/**
* delivers file contents and directory listing for a ZIP/JAR file into sb
*
* @param name
* @param header
* @param fileData
* @return name of entry
*/
private String getObjectAsSections(String name, String header, Map<String, String> fileData) {
if (name == null) return null;
String[] subFileList = null;
boolean asBinaryString = false;
String name0 = name.replace('\\', '/');
if (name.indexOf(":asBinaryString") >= 0) {
asBinaryString = true;
name = name.substring(0, name.indexOf(":asBinaryString"));
}
SB sb = null;
if (fileData.containsKey(name0)) return name0;
if (name.indexOf("#JMOL_MODEL ") >= 0) {
fileData.put(name0, name0 + "\n");
return name0;
}
String fullName = name;
if (name.indexOf("|") >= 0) {
subFileList = PT.split(name, "|");
name = subFileList[0];
}
BufferedInputStream bis = null;
try {
Object t =
getBufferedInputStreamOrErrorMessageFromName(name, fullName, false, false, null, false);
if (t instanceof String) {
fileData.put(name0, (String) t + "\n");
return name0;
}
bis = (BufferedInputStream) t;
if (JmolBinary.isCompoundDocumentS(bis)) {
JmolDocument doc = (JmolDocument) Interface.getOptionInterface("io2.CompoundDocument");
doc.setStream(bis, true);
doc.getAllDataMapped(name.replace('\\', '/'), "Molecule", fileData);
} else if (JmolBinary.isZipS(bis)) {
JmolBinary.getAllZipData(bis, subFileList, name.replace('\\', '/'), "Molecule", fileData);
} else if (asBinaryString) {
// used for Spartan binary file reading
JmolDocument bd = (JmolDocument) Interface.getOptionInterface("io2.BinaryDocument");
bd.setStream(bis, false);
sb = new SB();
// note -- these headers must match those in ZipUtil.getAllData and
// CompoundDocument.getAllData
if (header != null) sb.append("BEGIN Directory Entry " + name0 + "\n");
try {
while (true) sb.append(Integer.toHexString(bd.readByte() & 0xFF)).appendC(' ');
} catch (Exception e1) {
sb.appendC('\n');
}
if (header != null) sb.append("\nEND Directory Entry " + name0 + "\n");
fileData.put(name0, sb.toString());
} else {
BufferedReader br =
JmolBinary.getBufferedReader(
JmolBinary.isGzipS(bis)
? new BufferedInputStream(JmolBinary.newGZIPInputStream(bis))
: bis,
null);
String line;
sb = new SB();
if (header != null) sb.append("BEGIN Directory Entry " + name0 + "\n");
while ((line = br.readLine()) != null) {
sb.append(line);
sb.appendC('\n');
}
br.close();
if (header != null) sb.append("\nEND Directory Entry " + name0 + "\n");
fileData.put(name0, sb.toString());
}
} catch (Exception ioe) {
fileData.put(name0, ioe.toString());
}
if (bis != null)
try {
bis.close();
} catch (Exception e) {
//
}
if (!fileData.containsKey(name0)) fileData.put(name0, "FILE NOT FOUND: " + name0 + "\n");
return name0;
}
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();
}
}
