private SB getShortStringData(int shortSID, int nBytes, boolean asBinaryString) {
SB data = new SB();
if (rootEntry == null) return data;
int thisSID = rootEntry.SIDfirstSector;
int ptShort = 0;
byte[] byteBuf = new byte[shortSectorSize];
ZipData gzipData = new ZipData(nBytes);
try {
// System.out.println("CD shortSID=" + shortSID);
// point to correct short data sector, 512/64 = 4 per page
while (thisSID >= 0 && shortSID >= 0 && nBytes > 0) {
while (shortSID - ptShort >= nShortSectorsPerStandardSector) {
ptShort += nShortSectorsPerStandardSector;
thisSID = SAT[thisSID];
}
seek(getOffset(thisSID) + (shortSID - ptShort) * shortSectorSize);
nBytes = getSectorData(data, byteBuf, shortSectorSize, nBytes, asBinaryString, gzipData);
shortSID = SSAT[shortSID];
// System.out.println("CD shortSID=" + shortSID);
}
} catch (Exception e) {
Logger.error(data.toString());
Logger.errorEx(null, e);
}
if (gzipData.isEnabled) gzipData.addTo(data);
return data;
}
private int getSectorData(
SB data,
byte[] byteBuf,
int nSectorBytes,
int nBytes,
boolean asBinaryString,
ZipData gzipData)
throws Exception {
readByteArray(byteBuf, 0, byteBuf.length);
int n = gzipData.addBytes(byteBuf, nSectorBytes, nBytes);
if (n >= 0) return n;
if (asBinaryString) {
for (int i = 0; i < nSectorBytes; i++) {
data.append(Integer.toHexString(byteBuf[i] & 0xFF)).appendC(' ');
if (--nBytes < 1) break;
}
} else {
for (int i = 0; i < nSectorBytes; i++) {
if (byteBuf[i] == 0) return -9999; // don't allow binary data
data.appendC((char) byteBuf[i]);
if (--nBytes < 1) break;
}
}
return nBytes;
}
@SuppressWarnings("unchecked")
@Override
public Object getProperty(String propertyName, int param) {
if (propertyName.equals("list")) {
String s = (String) getPropI("list");
if (s.length() > 1) s += "cutoff = " + getPropI("cutoff") + "\n";
return vwr.getMoInfo(-1) + "\n" + s;
}
if (propertyName == "moNumber") return Integer.valueOf(moNumber);
if (propertyName == "moLinearCombination") return moLinearCombination;
if (propertyName == "showMO") {
SB str = new SB();
Lst<Map<String, Object>> mos = (Lst<Map<String, Object>>) (sg.getMoData().get("mos"));
int nOrb = (mos == null ? 0 : mos.size());
int thisMO = param;
int currentMO = moNumber;
boolean isShowCurrent = (thisMO == Integer.MIN_VALUE);
if (thisMO == Integer.MAX_VALUE) {
thisMO = currentMO;
}
if (nOrb == 0 || isShowCurrent && currentMO == 0) return "";
boolean doOneMo = (thisMO != 0);
if (currentMO == 0) thisMO = 0;
boolean haveHeader = false;
int nTotal = (thisMO > 0 ? 1 : nOrb);
int i0 = (nTotal == 1 && currentMO > 0 ? currentMO : 1);
for (int i = i0; i <= nOrb; i++)
if (thisMO == 0 || thisMO == i || !doOneMo && i == currentMO) {
if (!doOneMo) {
Parameters params = sg.getParams();
setPropI("init", params, null);
setOrbital(i, null);
}
jvxlData.moleculeXml =
vwr.getModelCml(vwr.getModelUndeletedAtomsBitSet(thisMesh.modelIndex), 100, true);
if (!haveHeader) {
str.append(
JvxlCoder.jvxlGetFile(
jvxlData, null, null, "HEADERONLY", true, nTotal, null, null));
haveHeader = true;
}
str.append(
JvxlCoder.jvxlGetFile(
jvxlData,
null,
jvxlData.title,
null,
false,
1,
thisMesh.getState("mo"),
(thisMesh.scriptCommand == null ? "" : thisMesh.scriptCommand)));
if (!doOneMo) setPropI("delete", "mo_show", null);
if (nTotal == 1) break;
}
str.append(JvxlCoder.jvxlGetFile(jvxlData, null, null, "TRAILERONLY", true, 0, null, null));
return str.toString();
}
return getPropI(propertyName);
}
@Override
void dump(int level, SB sb) {
sb.append("\nnode LEFT" + level);
eleLeft.dump(level + 1, sb);
for (int i = 0; i < level; ++i) sb.append("->");
sb.append(" RIGHT" + level);
eleRight.dump(level + 1, sb);
}
@Override
public String getShapeState() {
if (!isActive()) return "";
SB sb = new SB();
sb.append("\n");
if (!simpleEllipsoids.isEmpty()) getStateID(sb);
if (!atomEllipsoids.isEmpty()) getStateAtoms(sb);
return sb.toString();
}
@Override
public String getShapeState() {
if (htModels == null) return "";
SB s = new SB();
int modelCount = vwr.getModelCount();
for (int i = 0; i < modelCount; i++) s.append(getMoState(i));
// System.out.println("molecular orbital state " + s.length());
return s.toString();
}
String getSavedOrientationText(String saveName) {
Orientation o;
if (saveName != null) {
o = getOrientationFor(saveName);
return (o == null ? "" : o.getMoveToText(true));
}
SB sb = new SB();
for (Entry<String, Object> e : saved.entrySet()) {
String name = e.getKey();
if (name.startsWith("Orientation_"))
sb.append(((Orientation) e.getValue()).getMoveToText(true));
}
return sb.toString();
}
/**
* checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR
* (similar to Gaussian CUBE files).
*
* @param isXLowToHigh
* @param isAngstroms
* @param strAtomCount
* @param atomLine
* @param bs
* @return isAngstroms
*/
protected static boolean checkAtomLine(
boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, SB bs) {
if (atomLine.indexOf("ANGSTROMS") >= 0) isAngstroms = true;
int ac = (strAtomCount == null ? Integer.MAX_VALUE : javajs.util.PT.parseInt(strAtomCount));
switch (ac) {
case Integer.MIN_VALUE:
ac = 0;
atomLine = " " + atomLine.substring(atomLine.indexOf(" ") + 1);
break;
case Integer.MAX_VALUE:
ac = Integer.MIN_VALUE;
break;
default:
String s = "" + ac;
atomLine = atomLine.substring(atomLine.indexOf(s) + s.length());
}
if (isAngstroms) {
if (atomLine.indexOf("ANGSTROM") < 0) atomLine += " ANGSTROMS";
} else {
if (atomLine.indexOf("BOHR") < 0) atomLine += " BOHR";
}
atomLine =
(ac == Integer.MIN_VALUE ? "" : (isXLowToHigh ? "+" : "-") + Math.abs(ac))
+ atomLine
+ "\n";
bs.append(atomLine);
return isAngstroms;
}
private void getStateAtoms(SB sb) {
BS bsDone = new BS();
Map<String, BS> temp = new Hashtable<String, BS>();
Map<String, BS> temp2 = new Hashtable<String, BS>();
for (Ellipsoid e : atomEllipsoids.values()) {
int iType = e.tensor.iType;
if (bsDone.get(iType + 1)) continue;
bsDone.set(iType + 1);
boolean isADP = (e.tensor.iType == Tensor.TYPE_ADP);
String cmd = (isADP ? null : "Ellipsoids set " + PT.esc(e.tensor.type));
for (Ellipsoid e2 : atomEllipsoids.values()) {
if (e2.tensor.iType != iType || isADP && !e2.isOn) continue;
int i = e2.tensor.atomIndex1;
//
BSUtil.setMapBitSet(
temp,
i,
i,
(isADP
? "Ellipsoids " + e2.percent
: cmd
+ " scale "
+ e2.scale
+ (e2.options == null ? "" : " options " + PT.esc(e2.options))
+ (e2.isOn ? " ON" : " OFF")));
if (e2.colix != C.INHERIT_ALL)
BSUtil.setMapBitSet(
temp2, i, i, getColorCommand(cmd, e2.pid, e2.colix, translucentAllowed));
}
}
sb.append(vwr.getCommands(temp, temp2, "select"));
}
@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;
}
private String getMoState(int modelIndex) {
strID = getId(modelIndex);
if (!getSettings(strID)) return "";
SB s = new SB();
int modelCount = vwr.getModelCount();
if (modelCount > 1) appendCmd(s, "frame " + vwr.getModelNumberDotted(modelIndex));
if (moCutoff != null)
appendCmd(s, "mo cutoff " + (sg.getIsPositiveOnly() ? "+" : "") + moCutoff);
if (moScale != null) appendCmd(s, "mo scale " + moScale);
if (moMonteCarloCount != null)
appendCmd(s, "mo points " + moMonteCarloCount + " " + moRandomSeed);
if (moResolution != null) appendCmd(s, "mo resolution " + moResolution);
if (moPlane != null)
appendCmd(
s, "mo plane {" + moPlane.x + " " + moPlane.y + " " + moPlane.z + " " + moPlane.w + "}");
if (moTitleFormat != null) appendCmd(s, "mo titleFormat " + PT.esc(moTitleFormat));
// the following is a correct object==object test
if (moColorNeg != null)
appendCmd(
s,
"mo color "
+ Escape.escapeColor(moColorNeg.intValue())
+ (moColorNeg.equals(moColorPos)
? ""
: " " + Escape.escapeColor(moColorPos.intValue())));
if (moSlab != null) {
if (thisMesh.slabOptions != null) appendCmd(s, thisMesh.slabOptions.toString());
if (thisMesh.jvxlData.slabValue != Integer.MIN_VALUE)
appendCmd(s, "mo slab " + thisMesh.jvxlData.slabValue);
}
if (moLinearCombination == null) {
appendCmd(s, "mo " + (moSquareData == Boolean.TRUE ? "squared " : "") + moNumber);
} else {
appendCmd(
s,
"mo "
+ QS.getMOString(moLinearCombination)
+ (moSquareLinear == Boolean.TRUE ? " squared" : ""));
}
if (moTranslucency != null) appendCmd(s, "mo translucent " + moTranslucentLevel);
appendCmd(s, ((IsosurfaceMesh) thisModel.get("mesh")).getState("mo"));
return s.toString();
}
/**
* 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();
}
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();
}
public static String getVariableList(
Map<String, SV> htVariables, int nMax, boolean withSites, boolean definedOnly) {
SB sb = new SB();
// user variables only:
int n = 0;
String[] list = new String[htVariables.size()];
for (Map.Entry<String, SV> entry : htVariables.entrySet()) {
String key = entry.getKey();
SV var = entry.getValue();
if ((withSites || !key.startsWith("site_")) && (!definedOnly || key.charAt(0) == '@'))
list[n++] =
key
+ (key.charAt(0) == '@'
? " " + var.asString()
: " = " + varClip(key, var.escape(), nMax));
}
Arrays.sort(list, 0, n);
for (int i = 0; i < n; i++) if (list[i] != null) sb.append(" ").append(list[i]).append(";\n");
if (n == 0 && !definedOnly) sb.append("# --no global user variables defined--;\n");
return sb.toString();
}
protected void jvxlDecodeContourData(JvxlData jvxlData, String data) throws Exception {
List<List<Object>> vs = new List<List<Object>>();
SB values = new SB();
SB colors = new SB();
int pt = -1;
jvxlData.vContours = null;
if (data == null) return;
while ((pt = data.indexOf("<jvxlContour", pt + 1)) >= 0) {
List<Object> v = new List<Object>();
String s = xr.getXmlData("jvxlContour", data.substring(pt), true, false);
float value = parseFloatStr(XmlReader.getXmlAttrib(s, "value"));
values.append(" ").appendF(value);
int color = getColor(XmlReader.getXmlAttrib(s, "color"));
short colix = C.getColix(color);
colors.append(" ").append(Escape.escapeColor(color));
String fData = JvxlCoder.jvxlDecompressString(XmlReader.getXmlAttrib(s, "data"));
BS bs = JvxlCoder.jvxlDecodeBitSet(xr.getXmlData("jvxlContour", s, false, false));
int n = bs.length();
IsosurfaceMesh.setContourVector(v, n, bs, value, colix, color, SB.newS(fData));
vs.addLast(v);
}
int n = vs.size();
if (n > 0) {
jvxlData.vContours = AU.createArrayOfArrayList(n);
// 3D contour values and colors
jvxlData.contourColixes = params.contourColixes = new short[n];
jvxlData.contourValues = params.contoursDiscrete = new float[n];
for (int i = 0; i < n; i++) {
jvxlData.vContours[i] = vs.get(i);
jvxlData.contourValues[i] = ((Float) jvxlData.vContours[i].get(2)).floatValue();
jvxlData.contourColixes[i] = ((short[]) jvxlData.vContours[i].get(3))[0];
}
jvxlData.contourColors = C.getHexCodes(jvxlData.contourColixes);
Logger.info("JVXL read: " + n + " discrete contours");
Logger.info("JVXL read: contour values: " + values);
Logger.info("JVXL read: contour colors: " + colors);
}
}
@Override
protected void readParameters() throws Exception {
String s = xr.getXmlData("jvxlFileTitle", null, false, false);
jvxlFileHeaderBuffer = SB.newS(s);
xr.toTag("jvxlVolumeData");
String data = tempDataXml = xr.getXmlData("jvxlVolumeData", null, true, false);
volumetricOrigin.setT(xr.getXmlPoint(data, "origin"));
isAngstroms = true;
readVector(0);
readVector(1);
readVector(2);
line = xr.toTag("jvxlSurfaceSet");
nSurfaces = parseIntStr(XmlReader.getXmlAttrib(line, "count"));
Logger.info("jvxl file surfaces: " + nSurfaces);
Logger.info("using default edge fraction base and range");
Logger.info("using default color fraction base and range");
cJvxlEdgeNaN = (char) (edgeFractionBase + edgeFractionRange);
}
private void getStateID(SB sb) {
V3 v1 = new V3();
for (Ellipsoid ellipsoid : simpleEllipsoids.values()) {
Tensor t = ellipsoid.tensor;
if (!ellipsoid.isValid || t == null) continue;
sb.append(" Ellipsoid ID ")
.append(ellipsoid.id)
.append(" modelIndex ")
.appendI(t.modelIndex)
.append(" center ")
.append(Escape.eP(ellipsoid.center))
.append(" axes");
for (int i = 0; i < 3; i++) {
v1.setT(t.eigenVectors[i]);
v1.scale(ellipsoid.lengths[i]);
sb.append(" ").append(Escape.eP(v1));
}
sb.append(" " + getColorCommandUnk("", ellipsoid.colix, translucentAllowed));
if (ellipsoid.options != null) sb.append(" options ").append(PT.esc(ellipsoid.options));
if (!ellipsoid.isOn) sb.append(" off");
sb.append(";\n");
}
}
/**
* 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 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;
}
protected String skipComments(boolean allowBlankLines) throws Exception {
SB sb = new SB();
while (readLine() != null && (allowBlankLines && line.length() == 0 || line.indexOf("#") == 0))
sb.append(line).appendC('\n');
return sb.toString();
}
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 boolean slabPolygons(Object[] slabObject, boolean allowCap) {
if (polygonCount0 < 0) return false; // disabled for some surface types
int slabType = ((Integer) slabObject[0]).intValue();
if (slabType == T.none || slabType == T.brillouin) {
if (bsSlabDisplay != null && (polygonCount0 != 0 || vertexCount0 != 0)) {
pc = polygonCount0;
vc = vertexCount0;
polygonCount0 = vertexCount0 = 0;
normixCount = (isTriangleSet ? pc : vc);
bsSlabDisplay.setBits(0, (pc == 0 ? vc : pc));
slabOptions = new SB().append(meshType + " slab none");
bsSlabGhost = null;
slabMeshType = T.none;
}
if (slabType == T.none) return false;
}
Object slabbingObject = slabObject[1];
boolean andCap = ((Boolean) slabObject[2]).booleanValue() && !(slabType == T.brillouin);
if (andCap && !allowCap) return false;
Object[] colorData = (Object[]) slabObject[3];
boolean isGhost = (colorData != null);
if (bsSlabDisplay == null || polygonCount0 == 0 && vertexCount0 == 0) {
polygonCount0 = pc;
vertexCount0 = vc;
bsSlabDisplay = BSUtil.setAll(pc == 0 ? vc : pc);
bsSlabGhost = null;
if (pc == 0 && vc == 0) return false;
} else if (isMerged) {
if (pc == 0) bsSlabDisplay.setBits(mergeVertexCount0, vc);
else bsSlabDisplay.setBits(mergePolygonCount0, pc);
}
if (isGhost) {
if (bsSlabGhost == null) bsSlabGhost = new BS();
slabMeshType = ((Integer) colorData[0]).intValue();
slabColix = ((Short) colorData[1]).shortValue();
// if (C.isColixColorInherited(slabColix))
// slabColix = C.copyColixTranslucency(slabColix, colix);
andCap = false;
colix = C.getColixTranslucent3(colix, false, 0);
}
SB sb = new SB();
sb.append(andCap ? " cap " : " slab ");
if (isGhost) {
sb.append("translucent ").appendF(C.getColixTranslucencyFractional(slabColix)).append(" ");
String s = C.getHexCode(slabColix);
if (s != null) sb.append(s).append(" ");
if (slabMeshType == T.mesh) sb.append("mesh ");
}
switch (slabType) {
case T.brillouin:
sb.append("brillouin");
slabBrillouin((P3[]) slabbingObject);
break;
case T.decimal:
getIntersection(
0,
null,
null,
null,
null,
(BS) slabbingObject,
null,
andCap,
false,
T.decimal,
isGhost);
break;
case T.plane:
P4 plane = (P4) slabbingObject;
sb.append(Escape.eP4(plane));
getIntersection(0, plane, null, null, null, null, null, andCap, false, T.plane, isGhost);
break;
case T.unitcell:
case T.boundbox:
P3[] box = (P3[]) slabbingObject;
sb.append("within ").append(Escape.eAP(box));
P4[] faces = BoxInfo.getFacesFromCriticalPoints(box);
for (int i = 0; i < faces.length; i++) {
getIntersection(
0, faces[i], null, null, null, null, null, andCap, false, T.plane, isGhost);
}
break;
case T.data:
getIntersection(
0,
null,
null,
null,
(float[]) slabbingObject,
null,
null,
false,
false,
T.min,
isGhost);
break;
case T.within:
case T.range:
case T.mesh:
Object[] o = (Object[]) slabbingObject;
float distance = ((Float) o[0]).floatValue();
switch (slabType) {
case T.within:
P3[] points = (P3[]) o[1];
BS bs = (BS) o[2];
sb.append("within ")
.appendF(distance)
.append(bs == null ? Escape.e(points) : Escape.e(bs));
getIntersection(
distance,
null,
points,
null,
null,
null,
null,
andCap,
false,
(distance > 0 ? T.distance : T.sphere),
isGhost);
break;
case T.range:
// isosurface slab within range x.x y.y
// if y.y < x.x then this effectively means "NOT within range y.y x.x"
if (vvs == null) return false;
float distanceMax = ((Float) o[1]).floatValue();
sb.append("within range ").appendF(distance).append(" ").appendF(distanceMax);
bs = (distanceMax < distance ? BSUtil.copy(bsSlabDisplay) : null);
getIntersection(
distance, null, null, null, null, null, null, andCap, false, T.min, isGhost);
BS bsA = (bs == null ? null : BSUtil.copy(bsSlabDisplay));
BSUtil.copy2(bs, bsSlabDisplay);
getIntersection(
distanceMax, null, null, null, null, null, null, andCap, false, T.max, isGhost);
if (bsA != null) bsSlabDisplay.or(bsA);
break;
case T.mesh:
// NOT IMPLEMENTED
MeshSurface mesh = (MeshSurface) o[1];
// distance = -1;
getIntersection(
0,
null,
null,
null,
null,
null,
mesh,
andCap,
false,
distance < 0 ? T.min : T.max,
isGhost);
// TODO: unresolved how exactly to store this in the state
// -- must indicate exact set of triangles to slab and how!
break;
}
break;
}
String newOptions = sb.toString();
if (slabOptions == null) slabOptions = new SB();
if (slabOptions.indexOf(newOptions) < 0)
slabOptions.append(slabOptions.length() > 0 ? "; " : "").append(meshType).append(newOptions);
return true;
}