Revision: 18315
http://sourceforge.net/p/jmol/code/18315
Author: hansonr
Date: 2013-06-08 12:30:43 +0000 (Sat, 08 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.07"
TODO: PyMOL EDM data saved from PyMOL 1.6?
TODO: PyMOL uniqueAtomSettings for mesh_color, surface_color, and transparency
-- color isosurface {xxxx} red translucent 0.5 ??
bug fix: jvxl reader ignores jvxlVertexColorData
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2013-06-08
12:30:13 UTC (rev 18314)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2013-06-08
12:30:43 UTC (rev 18315)
@@ -1169,6 +1169,10 @@
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: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-06-08
12:30:13 UTC (rev 18314)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-06-08
12:30:43 UTC (rev 18315)
@@ -267,15 +267,32 @@
// color $id red ({0:30 ....}) (atoms)
// color $id red [{0:30 ....}] (vertices)
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 "
- + C.getHexCode(colix);
- setProperty("color", Integer.valueOf(C.getArgb(colix)), null);
+ if (source == null) {
+ if (colix != 0) {
+ thisMesh.colorCommand = "color isosurface "
+ + C.getHexCode(colix);
+ setProperty("color", Integer.valueOf(C.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(C.getColixO(value), bs);
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2013-06-08
12:30:13 UTC (rev 18314)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2013-06-08
12:30:43 UTC (rev 18315)
@@ -528,7 +528,10 @@
// 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);
}
@@ -657,27 +660,30 @@
meshColix = C.getColixS(jvxlData.meshColor);
setJvxlDataRendering();
- isColorSolid = !jvxlData.isBicolorMap && jvxlData.vertexColors == null;
+ isColorSolid = !jvxlData.isBicolorMap && jvxlData.vertexColors == null
+ && 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, null, Float.NaN);
- }
- if (jvxlData.vertexColorMap != null)
- for (Map.Entry<String, BS> entry : jvxlData.vertexColorMap
- .entrySet()) {
+ 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, null, Float.NaN);
+ }
+ } else {
+ for (Map.Entry<String, BS> entry : jvxlData.vertexColorMap.entrySet())
{
BS bsMap = entry.getValue();
- short colix = C.copyColixTranslucency(this.colix, C
- .getColixS(entry.getKey()));
+ short colix = C.copyColixTranslucency(this.colix, C.getColixS(entry
+ .getKey()));
for (int i = bsMap.nextSetBit(0); i >= 0; i = bsMap.nextSetBit(i +
1))
vertexColixes[i] = colix;
}
- }
+ }
+ }
+
}
void setJvxlDataRendering() {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-08 12:30:13 UTC
(rev 18314)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-08 12:30:43 UTC
(rev 18315)
@@ -14,7 +14,8 @@
TODO: PyMOL EDM data saved from PyMOL 1.6?
TODO: PyMOL uniqueAtomSettings for mesh_color, surface_color, and transparency
-- color isosurface {xxxx} red translucent 0.5 ??
-
+
+bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems
new feature: set translucent
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