@Override
public SB getAllDataFiles(String binaryFileList, String firstFile) {
if (firstFile != null) {
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
if (thisEntry.entryName.equals(firstFile)) {
directory.remove(i);
directory.add(1, thisEntry); // after ROOT_ENTRY
break;
}
}
}
data = new SB();
data.append("Compound Document File Directory: ");
data.append(getDirectoryListing("|"));
data.append("\n");
binaryFileList = "|" + binaryFileList + "|";
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
Logger.info("reading " + thisEntry.entryName);
if (!thisEntry.isEmpty && thisEntry.entryType != 5) {
String name = thisEntry.entryName;
if (name.endsWith(".gz")) name = name.substring(0, name.length() - 3);
data.append("BEGIN Directory Entry ").append(name).append("\n");
data.appendSB(
getEntryAsString(
thisEntry, binaryFileList.indexOf("|" + thisEntry.entryName + "|") >= 0));
data.append("\n");
data.append("END Directory Entry ").append(thisEntry.entryName).append("\n");
}
}
close();
return data;
}
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();
}
/**
* reads a compound document directory 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.
*
* <p>Files are bracketed by BEGIN Directory Entry and END Directory Entry lines, similar to
* ZipUtil.getAllData.
*
* @param prefix
* @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 getAllDataMapped(String prefix, String binaryFileList, Map<String, String> fileData) {
fileData.put("#Directory_Listing", getDirectoryListing("|"));
binaryFileList = "|" + binaryFileList + "|";
for (int i = 0; i < directory.size(); i++) {
CompoundDocDirEntry thisEntry = directory.get(i);
if (!thisEntry.isEmpty && thisEntry.entryType != 5) {
String name = thisEntry.entryName;
Logger.info("CompoundDocument file " + name);
boolean isBinary = (binaryFileList.indexOf("|" + name + "|") >= 0);
if (isBinary) name += ":asBinaryString";
SB data = new SB();
data.append("BEGIN Directory Entry ").append(name).append("\n");
data.appendSB(getEntryAsString(thisEntry, isBinary));
data.append("\nEND Directory Entry ").append(name).append("\n");
fileData.put(prefix + "/" + name, data.toString());
}
}
close();
}
