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"));
}
public static String fixFileNameVariables(String format, String fname) {
String str = PT.simpleReplace(format, "%FILE", fname);
if (str.indexOf("%LC") < 0) return str;
fname = fname.toLowerCase();
str = PT.simpleReplace(str, "%LCFILE", fname);
if (fname.length() == 4) str = PT.simpleReplace(str, "%LC13", fname.substring(1, 3));
return str;
}
private boolean checkID(String thisID) {
ellipsoidSet = new Lst<Ellipsoid>();
if (thisID == null) return false;
thisID = thisID.toLowerCase();
if (PT.isWild(thisID)) {
for (Entry<String, Ellipsoid> e : simpleEllipsoids.entrySet()) {
String key = e.getKey().toLowerCase();
if (PT.isMatch(key, thisID, true, true)) ellipsoidSet.addLast(e.getValue());
}
}
Ellipsoid e = simpleEllipsoids.get(thisID);
if (e != null) ellipsoidSet.addLast(e);
return (ellipsoidSet.size() > 0);
}
public static String setScriptFileReferences(
String script, String localPath, String remotePath, String scriptPath) {
if (localPath != null) script = setScriptFileRefs(script, localPath, true);
if (remotePath != null) script = setScriptFileRefs(script, remotePath, false);
script = PT.simpleReplace(script, "\1\"", "\"");
if (scriptPath != null) {
while (scriptPath.endsWith("/"))
scriptPath = scriptPath.substring(0, scriptPath.length() - 1);
for (int ipt = 0; ipt < scriptFilePrefixes.length; ipt++) {
String tag = scriptFilePrefixes[ipt];
script = PT.simpleReplace(script, tag + ".", tag + scriptPath);
}
}
return script;
}
public Object getFileAsBytes(String name, OC out, boolean allowZip) {
// ?? used by eval of "WRITE FILE"
// will be full path name
if (name == null) return null;
String fullName = name;
String[] subFileList = null;
if (name.indexOf("|") >= 0) {
subFileList = PT.split(name, "|");
name = subFileList[0];
allowZip = true;
}
Object t =
getBufferedInputStreamOrErrorMessageFromName(name, fullName, false, false, null, false);
if (t instanceof String) return "Error:" + t;
try {
BufferedInputStream bis = (BufferedInputStream) t;
Object bytes =
(out != null
|| !allowZip
|| subFileList == null
|| subFileList.length <= 1
|| !JmolBinary.isZipS(bis) && !JmolBinary.isPngZipStream(bis)
? JmolBinary.getStreamAsBytes(bis, out)
: JmolBinary.getZipFileContentsAsBytes(bis, subFileList, 1));
bis.close();
return bytes;
} catch (Exception ioe) {
return ioe.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;
}
@Override
protected void readParameters() throws Exception {
jvxlFileHeaderBuffer = new SB();
jvxlFileHeaderBuffer.append(readLine()).appendC('\n');
jvxlFileHeaderBuffer.append(readLine()).appendC('\n');
String atomLine = readLine();
String[] tokens = PT.getTokensAt(atomLine, 0);
ac = parseIntStr(tokens[0]);
negativeAtomCount = (ac < 0); // MO list
if (negativeAtomCount) ac = -ac;
volumetricOrigin.set(
parseFloatStr(tokens[1]), parseFloatStr(tokens[2]), parseFloatStr(tokens[3]));
VolumeFileReader.checkAtomLine(
isXLowToHigh, isAngstroms, tokens[0], atomLine, jvxlFileHeaderBuffer);
if (!isAngstroms) volumetricOrigin.scale(ANGSTROMS_PER_BOHR);
for (int i = 0; i < 3; ++i) readVoxelVector(i);
for (int i = 0; i < ac; ++i) jvxlFileHeaderBuffer.append(readLine() + "\n");
if (!negativeAtomCount) {
nSurfaces = 1;
} else {
readLine();
Logger.info("Reading extra CUBE information line: " + line);
nSurfaces = parseIntStr(line);
}
}
private DataReader newDataReader(Object data) {
String reader =
(data instanceof String
? "String"
: PT.isAS(data) ? "Array" : data instanceof List<?> ? "List" : null);
if (reader == null) return null;
DataReader dr = (DataReader) Interface.getOptionInterface("io2." + reader + "DataReader");
return dr.setData(data);
}
private static String fixPath(String path) {
path = path.replace('\\', '/');
path = PT.simpleReplace(path, "/./", "/");
int pt = path.lastIndexOf("//") + 1;
if (pt < 1) pt = path.indexOf(":/") + 1;
if (pt < 1) pt = path.indexOf("/");
if (pt < 0) return null;
String protocol = path.substring(0, pt);
path = path.substring(pt);
while ((pt = path.lastIndexOf("/../")) >= 0) {
int pt0 = path.substring(0, pt).lastIndexOf("/");
if (pt0 < 0) return PT.simpleReplace(protocol + path, "/../", "/");
path = path.substring(0, pt0) + path.substring(pt + 3);
}
if (path.length() == 0) path = "/";
return protocol + path;
}
private static int getColor(String c) {
int n = 0;
try {
switch (c.charAt(0)) {
case '[':
n = CU.getArgbFromString(c);
break;
case '0': // 0x
n = PT.parseIntRadix(c.substring(2), 16);
break;
default:
n = PT.parseIntRadix(c, 10);
}
// if (n < 0x1000000)
// n |= 0xFF000000;
} catch (Exception e) {
}
return n;
}
Map<String, Integer> cacheList() {
Map<String, Integer> map = new Hashtable<String, Integer>();
for (Map.Entry<String, Object> entry : cache.entrySet())
map.put(
entry.getKey(),
Integer.valueOf(
PT.isAB(entry.getValue())
? ((byte[]) entry.getValue()).length
: entry.getValue().toString().length()));
return map;
}
/**
* decode vertex data found within <jvxlVertexData> element as created by jvxlEncodeVertexData
* (see above)
*
* @param data tag and contents
* @param asArray or just addVertexCopy
* @return Point3f[] if desired
* @throws Exception
*/
public P3[] jvxlDecodeVertexData(String data, boolean asArray) throws Exception {
int vertexCount = parseIntStr(XmlReader.getXmlAttrib(data, "count"));
if (!asArray) Logger.info("Reading " + vertexCount + " vertices");
int ptCount = vertexCount * 3;
P3[] vertices = (asArray ? new P3[vertexCount] : null);
P3 p = (asArray ? null : new P3());
float fraction;
String vData = XmlReader.getXmlAttrib(data, "data");
String encoding = getEncoding(data);
if ("none".equals(encoding)) {
if (vData.length() == 0) vData = xr.getXmlData("jvxlVertexData", data, false, false);
float[] fdata = PT.parseFloatArray(vData);
// first point is count -- ignored.
if (fdata[0] != vertexCount * 3)
Logger.info(
"JvxlXmlReader: vertexData count="
+ ((int) fdata[0])
+ "; expected "
+ (vertexCount * 3));
for (int i = 0, pt = 1; i < vertexCount; i++) {
p = P3.new3(fdata[pt++], fdata[pt++], fdata[pt++]);
if (asArray) vertices[i] = p;
else addVertexCopy(p, 0, i);
}
} else {
P3 min = xr.getXmlPoint(data, "min");
P3 range = xr.getXmlPoint(data, "max");
range.sub(min);
int colorFractionBase = jvxlData.colorFractionBase;
int colorFractionRange = jvxlData.colorFractionRange;
String s = JvxlCoder.jvxlDecompressString(vData);
if (s.length() == 0) s = xr.getXmlData("jvxlVertexData", data, false, false);
for (int i = 0, pt = -1; i < vertexCount; i++) {
if (asArray) p = vertices[i] = new P3();
fraction =
JvxlCoder.jvxlFractionFromCharacter2(
s.charAt(++pt), s.charAt(pt + ptCount), colorFractionBase, colorFractionRange);
p.x = min.x + fraction * range.x;
fraction =
JvxlCoder.jvxlFractionFromCharacter2(
s.charAt(++pt), s.charAt(pt + ptCount), colorFractionBase, colorFractionRange);
p.y = min.y + fraction * range.y;
fraction =
JvxlCoder.jvxlFractionFromCharacter2(
s.charAt(++pt), s.charAt(pt + ptCount), colorFractionBase, colorFractionRange);
p.z = min.z + fraction * range.z;
if (!asArray) addVertexCopy(p, 0, i);
}
}
return vertices;
}
@Override
public void processStartElement(String localName) {
String[] tokens;
// System.out.println( " " + localName + " " + atts);
// System.out.println("xmlchem3d: start " + localName);
if ("Molecule".equalsIgnoreCase(localName)) {
asc.newAtomSet();
asc.setAtomSetName(atts.get("Name"));
return;
}
if ("LinearChain".equalsIgnoreCase(localName)) {
iGroup = 0;
iChain++;
}
if ("RepeatUnit".equalsIgnoreCase(localName)) {
iGroup++;
}
if ("Atom3d".equalsIgnoreCase(localName)) {
atom = new Atom();
atom.elementSymbol = atts.get("Components");
atom.atomName = atts.get("ID");
atom.atomSerial = ++iAtom;
if (iChain >= 0) parent.setChainID(atom, "" + (char) ((iChain - 1) % 26 + 'A'));
atom.group3 = "UNK";
if (iGroup == 0) iGroup = 1;
atom.sequenceNumber = iGroup;
String xyz = atts.get("XYZ");
if (xyz != null) {
tokens = getTokensStr(xyz.replace(',', ' '));
atom.set(parseFloatStr(tokens[0]), parseFloatStr(tokens[1]), parseFloatStr(tokens[2]));
}
boolean isBackbone = "1".equals(atts.get("IsBackboneAtom"));
if (isBackbone) bsBackbone.set(iAtom);
return;
}
if ("Bond".equalsIgnoreCase(localName)) {
String[] atoms = PT.split(atts.get("Connects"), ",");
int order = 1;
if (atts.containsKey("Type")) {
String type = atts.get("Type");
if (type.equals("Double")) order = 2;
else if (type.equals("Triple")) order = 3;
}
asc.addNewBondFromNames(atoms[0], atoms[1], order);
return;
}
}
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);
}
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();
}
public static String prompt(String label, String data, String[] list, boolean asButtons) {
try {
if (!asButtons) return JOptionPane.showInputDialog(label, data);
if (data != null) list = PT.split(data, "|");
int i =
JOptionPane.showOptionDialog(
null,
label,
"Jmol prompt",
JOptionPane.DEFAULT_OPTION,
JOptionPane.INFORMATION_MESSAGE,
null,
list,
list[0]);
// ESCAPE will close the panel with no option selected.
return (data == null ? "" + i : i == JOptionPane.CLOSED_OPTION ? "null" : list[i]);
} catch (Throwable e) {
return "null";
}
}
/**
* legacy -- for some scripts with early isosurface slabbing
*
* @param s
* @param isCap
* @return slabInfo object
*/
public static Object[] getCapSlabObject(String s, boolean isCap) {
try {
if (s.indexOf("array") == 0) {
String[] pts = PT.split(s.substring(6, s.length() - 1), ",");
return TempArray.getSlabObjectType(
T.boundbox,
new P3[] {
(P3) Escape.uP(pts[0]),
(P3) Escape.uP(pts[1]),
(P3) Escape.uP(pts[2]),
(P3) Escape.uP(pts[3])
},
isCap,
null);
}
Object plane = Escape.uP(s);
if (plane instanceof P4) return TempArray.getSlabObjectType(T.plane, plane, isCap, null);
} catch (Exception e) {
//
}
return null;
}
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");
}
}
void loadImage(String name, String echoName) {
Object image = null;
Object info = null;
String fullPathName = "";
while (true) {
if (name == null) break;
String[] names = classifyName(name, true);
if (names == null) {
fullPathName = "cannot read file name: " + name;
break;
}
GenericPlatform apiPlatform = viewer.apiPlatform;
fullPathName = names[0].replace('\\', '/');
if (fullPathName.indexOf("|") > 0) {
Object ret = getFileAsBytes(fullPathName, null, true);
if (!PT.isAB(ret)) {
fullPathName = "" + ret;
break;
}
image = (viewer.isJS ? ret : apiPlatform.createImage(ret));
} else if (viewer.isJS) {
} else if (urlTypeIndex(fullPathName) >= 0) {
try {
image = apiPlatform.createImage(new URL((URL) null, fullPathName, null));
} catch (Exception e) {
fullPathName = "bad URL: " + fullPathName;
break;
}
} else {
image = apiPlatform.createImage(fullPathName);
}
/** @j2sNative info = [echoName, fullPathName]; */
{
if (image == null) break;
}
try {
if (!apiPlatform.waitForDisplay(info, image)) {
image = null;
break;
}
/**
* note -- JavaScript just returns immediately, because we must wait for the image to load,
* and it is single-threaded
*
* @j2sNative fullPathName = null; break;
*/
{
if (apiPlatform.getImageWidth(image) < 1) {
fullPathName = "invalid or missing image " + fullPathName;
image = null;
}
break;
}
} catch (Exception e) {
System.out.println(e.toString());
fullPathName = e.toString() + " opening 4 " + fullPathName;
image = null;
break;
}
}
viewer.loadImageData(image, fullPathName, echoName, null);
}
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;
}
@Override
protected String readColorData() {
if (!jvxlDataIsColorMapped) return "";
// overloads SurfaceReader
// standard jvxl file read for color
int vertexCount = jvxlData.vertexCount = meshData.vertexCount;
// the problem is that the new way to read data in Marching Cubes
// is to ignore all points that are NaN. But then we also have to
// remove those points from the color string.
short[] colixes = meshData.vertexColixes;
float[] vertexValues = meshData.vertexValues;
/*
* haveReadColorData?
= (isJvxl ? jvxlColorDataRead : "");
if (isJvxl && strValueTemp.length() == 0) {
Logger
.error("You cannot use JVXL data to map onto OTHER data, because it only contains the data for one surface. Use ISOSURFACE \"file.jvxl\" not ISOSURFACE .... MAP \"file.jvxl\".");
return "";
}
*/
if ("none".equals(jvxlColorEncodingRead)) {
jvxlData.vertexColors = new int[vertexCount];
int[] nextc = new int[1];
int n = PT.parseIntNext(jvxlColorDataRead, nextc);
n = Math.min(n, vertexCount);
String[] tokens = PT.getTokens(jvxlColorDataRead.substring(nextc[0]));
boolean haveTranslucent = false;
float trans = jvxlData.translucency;
int lastColor = 0;
for (int i = 0; i < n; i++)
// colix will be one of 8 shades of translucent if A in ARGB is not FF.
try {
int c = getColor(tokens[i]);
if (c == 0) c = lastColor;
else lastColor = c;
colixes[i] = C.getColixTranslucent(jvxlData.vertexColors[i] = c);
if (C.isColixTranslucent(colixes[i])) haveTranslucent = true;
else if (trans != 0) colixes[i] = C.getColixTranslucent3(colixes[i], true, trans);
} catch (Exception e) {
Logger.info("JvxlXmlReader: Cannot interpret color code: " + tokens[i]);
// ignore this color if parsing error
}
if (haveTranslucent && trans == 0) {
// set to show in pass2
jvxlData.translucency = 0.5f;
}
return "-";
}
if (params.colorEncoder == null) params.colorEncoder = new ColorEncoder(null);
params.colorEncoder.setColorScheme(null, false);
params.colorEncoder.setRange(
params.valueMappedToRed, params.valueMappedToBlue, params.isColorReversed);
Logger.info(
"JVXL reading color data mapped min/max: "
+ params.mappedDataMin
+ "/"
+ params.mappedDataMax
+ " for "
+ vertexCount
+ " vertices."
+ " using encoding keys "
+ colorFractionBase
+ " "
+ colorFractionRange);
Logger.info(
"mapping red-->blue for "
+ params.valueMappedToRed
+ " to "
+ params.valueMappedToBlue
+ " colorPrecision:"
+ jvxlData.isJvxlPrecisionColor);
boolean getValues = (Float.isNaN(valueMin));
if (getValues) setValueMinMax();
float contourPlaneMinimumValue = Float.MAX_VALUE;
float contourPlaneMaximumValue = -Float.MAX_VALUE;
if (colixes == null || colixes.length < vertexCount)
meshData.vertexColixes = colixes = new short[vertexCount];
// hasColorData = true;
short colixNeg = 0, colixPos = 0;
if (params.colorBySign) {
colixPos = C.getColix(params.isColorReversed ? params.colorNeg : params.colorPos);
colixNeg = C.getColix(params.isColorReversed ? params.colorPos : params.colorNeg);
}
int vertexIncrement = meshData.vertexIncrement;
// here's the problem: we are assuming here that vertexCount == nPointsRead
boolean needContourMinMax = (params.mappedDataMin == Float.MAX_VALUE);
for (int i = 0; i < vertexCount; i += vertexIncrement) {
float value;
if (getValues) value = vertexValues[i] = getNextValue();
else value = vertexValues[i];
if (needContourMinMax) {
if (value < contourPlaneMinimumValue) contourPlaneMinimumValue = value;
if (value > contourPlaneMaximumValue) contourPlaneMaximumValue = value;
}
}
if (needContourMinMax) {
params.mappedDataMin = contourPlaneMinimumValue;
params.mappedDataMax = contourPlaneMaximumValue;
}
if (jvxlData.colorScheme != null)
for (int i = 0; i < vertexCount; i += vertexIncrement) {
float value = vertexValues[i];
// note: these are just default colorings
// orbital color had a bug through 11.2.6/11.3.6
if (marchingSquares != null && params.isContoured) {
marchingSquares.setContourData(i, value);
continue;
}
short colix =
(!params.colorBySign
? params.colorEncoder.getColorIndex(value)
: (params.isColorReversed ? value > 0 : value <= 0) ? colixNeg : colixPos);
colixes[i] = C.getColixTranslucent3(colix, true, jvxlData.translucency);
}
return jvxlColorDataRead + "\n";
}
private WebExport(JmolViewer vwr, HistoryFile hFile) {
super(new BorderLayout());
historyFile = hFile;
remoteAppletPath = historyFile.getProperty("webMakerAppletPath", "..");
localAppletPath = historyFile.getProperty("webMakerLocalAppletPath", "..");
pageAuthorName = historyFile.getProperty("webMakerPageAuthorName",
GT._("Jmol Web Page Maker"));
popInWidth=PT.parseInt(historyFile.getProperty("webMakerPopInWidth", "300"));
popInHeight=PT.parseInt(historyFile.getProperty("webMakerPopInHeight", "300"));
scriptButtonPercent = PT.parseInt(historyFile.getProperty(
"webMakerScriptButtonPercent", "60"));
//Define the tabbed pane
JTabbedPane mainTabs = new JTabbedPane();
//Create file chooser
JFileChooser fc = new JFileChooser();
webPanels = new WebPanel[2];
if (runStatus != STAND_ALONE) {
//Add tabs to the tabbed pane
JPanel introPanel = new JPanel();
String introFileName = "WebExportIntro";
URL url = GuiMap.getHtmlResource(this, introFileName);
if (url == null) {
System.err.println(GT.o(GT._("Couldn't find file: {0}"), introFileName+".html"));
}
JEditorPane intro = new JEditorPane();
if (url != null) {
try {
intro.setPage(url);
} catch (IOException e) {
System.err.println("Attempted to read a bad URL: " + url);
}
}
intro.setEditable(false);
JScrollPane introPane = new JScrollPane(intro);
introPane.setMaximumSize(new Dimension(450, 350));
introPane.setPreferredSize(new Dimension(400, 300));
introPanel.setLayout(new BorderLayout());
introPanel.add(introPane);
introPanel.setMaximumSize(new Dimension(450, 350));
introPanel.setPreferredSize(new Dimension(400, 300));
mainTabs.add(GT._("Introduction"), introPanel);
webPanels[0] = new PopInJmol(vwr, fc, webPanels, 0);
webPanels[1] = new ScriptButtons(vwr, fc, webPanels, 1);
int w = Integer.parseInt(historyFile.getProperty("webMakerInfoWidth",
"300"));
int h = Integer.parseInt(historyFile.getProperty("webMakerInfoHeight",
"350"));
mainTabs.addTab(GT._("Pop-In Jmol"), webPanels[0].getPanel(w, h));
mainTabs.addTab(GT._("ScriptButton Jmol"), webPanels[1].getPanel(w, h));
// Uncomment to activate the test panel
// Test TestCreator = new Test((Viewer)vwr);
// JComponent Test = TestCreator.Panel();
// Maintabs.addTab("Tests",Test);
}
showMoleculesAndOrbitals = (runStatus == STAND_ALONE || JmolViewer
.checkOption(vwr, "webMakerAllTabs"));
if (showMoleculesAndOrbitals) {
//mainTabs.addTab("Orbitals", (new Orbitals()).getPanel());
//mainTabs.addTab("Molecules", (new Molecules()).getPanel());
}
//The LogPanel should always be the last one
mainTabs.addTab(GT._("Log"), LogPanel.getPanel());
//Add the tabbed pane to this panel
add(mainTabs);
//Create the small log
add(LogPanel.getMiniPanel(), BorderLayout.SOUTH);
//Uncomment the following line to use scrolling tabs.
//tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
}
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();
}
}
/**
* 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;
}
/**
* decode triangle data found within <jvxlTriangleData> element as created with
* jvxlEncodeTriangleData (see above)
*
* @param tdata tag and contents
* @param edgeData
* @param colorData
* @throws Exception
*/
void jvxlDecodeTriangleData(String tdata, String edgeData, String colorData) throws Exception {
int nTriangles = parseIntStr(XmlReader.getXmlAttrib(tdata, "count"));
if (nTriangles < 0) return;
int[] nextc = new int[1];
int nColors = (colorData == null ? -1 : PT.parseIntNext(colorData, nextc));
int color = 0;
Logger.info("Reading " + nTriangles + " triangles");
String encoding = getEncoding(tdata);
tdata = getData(tdata, "jvxlTriangleData");
String edata = getData(edgeData, "jvxlTriangleEdgeData");
int[] vertex = new int[3];
int[] nextp = new int[1];
int[] nexte = null;
int edgeMask = 7;
boolean haveEdgeInfo;
boolean haveEncoding = !"none".equals(encoding);
if (haveEncoding) {
tdata = JvxlCoder.jvxlDecompressString(tdata);
edata = JvxlCoder.jvxlDecompressString(edata).trim();
haveEdgeInfo = (edata.length() == nTriangles);
} else {
int n = PT.parseIntNext(tdata, nextp);
haveEdgeInfo = (edata.length() > 0);
if (haveEdgeInfo) {
nexte = new int[1];
PT.parseIntNext(edata, nexte); // throw away count
} else if (n > 0) {
Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count=" + n + "; expected " + nTriangles);
}
}
for (int i = 0, v = 0, p = 0, pt = -1; i < nTriangles; ) {
if (haveEncoding) {
char ch = tdata.charAt(++pt);
int diff;
switch (ch) {
case '!':
diff = 0;
break;
case '+':
case '.':
case ' ':
case '\n':
case '\r':
case '\t':
case ',':
continue;
case '-':
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
nextp[0] = pt;
diff = PT.parseIntNext(tdata, nextp);
pt = nextp[0] - 1;
break;
default:
diff = ch - 92; // '\' character
}
v += diff;
} else {
v = PT.parseIntNext(tdata, nextp) - 1;
}
vertex[p] = v;
if (++p == 3) {
p = 0;
if (haveEdgeInfo) {
edgeMask =
(nexte == null ? edata.charAt(i) - '0' : javajs.util.PT.parseIntNext(edata, nexte));
if (edgeMask < 0 || edgeMask > 7) edgeMask = 7;
}
if (nColors > 0) {
int c = PT.parseIntNext(colorData, nextc);
if (c == Integer.MIN_VALUE) nColors = 0;
else color = c;
nColors--;
}
addTriangleCheck(vertex[0], vertex[1], vertex[2], edgeMask, 0, false, color);
i++;
}
}
}
static String nextStringToken(ScriptTokenizer eachParam, boolean removeQuotes) {
String s = eachParam.nextToken();
return (removeQuotes && s.charAt(0) == '"' && s.endsWith("\"") && s.length() > 1
? PT.trimQuotes(s)
: s);
}
/**
* [0] and [2] may return same as [1] in the case of a local unsigned applet.
*
* @param name
* @param isFullLoad false only when just checking path
* @return [0] full path name, [1] file name without path, [2] full URL
*/
private String[] classifyName(String name, boolean isFullLoad) {
if (name == null) return new String[] {null};
boolean doSetPathForAllFiles = (pathForAllFiles.length() > 0);
if (name.startsWith("?")) {
if ((name = viewer.dialogAsk("Load", name.substring(1))) == null)
return new String[] {isFullLoad ? "#CANCELED#" : null};
doSetPathForAllFiles = false;
}
GenericFileInterface file = null;
URL url = null;
String[] names = null;
if (name.startsWith("cache://")) {
names = new String[3];
names[0] = names[2] = name;
names[1] = stripPath(names[0]);
return names;
}
name = viewer.resolveDatabaseFormat(name);
if (name.indexOf(":") < 0 && name.indexOf("/") != 0)
name = addDirectory(viewer.getDefaultDirectory(), name);
if (appletDocumentBaseURL == null) {
// This code is for the app or signed local applet
// -- no local file reading for headless
if (urlTypeIndex(name) >= 0
|| viewer.haveAccess(ACCESS.NONE)
|| viewer.haveAccess(ACCESS.READSPT) && !name.endsWith(".spt") && !name.endsWith("/")) {
try {
url = new URL((URL) null, name, null);
} catch (MalformedURLException e) {
return new String[] {isFullLoad ? e.toString() : null};
}
} else {
file = viewer.apiPlatform.newFile(name);
String s = file.getFullPath();
// local unsigned applet may have access control issue here and get a null return
String fname = file.getName();
names =
new String[] {
(s == null ? fname : s), fname, (s == null ? fname : "file:/" + s.replace('\\', '/'))
};
}
} else {
// This code is only for the non-local applet
try {
if (name.indexOf(":\\") == 1 || name.indexOf(":/") == 1) name = "file:/" + name;
// else if (name.indexOf("/") == 0 && viewer.isSignedApplet())
// name = "file:" + name;
url = new URL(appletDocumentBaseURL, name, null);
} catch (MalformedURLException e) {
return new String[] {isFullLoad ? e.toString() : null};
}
}
if (url != null) {
names = new String[3];
names[0] = names[2] = url.toString();
names[1] = stripPath(names[0]);
}
if (doSetPathForAllFiles) {
String name0 = names[0];
names[0] = pathForAllFiles + names[1];
Logger.info("FileManager substituting " + name0 + " --> " + names[0]);
}
if (isFullLoad && (file != null || urlTypeIndex(names[0]) == URL_LOCAL)) {
String path = (file == null ? PT.trim(names[0].substring(5), "/") : names[0]);
int pt = path.length() - names[1].length() - 1;
if (pt > 0) {
path = path.substring(0, pt);
setLocalPath(viewer, path, true);
}
}
return names;
}