsGiven[i] = nameAsGiven;
   }
   htParams.put("fullPathNames", fullPathNames);
   htParams.put("fileTypes", fileTypes);
   JmolFilesReaderInterface filesReader =
       newFilesReader(fullPathNames, namesAsGiven, fileTypes, null, htParams, isAppend);
   filesReader.run();
   return filesReader.getAtomSetCollection();
 }