Revision: 18314
http://sourceforge.net/p/jmol/code/18314
Author: hansonr
Date: 2013-06-08 12:30:13 +0000 (Sat, 08 Jun 2013)
Log Message:
-----------
___version=13.0.17_dev_2013.06.07
bug fix: jvxl reader ignores jvxlVertexColorData
Modified Paths:
--------------
branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java
branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2013-06-07 23:32:18 UTC (rev 18313)
+++ branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2013-06-08 12:30:13 UTC (rev 18314)
@@ -1126,6 +1126,10 @@
params.state = Parameters.STATE_DATA_COLORED;
surfaceReader.applyColorScale();
}
+ if (jvxlData.vertexColorMap != null) {
+ jvxlData.vertexColorMap = null;
+ surfaceReader.hasColorData = false;
+ }
surfaceReader.jvxlUpdateInfo();
setMarchingSquares(surfaceReader.marchingSquares);
surfaceReader.discardTempData(false);
Modified: branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java
2013-06-07 23:32:18 UTC (rev 18313)
+++ branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java
2013-06-08 12:30:13 UTC (rev 18314)
@@ -233,15 +233,32 @@
if ("atomcolor" == propertyName) {
if (thisMesh != null) {
- if (thisMesh.vertexSource == null) {
+ boolean haveColors = (thisMesh.vertexSource != null);
+ if (haveColors)
+ for (int i = thisMesh.vertexCount; --i >= 0;)
+ if (thisMesh.vertexSource[i] < 0) {
+ haveColors = false;
+ break;
+ }
+ if (!haveColors) {
+ int[] source = thisMesh.vertexSource;
+ short[] vertexColixes = thisMesh.vertexColixes;
short colix = (!thisMesh.isColorSolid ? 0 : thisMesh.colix);
setProperty("init", null, null);
setProperty("map", Boolean.FALSE, null);
setProperty("property", new float[viewer.getAtomCount()], null);
- if (colix != 0) {
- thisMesh.colorCommand = "color isosurface "
- + Graphics3D.getHexCode(colix);
- setProperty("color", new Integer(Graphics3D.getArgb(colix)), null);
+ if (source == null) {
+ if (colix != 0) {
+ thisMesh.colorCommand = "color isosurface "
+ + Graphics3D.getHexCode(colix);
+ setProperty("color", Integer.valueOf(Graphics3D.getArgb(colix)),
null);
+ }
+ } else {
+ for (int i = thisMesh.vertexCount; --i >= 0;)
+ if (source[i] < 0)
+ source[i] = thisMesh.vertexSource[i];
+ thisMesh.vertexSource = source;
+ thisMesh.vertexColixes = vertexColixes;
}
}
thisMesh.colorAtoms(Graphics3D.getColix(value), bs);
Modified: branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2013-06-07 23:32:18 UTC (rev 18313)
+++ branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2013-06-08 12:30:13 UTC (rev 18314)
@@ -527,7 +527,10 @@
// TODO: color translucency?
if (isAtoms)
for (int i = 0; i < vertexCount; i++) {
- if (bs.get(vertexSource[i])) {
+ int pt = vertexSource[i];
+ if (pt < 0)
+ continue;
+ if (bs.get(pt)) {
vertexColixes[i] = colix;
bsVertices.set(i);
}
@@ -632,7 +635,8 @@
* scheme information, and vertex color mappings (as from COLOR ISOSURFACE
* {hydrophobic} WHITE), returning these settings when the JVXL file is
* opened.
- * @param colorRgb
+ *
+ * @param colorRgb
*/
void setColorsFromJvxlData(int colorRgb) {
diameter = jvxlData.diameter;
@@ -649,19 +653,20 @@
if (jvxlData.meshColor != null)
meshColix = Graphics3D.getColix(jvxlData.meshColor);
setJvxlDataRendering();
-
- isColorSolid = !jvxlData.isBicolorMap;
+
+ isColorSolid = !jvxlData.isBicolorMap && jvxlData.vertexColorMap == null;
if (colorEncoder != null) {
// bicolor map will be taken care of with params.isBicolorMap
- if (jvxlData.colorScheme != null) {
- String colorScheme = jvxlData.colorScheme;
- boolean isTranslucent = colorScheme.startsWith("translucent ");
- if (isTranslucent)
- colorScheme = colorScheme.substring(12);
- colorEncoder.setColorScheme(colorScheme, isTranslucent);
- remapColors(null, Float.NaN);
- }
- if (jvxlData.vertexColorMap != null)
+ if (jvxlData.vertexColorMap == null) {
+ if (jvxlData.colorScheme != null) {
+ String colorScheme = jvxlData.colorScheme;
+ boolean isTranslucent = colorScheme.startsWith("translucent ");
+ if (isTranslucent)
+ colorScheme = colorScheme.substring(12);
+ colorEncoder.setColorScheme(colorScheme, isTranslucent);
+ remapColors(null, Float.NaN);
+ }
+ } else {
for (Map.Entry<String, BitSet> entry : jvxlData.vertexColorMap
.entrySet()) {
BitSet bsMap = entry.getValue();
@@ -670,7 +675,8 @@
for (int i = bsMap.nextSetBit(0); i >= 0; i = bsMap.nextSetBit(i +
1))
vertexColixes[i] = colix;
}
- }
+ }
+ }
}
void setJvxlDataRendering() {
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-07
23:32:18 UTC (rev 18313)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-08
12:30:13 UTC (rev 18314)
@@ -11,6 +11,7 @@
___version=13.0.17_dev_2013.06.07
+bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems
=============================================================================
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