private void setProp(Ellipsoid e, int mode, Object value) {
// "ax ce co de eq mo on op sc tr"
// 0 1 2 3 4 5 6 7 8 9
switch (mode) {
case 0: // axes
e.setTensor(
((Tensor) Interface.getUtil("Tensor", vwr, "script")).setFromAxes((V3[]) value));
return;
case 1: // center
e.setCenter((P3) value);
return;
case 2: // color
e.colix = C.getColixO(value);
return;
case 3: // delete
simpleEllipsoids.remove(e.id);
return;
case 4: // equation
e.setTensor(
((Tensor) Interface.getUtil("Tensor", vwr, "script"))
.setFromThermalEquation((double[]) value, null));
return;
case 5: // modelindex
e.tensor.modelIndex = ((Integer) value).intValue();
return;
case 6: // on
e.isOn = ((Boolean) value).booleanValue();
return;
case 7: // options
e.options = ((String) value).toLowerCase();
return;
case 8: // scale
e.setScale(((Float) value).floatValue(), false);
return;
case 9: // translucency
e.colix = C.getColixTranslucent3(e.colix, value.equals("translucent"), translucentLevel);
return;
}
return;
}
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);
}
}
private void drawSegment(Atom atomA, Atom atomB, short colixA, short colixB, float max) {
if (atomA.getNBackbonesDisplayed() == 0
|| atomB.getNBackbonesDisplayed() == 0
|| ms.isAtomHidden(atomB.i)
|| !isDataFrame && atomA.distanceSquared(atomB) > max) return;
colixA = C.getColixInherited(colixA, atomA.colixAtom);
colixB = C.getColixInherited(colixB, atomB.colixAtom);
if (!isExport && !isPass2 && !setBioColix(colixA) && !setBioColix(colixB)) return;
int xA = atomA.sX, yA = atomA.sY, zA = atomA.sZ;
int xB = atomB.sX, yB = atomB.sY, zB = atomB.sZ;
int mad = this.mad;
if (max == 1000) mad = mad >> 1;
if (mad < 0) {
g3d.drawLine(colixA, colixB, xA, yA, zA, xB, yB, zB);
} else {
int width =
(int)
(exportType == GData.EXPORT_CARTESIAN
? mad
: vwr.tm.scaleToScreen((zA + zB) / 2, mad));
g3d.fillCylinderXYZ(colixA, colixB, GData.ENDCAPS_SPHERICAL, width, xA, yA, zA, xB, yB, zB);
}
}
@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";
}
protected void jvxlReadSurfaceInfo() throws Exception {
String s;
String data = xr.getXmlData("jvxlSurfaceInfo", null, true, true);
isXLowToHigh = XmlReader.getXmlAttrib(data, "isXLowToHigh").equals("true");
jvxlCutoff = parseFloatStr(XmlReader.getXmlAttrib(data, "cutoff"));
if (!Float.isNaN(jvxlCutoff)) Logger.info("JVXL read: cutoff " + jvxlCutoff);
int nContourData = parseIntStr(XmlReader.getXmlAttrib(data, "nContourData"));
haveContourData = (nContourData > 0);
params.isContoured = XmlReader.getXmlAttrib(data, "contoured").equals("true");
if (params.isContoured) {
int nContoursRead = parseIntStr(XmlReader.getXmlAttrib(data, "nContours"));
if (nContoursRead <= 0) {
nContoursRead = 0;
} else {
s = XmlReader.getXmlAttrib(data, "contourValues");
if (s.length() > 0) {
jvxlData.contourValues = params.contoursDiscrete = parseFloatArrayStr(s);
Logger.info("JVXL read: contourValues " + Escape.eAF(jvxlData.contourValues));
}
s = XmlReader.getXmlAttrib(data, "contourColors");
if (s.length() > 0) {
jvxlData.contourColixes = params.contourColixes = C.getColixArray(s);
jvxlData.contourColors = C.getHexCodes(jvxlData.contourColixes);
Logger.info("JVXL read: contourColixes " + C.getHexCodes(jvxlData.contourColixes));
}
params.contourFromZero = XmlReader.getXmlAttrib(data, "contourFromZero").equals("true");
}
params.nContours = (haveContourData ? nContourData : nContoursRead);
// TODO ? params.contourFromZero = false; // MEP data to complete the plane
}
jvxlData.nVertexColors = parseIntStr(XmlReader.getXmlAttrib(data, "nVertexColors"));
params.isBicolorMap = XmlReader.getXmlAttrib(data, "bicolorMap").equals("true");
if (params.isBicolorMap) {
// TODO -- not quite right, because
s = XmlReader.getXmlAttrib(data, "colorPositive");
if (s.length() > 0
&& params.colorRgb == Integer.MIN_VALUE
&& params.colorPos == Parameters.defaultColorPositive)
params.colorPos = CU.getArgbFromString(s);
s = XmlReader.getXmlAttrib(data, "colorNegative");
if (s.length() > 0
&& params.colorRgb == Integer.MIN_VALUE
&& params.colorNeg == Parameters.defaultColorNegative)
params.colorNeg = CU.getArgbFromString(s);
}
if (params.isBicolorMap || params.colorBySign) jvxlCutoff = 0;
jvxlDataIsColorMapped =
((params.colorRgb == Integer.MIN_VALUE || params.colorRgb == Integer.MAX_VALUE)
&& (params.isBicolorMap || XmlReader.getXmlAttrib(data, "colorMapped").equals("true")));
// isJvxlPrecisionColor is for information only -- will be superceded by encoding attribute of
// jvxlColorData
jvxlData.isJvxlPrecisionColor = XmlReader.getXmlAttrib(data, "precisionColor").equals("true");
jvxlData.jvxlDataIsColorDensity =
params.colorDensity =
(params.colorRgb == Integer.MIN_VALUE
&& XmlReader.getXmlAttrib(data, "colorDensity").equals("true"));
if (jvxlData.jvxlDataIsColorDensity && Float.isNaN(params.pointSize)) {
s = XmlReader.getXmlAttrib(data, "pointSize");
if (s.length() > 0) jvxlData.pointSize = params.pointSize = parseFloatStr(s);
}
s = XmlReader.getXmlAttrib(data, "allowVolumeRender");
jvxlData.allowVolumeRender =
params.allowVolumeRender = (s.length() == 0 || s.equalsIgnoreCase("true"));
s = XmlReader.getXmlAttrib(data, "plane");
if (s.indexOf("{") >= 0) {
params.thePlane = null;
params.mapLattice = null;
try {
params.thePlane = (P4) Escape.uP(s);
s = XmlReader.getXmlAttrib(data, "maplattice");
Logger.info("JVXL read: plane " + params.thePlane);
if (s.indexOf("{") >= 0) {
params.mapLattice = (P3) Escape.uP(s);
Logger.info("JVXL read: mapLattice " + params.mapLattice);
}
if (params.scale3d == 0)
params.scale3d = parseFloatStr(XmlReader.getXmlAttrib(data, "scale3d"));
if (Float.isNaN(params.scale3d)) params.scale3d = 0;
} catch (Exception e) {
if (params.thePlane == null) {
Logger.error("JVXL Error reading plane definition -- setting to 0 0 1 0 (z=0)");
params.thePlane = P4.new4(0, 0, 1, 0);
} else {
Logger.error("JVXL Error reading mapLattice definition -- ignored");
}
}
surfaceDataCount = 0;
edgeDataCount = 0;
} else {
params.thePlane = null;
surfaceDataCount = parseIntStr(XmlReader.getXmlAttrib(data, "nSurfaceInts"));
edgeDataCount = parseIntStr(XmlReader.getXmlAttrib(data, "nBytesUncompressedEdgeData"));
}
excludedVertexCount = parseIntStr(XmlReader.getXmlAttrib(data, "nExcludedVertexes"));
excludedTriangleCount = parseIntStr(XmlReader.getXmlAttrib(data, "nExcludedTriangles"));
invalidatedVertexCount = parseIntStr(XmlReader.getXmlAttrib(data, "nInvalidatedVertexes"));
s = XmlReader.getXmlAttrib(data, "slabInfo");
if (s.length() > 0) jvxlData.slabInfo = s;
colorDataCount =
Math.max(0, parseIntStr(XmlReader.getXmlAttrib(data, "nBytesUncompressedColorData")));
jvxlDataIs2dContour = (params.thePlane != null && jvxlDataIsColorMapped);
// new Jmol 12.1.50
jvxlData.color = XmlReader.getXmlAttrib(data, "color");
if (jvxlData.color.length() == 0 || jvxlData.color.indexOf("null") >= 0)
jvxlData.color = "orange";
jvxlData.translucency = parseFloatStr(XmlReader.getXmlAttrib(data, "translucency"));
if (Float.isNaN(jvxlData.translucency)) jvxlData.translucency = 0;
s = XmlReader.getXmlAttrib(data, "meshColor");
if (s.length() > 0) jvxlData.meshColor = s;
s = XmlReader.getXmlAttrib(data, "rendering");
if (s.length() > 0) jvxlData.rendering = s;
jvxlData.colorScheme = XmlReader.getXmlAttrib(data, "colorScheme");
if (jvxlData.colorScheme.length() == 0) jvxlData.colorScheme = null;
if (jvxlData.thisSet < 0) {
int n = parseIntStr(XmlReader.getXmlAttrib(data, "set"));
if (n > 0) jvxlData.thisSet = n - 1;
}
jvxlData.slabValue = parseIntStr(XmlReader.getXmlAttrib(data, "slabValue"));
jvxlData.isSlabbable = (XmlReader.getXmlAttrib(data, "slabbable").equalsIgnoreCase("true"));
jvxlData.diameter = parseIntStr(XmlReader.getXmlAttrib(data, "diameter"));
if (jvxlData.diameter == Integer.MIN_VALUE) jvxlData.diameter = 0;
if (jvxlDataIs2dContour) params.isContoured = true;
if (params.colorBySign) params.isBicolorMap = true;
boolean insideOut = XmlReader.getXmlAttrib(data, "insideOut").equals("true");
float dataMin = Float.NaN;
float dataMax = Float.NaN;
float red = Float.NaN;
float blue = Float.NaN;
if (jvxlDataIsColorMapped) {
dataMin = parseFloatStr(XmlReader.getXmlAttrib(data, "dataMinimum"));
dataMax = parseFloatStr(XmlReader.getXmlAttrib(data, "dataMaximum"));
red = parseFloatStr(XmlReader.getXmlAttrib(data, "valueMappedToRed"));
blue = parseFloatStr(XmlReader.getXmlAttrib(data, "valueMappedToBlue"));
if (Float.isNaN(dataMin)) {
dataMin = red = -1f;
dataMax = blue = 1f;
}
}
jvxlSetColorRanges(dataMin, dataMax, red, blue, insideOut);
}
protected short getLeadColix(int i) {
return C.getColixInherited(colixes[i], monomers[i].getLeadAtom().colixAtom);
}
@Override
public void setProperty(String propertyName, Object value, BS bs) {
// System.out.println(propertyName + " " + value + " " + bs);
if (propertyName == "thisID") {
if (initEllipsoids(value) && ellipsoidSet.size() == 0) {
String id = (String) value;
Ellipsoid e = Ellipsoid.getEmptyEllipsoid(id, vwr.am.cmi);
ellipsoidSet.addLast(e);
simpleEllipsoids.put(id, e);
}
return;
}
if ("atoms" == propertyName) {
selectedAtoms = (BS) value;
return;
}
if (propertyName == "deleteModelAtoms") {
int modelIndex = ((int[]) ((Object[]) value)[2])[0];
Iterator<Ellipsoid> e = simpleEllipsoids.values().iterator();
while (e.hasNext()) if (e.next().tensor.modelIndex == modelIndex) e.remove();
e = atomEllipsoids.values().iterator();
while (e.hasNext()) if (e.next().modelIndex == modelIndex) e.remove();
ellipsoidSet.clear();
return;
}
int mode = PROPERTY_MODES.indexOf((propertyName + " ").substring(0, 2));
if (ellipsoidSet.size() > 0) {
if ("translucentLevel" == propertyName) {
setPropS(propertyName, value, bs);
return;
}
if (mode >= 0)
for (int i = ellipsoidSet.size(); --i >= 0; ) setProp(ellipsoidSet.get(i), mode / 3, value);
return;
}
if ("color" == propertyName) {
short colix = C.getColixO(value);
byte pid = PAL.pidOf(value);
if (selectedAtoms != null) bs = selectedAtoms;
for (Ellipsoid e : atomEllipsoids.values())
if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1)) {
e.colix = getColixI(colix, pid, e.tensor.atomIndex1);
e.pid = pid;
}
return;
}
if ("on" == propertyName) {
boolean isOn = ((Boolean) value).booleanValue();
if (selectedAtoms != null) bs = selectedAtoms;
if (isOn) setSize(Integer.MAX_VALUE, bs);
for (Ellipsoid e : atomEllipsoids.values()) {
Tensor t = e.tensor;
if ((t.type.equals(typeSelected) || typeSelected.equals(t.altType))
&& t.isSelected(bs, -1)) {
e.isOn = isOn;
}
}
return;
}
if ("options" == propertyName) {
String options = ((String) value).toLowerCase().trim();
if (options.length() == 0) options = null;
if (selectedAtoms != null) bs = selectedAtoms;
if (options != null) setSize(Integer.MAX_VALUE, bs);
for (Ellipsoid e : atomEllipsoids.values())
if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1)) e.options = options;
return;
}
if ("params" == propertyName) {
Object[] data = (Object[]) value;
data[2] = null; // Jmol does not allow setting sizes this way from PyMOL yet
typeSelected = "0";
setSize(50, bs);
// onward...
}
if ("points" == propertyName) {
// Object[] o = (Object[]) value;
// setPoints((P3[]) o[1], (BS) o[2]);
return;
}
if ("scale" == propertyName) {
setSize((int) (((Float) value).floatValue() * 100), bs);
return;
}
if ("select" == propertyName) {
typeSelected = ((String) value).toLowerCase();
return;
}
if ("translucency" == propertyName) {
boolean isTranslucent = (value.equals("translucent"));
for (Ellipsoid e : atomEllipsoids.values())
if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
e.colix = C.getColixTranslucent3(e.colix, isTranslucent, translucentLevel);
return;
}
setPropS(propertyName, value, bs);
}
short getColix2() {
return C.getColixInherited(colix, atom2.colixAtom);
}
short getColix1() {
return C.getColixInherited(colix, atom1.colixAtom);
}
public void setTranslucent(boolean isTranslucent, float translucentLevel) {
colix = C.getColixTranslucent3(colix, isTranslucent, translucentLevel);
}