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();
}
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);
}
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();
}
}
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;
}