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;
}
@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";
}
@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);
}
public void setTranslucent(boolean isTranslucent, float translucentLevel) {
colix = C.getColixTranslucent3(colix, isTranslucent, translucentLevel);
}