Revision: 18322
http://sourceforge.net/p/jmol/code/18322
Author: hansonr
Date: 2013-06-12 03:17:30 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
___version=13.0.17_dev_2013.06.11
bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx
INTERSECT yyy)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/render/MeshRenderer.java
trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
trunk/Jmol/src/org/jmol/shape/Mesh.java
trunk/Jmol/src/org/jmol/shape/MeshCollection.java
trunk/Jmol/src/org/jmol/shapespecial/Draw.java
trunk/Jmol/src/org/jmol/util/MeshSurface.java
trunk/Jmol/src/org/jmol/util/P4.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2013-06-12 03:17:05 UTC
(rev 18321)
+++ trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2013-06-12 03:17:30 UTC
(rev 18322)
@@ -57,8 +57,8 @@
protected boolean frontOnly;
protected boolean antialias;
protected boolean haveBsDisplay;
- protected boolean haveBsSlabDisplay;
- protected boolean haveBsSlabGhost;
+ protected boolean selectedPolyOnly;
+ protected boolean isGhostPass;
protected P4 thePlane;
protected P3 latticeOffset = new P3();
@@ -133,7 +133,7 @@
private boolean doRender;
protected boolean volumeRender;
- protected BS bsSlab;
+ protected BS bsPolygons;
private boolean setVariables() {
@@ -141,19 +141,20 @@
return false;
if (mesh.bsSlabGhost != null)
g3d.setColix(mesh.slabColix); // forces a second pass
- haveBsSlabGhost = (mesh.bsSlabGhost != null && (isExport ? exportPass == 2
+ isGhostPass = (mesh.bsSlabGhost != null && (isExport ? exportPass == 2
: g3d.isPass2()));
- isTranslucent = haveBsSlabGhost
+ isTranslucent = isGhostPass
|| C.isColixTranslucent(mesh.colix);
if (isTranslucent || volumeRender || mesh.bsSlabGhost != null)
needTranslucent = true;
doRender = (setColix(mesh.colix) || mesh.showContourLines);
- if (!doRender || haveBsSlabGhost && !(doRender =
g3d.setColix(mesh.slabColix))) {
+ if (!doRender || isGhostPass && !(doRender =
g3d.setColix(mesh.slabColix))) {
vertices = mesh.vertices;
return true;
}
vertices = (mesh.scale3d == 0 && mesh.mat4 == null ? mesh.vertices :
mesh.getOffsetVertices(thePlane));
if (mesh.lineData == null) {
+ // not a draw
if ((vertexCount = mesh.vertexCount) == 0)
return false;
normixes = mesh.normixes;
@@ -161,13 +162,15 @@
return false;
// this can happen when user switches windows
// during a surface calculation
-
haveBsDisplay = (mesh.bsDisplay != null);
- haveBsSlabDisplay = (haveBsSlabGhost || mesh.bsSlabDisplay != null);
- bsSlab = (haveBsSlabGhost ? mesh.bsSlabGhost
- : haveBsSlabDisplay ? mesh.bsSlabDisplay : null);
+ // mesh.bsSlabDisplay is a temporary slab effect
+ // that is reversible; these are the polygons to display
+ selectedPolyOnly = (isGhostPass || mesh.bsSlabDisplay != null);
+ bsPolygons = (isGhostPass ? mesh.bsSlabGhost
+ : selectedPolyOnly ? mesh.bsSlabDisplay : null);
+
frontOnly = !viewer.getSlabEnabled() && mesh.frontOnly
- && !mesh.isTwoSided && !haveBsSlabDisplay;
+ && !mesh.isTwoSided && !selectedPolyOnly;
screens = viewer.allocTempScreens(vertexCount);
if (frontOnly)
transformedVectors = g3d.getTransformedVertexVectors();
@@ -178,7 +181,7 @@
}
protected boolean setColix(short colix) {
- if (haveBsSlabGhost)
+ if (isGhostPass)
return true;
if (volumeRender && !isTranslucent)
colix = C.getColixTranslucent3(colix, true, 0.8f);
@@ -207,13 +210,13 @@
}
protected void render2b(boolean generateSet) {
- if (!g3d.setColix(haveBsSlabGhost ? mesh.slabColix : colix))
+ if (!g3d.setColix(isGhostPass ? mesh.slabColix : colix))
return;
if (mesh.showPoints || mesh.polygonCount == 0)
renderPoints();
- if (haveBsSlabGhost ? mesh.slabMeshType == T.mesh : mesh.drawTriangles)
+ if (isGhostPass ? mesh.slabMeshType == T.mesh : mesh.drawTriangles)
renderTriangles(false, mesh.showTriangles, false);
- if (haveBsSlabGhost ? mesh.slabMeshType == T.fill : mesh.fillTriangles)
+ if (isGhostPass ? mesh.slabMeshType == T.fill : mesh.fillTriangles)
renderTriangles(true, mesh.showTriangles, generateSet);
}
@@ -246,18 +249,18 @@
g3d.fillSphereI(4, screens[i]);
}
- protected BS bsPolygons = new BS();
+ protected BS bsPolygonsToExport = new BS();
protected void renderTriangles(boolean fill, boolean iShowTriangles,
boolean generateSet) {
int[][] polygonIndexes = mesh.polygonIndexes;
- colix = (haveBsSlabGhost ? mesh.slabColix : mesh.colix);
+ colix = (isGhostPass ? mesh.slabColix : mesh.colix);
// vertexColixes are only isosurface properties of IsosurfaceMesh, not Mesh
g3d.setColix(colix);
if (generateSet) {
if (frontOnly && fill)
frontOnly = false;
- bsPolygons.clearAll();
+ bsPolygonsToExport.clearAll();
}
for (int i = mesh.polygonCount; --i >= 0;) {
if (!isPolygonDisplayable(i))
@@ -318,7 +321,7 @@
case 3:
if (fill) {
if (generateSet) {
- bsPolygons.set(i);
+ bsPolygonsToExport.set(i);
continue;
}
if (iShowTriangles) {
@@ -339,7 +342,7 @@
continue;
if (fill) {
if (generateSet) {
- bsPolygons.set(i);
+ bsPolygonsToExport.set(i);
continue;
}
g3d.fillQuadrilateral3i(screens[iA], colix, nA, screens[iB], colix,
nB,
@@ -426,7 +429,7 @@
protected void exportSurface(short colix) {
mesh.normals = mesh.getNormals(vertices, null);
- mesh.bsPolygons = bsPolygons;
+ mesh.bsPolygons = bsPolygonsToExport;
mesh.offset = latticeOffset;
g3d.drawSurface(mesh, colix);
mesh.normals = null;
Modified: trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-06-12 03:17:05 UTC (rev 18321)
+++ trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-06-12 03:17:30 UTC (rev 18322)
@@ -23,9 +23,6 @@
*/
package org.jmol.rendersurface;
-
-
-
import org.jmol.jvxl.data.JvxlCoder;
import org.jmol.jvxl.readers.Parameters;
import org.jmol.render.MeshRenderer;
@@ -67,7 +64,9 @@
iShowNormals = viewer.getTestFlag(4);
showNumbers = viewer.getTestFlag(3);
isosurface = (Isosurface) shape;
- exportPass = (isExport ? 2 : 0);
+ // exporters will do two passes here if there is translucency
+ // first pass is #2 (translucent), then #1 (opaque).
+ exportPass = (isExport ? 2 : 0);
isNavigationMode = viewer.getBoolean(T.navigationmode);
int mySlabValue = Integer.MAX_VALUE;
int slabValue = g3d.getSlab();
@@ -84,7 +83,7 @@
if (renderMeshSlab(mySlabValue, slabValue)) {
if (!isExport)
renderInfo();
- if (isExport && haveBsSlabGhost) {
+ if (isExport && isGhostPass) {
exportPass = 1;
renderMeshSlab(mySlabValue, slabValue);
exportPass = 2;
@@ -274,7 +273,7 @@
try {
if (volumeRender)
g3d.volumeRender(true);
- boolean slabPoints = ((volumeRender || imesh.polygonCount == 0) &&
haveBsSlabDisplay);
+ boolean slabPoints = ((volumeRender || imesh.polygonCount == 0) &&
selectedPolyOnly);
int incr = imesh.vertexIncrement;
int diam;
if (imesh.diameter <= 0) {
@@ -297,7 +296,7 @@
&& imesh.vertexSets[i] != imesh.jvxlData.thisSet ||
!imesh.isColorSolid
&& imesh.vertexColixes != null && !setColix(imesh.vertexColixes[i])
|| haveBsDisplay && !imesh.bsDisplay.get(i)
- || slabPoints && !bsSlab.get(i))
+ || slabPoints && !bsPolygons.get(i))
continue;
hasColorRange = true; // maybe
if (showNumbers && screens[i].z > 10
@@ -346,7 +345,7 @@
protected void renderTriangles(boolean fill, boolean iShowTriangles,
boolean isExport) {
int[][] polygonIndexes = imesh.polygonIndexes;
- colix = (haveBsSlabGhost ? imesh.slabColix
+ colix = (isGhostPass ? imesh.slabColix
: !fill && imesh.meshColix != 0 ? imesh.meshColix : imesh.colix);
short[] vertexColixes = (!fill && imesh.meshColix != 0 ? null
: imesh.vertexColixes);
@@ -356,14 +355,14 @@
if (generateSet) {
if (frontOnly && fill)
frontOnly = false;
- bsPolygons.clearAll();
+ bsPolygonsToExport.clearAll();
}
if (exportType == GData.EXPORT_CARTESIAN) {
frontOnly = false;
}
- boolean colorSolid = (haveBsSlabGhost && (!isBicolorMap)
+ boolean colorSolid = (isGhostPass && (!isBicolorMap)
|| vertexColixes == null || imesh.isColorSolid);
- boolean noColor = (haveBsSlabGhost && !isBicolorMap
+ boolean noColor = (isGhostPass && !isBicolorMap
|| vertexColixes == null || !fill && imesh.meshColix != 0);
boolean isPlane = (imesh.jvxlData.jvxlPlane != null);
short colix = this.colix;
@@ -386,7 +385,7 @@
hasColorRange = !colorSolid && !isBicolorMap;
for (int i = imesh.polygonCount; --i >= 0;) {
int[] polygon = polygonIndexes[i];
- if (polygon == null || haveBsSlabDisplay && !bsSlab.get(i))
+ if (polygon == null || selectedPolyOnly && !bsPolygons.get(i))
continue;
int iA = polygon[0];
int iB = polygon[1];
@@ -420,7 +419,7 @@
if (isBicolorMap) {
if (colixA != colixB || colixB != colixC)
continue;
- if (haveBsSlabGhost)
+ if (isGhostPass)
colixA = colixB = colixC = C.copyColixTranslucency(
imesh.slabColix, colixA);
}
@@ -438,7 +437,7 @@
}
if (fill) {
if (generateSet) {
- bsPolygons.set(i);
+ bsPolygonsToExport.set(i);
continue;
}
if (iB == iC) {
Modified: trunk/Jmol/src/org/jmol/shape/Mesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Mesh.java 2013-06-12 03:17:05 UTC (rev
18321)
+++ trunk/Jmol/src/org/jmol/shape/Mesh.java 2013-06-12 03:17:30 UTC (rev
18322)
@@ -129,9 +129,9 @@
bsDisplay = null;
bsSlabDisplay = null;
bsSlabGhost = null;
+ bsTransPolygons = null;
cappingObject = null;
colix = C.GOLD;
- useColix = true;
colorDensity = false;
connections = null;
diameter = 0;
@@ -145,9 +145,10 @@
lattice = null;
mat4 = null;
normixes = null;
- scale3d = 0;
polygonIndexes = null;
+ polygonTranslucencies = null;
scale = 1;
+ scale3d = 0;
showContourLines = false;
showPoints = false;
showTriangles = false; //as distinct entities
@@ -156,6 +157,7 @@
spanningVectors = null;
title = null;
unitCell = null;
+ useColix = true;
vertexCount0 = polygonCount0 = vertexCount = polygonCount = 0;
vertices = null;
volumeRenderPointSize = 0.15f;
@@ -413,24 +415,24 @@
}
return bs;
}
+//
+// BS getVisibleGhostBitSet() {
+// BS bs = new BS();
+// if (polygonCount == 0 && bsSlabGhost != null)
+// BSUtil.copy2(bsSlabGhost, bs);
+// else
+// for (int i = polygonCount; --i >= 0;)
+// if (bsSlabGhost == null || bsSlabGhost.get(i)) {
+// int[] vertexIndexes = polygonIndexes[i];
+// if (vertexIndexes == null)
+// continue;
+// bs.set(vertexIndexes[0]);
+// bs.set(vertexIndexes[1]);
+// bs.set(vertexIndexes[2]);
+// }
+// return bs;
+// }
- BS getVisibleGhostBitSet() {
- BS bs = new BS();
- if (polygonCount == 0 && bsSlabGhost != null)
- BSUtil.copy2(bsSlabGhost, bs);
- else
- for (int i = polygonCount; --i >= 0;)
- if (bsSlabGhost == null || bsSlabGhost.get(i)) {
- int[] vertexIndexes = polygonIndexes[i];
- if (vertexIndexes == null)
- continue;
- bs.set(vertexIndexes[0]);
- bs.set(vertexIndexes[1]);
- bs.set(vertexIndexes[2]);
- }
- return bs;
- }
-
public void setTokenProperty(int tokProp, boolean bProp) {
switch (tokProp) {
case T.notfrontonly:
Modified: trunk/Jmol/src/org/jmol/shape/MeshCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2013-06-12 03:17:05 UTC
(rev 18321)
+++ trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2013-06-12 03:17:30 UTC
(rev 18322)
@@ -354,8 +354,12 @@
return;
case T.translucent:
m.setTranslucent(bProp, translucentLevel);
+ // color isosurface translucent clears the slab
if (bProp && m.bsSlabGhost != null)
m.resetSlab();
+ // color isosurface translucent or opaque clears all special translucent
polygons
+ if (m.bsTransPolygons != null)
+ m.resetTransPolygons();
return;
default:
m.setTokenProperty(tokProp, bProp);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2013-06-12 03:17:05 UTC
(rev 18321)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2013-06-12 03:17:30 UTC
(rev 18322)
@@ -435,27 +435,28 @@
}
private void initDraw() {
+ boundBox = null;
+ bsAllModels = null;
colix = C.ORANGE;
color = 0xFFFFFFFF;
- newScale = 0;
+ diameter = 0;
+ explicitID = false;
+ indicatedModelIndex = -1;
+ intersectID = null;
+ isCurve = isArc = isArrow = isPlane = isCircle = isCylinder = isLine =
false;
isFixed = isReversed = isRotated45 = isCrossed = noHead = isBarb = false;
- isCurve = isArc = isArrow = isPlane = isCircle = isCylinder = isLine =
false;
- isVertices = isPerpendicular = isVector = false;
+ isPerpendicular = isVertices = isVector = false;
isValid = true;
length = Float.MAX_VALUE;
- diameter = 0;
- width = 0;
- indicatedModelIndex = -1;
+ lineData = null;
+ newScale = 0;
+ nidentifiers = nbitsets = 0;
offset = null;
plane = null;
polygon = null;
- nidentifiers = nbitsets = 0;
+ slabData = null;
vData = new JmolList<Object[]>();
- bsAllModels = null;
- intersectID = null;
- slabData = null;
- boundBox = null;
- explicitID = false;
+ width = 0;
setPropertySuper("thisID", MeshCollection.PREVIOUS_MESH_ID, null);
}
@@ -638,7 +639,8 @@
@Override
protected void clean() {
for (int i = meshCount; --i >= 0;)
- if (meshes[i] == null || meshes[i].vertexCount == 0 &&
meshes[i].connections == null)
+ if (meshes[i] == null || meshes[i].vertexCount == 0
+ && meshes[i].connections == null && meshes[i].lineData == null)
deleteMeshI(i);
}
@@ -1356,9 +1358,11 @@
int n = dmesh.lineData.size();
for (int j = 0; j < n;) {
P3[] pts = dmesh.lineData.get(j);
- str.append(Escape.eP(pts[0]));
- str.append(" ");
- str.append(Escape.eP(pts[1]));
+ String s = Escape.eP(pts[0]);
+ str.append(s.substring(1, s.length() - 1));
+ str.append(",");
+ s = Escape.eP(pts[1]);
+ str.append(s.substring(1, s.length() - 1));
if (++j < n)
str.append(", ");
}
Modified: trunk/Jmol/src/org/jmol/util/MeshSurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshSurface.java 2013-06-12 03:17:05 UTC
(rev 18321)
+++ trunk/Jmol/src/org/jmol/util/MeshSurface.java 2013-06-12 03:17:30 UTC
(rev 18322)
@@ -20,6 +20,7 @@
public int polygonCount;
public int[][] polygonIndexes;
+ public float[] polygonTranslucencies;
public boolean isTriangleSet; // just a set of flat polygons
public boolean haveQuads;
@@ -215,8 +216,20 @@
public BS bsSlabDisplay;
public BS bsSlabGhost;
+ public BS bsTransPolygons;
public int slabMeshType;
public short slabColix;
+
+ /**
+ * Must create bsTransPolygons, polygonTranslucencies,
+ * and new triangle set for partially translucent polygons
+ *
+ * @param bsVertices
+ */
+ public void setTranslucentVertices(BS bsVertices) {
+ //TODO
+
+ }
public void setSlab(BS bsDisplay, BS bsGhost, String type,
String color, float translucency) {
@@ -249,6 +262,21 @@
new Float[] {Float.valueOf(min), Float.valueOf(max)}, Boolean.FALSE,
null };
}
+ public void resetTransPolygons() {
+ boolean isTranslucent = C.isColixTranslucent(colix);
+ float translucentLevel = C.getColixTranslucencyFractional(colix);
+ for (int i = 0; i < polygonCount; i++)
+ if (bsTransPolygons.get(i)) {
+ if (!setABC(i))
+ continue;
+ vertexColixes[iA] = C.getColixTranslucent3(vertexColixes[iA],
isTranslucent, translucentLevel);
+ vertexColixes[iB] = C.getColixTranslucent3(vertexColixes[iB],
isTranslucent, translucentLevel);
+ vertexColixes[iC] = C.getColixTranslucent3(vertexColixes[iC],
isTranslucent, translucentLevel);
+ }
+ bsTransPolygons = null;
+ polygonTranslucencies = null;
+ }
+
public void resetSlab() {
slabPolygons(getSlabObject(T.none, null, false, null), false);
}
Modified: trunk/Jmol/src/org/jmol/util/P4.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/P4.java 2013-06-12 03:17:05 UTC (rev
18321)
+++ trunk/Jmol/src/org/jmol/util/P4.java 2013-06-12 03:17:30 UTC (rev
18322)
@@ -46,7 +46,7 @@
public static P4 newPt(P4 value) {
P4 pt = new P4();
- pt.set(value.x, value.y, value.z, value.w);
+ pt.set(value.x, value.y, value.z, value.w);
return pt;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-12 03:17:05 UTC
(rev 18321)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-12 03:17:30 UTC
(rev 18322)
@@ -11,9 +11,14 @@
___JmolVersion="13.1.17_dev_2013.06.08"
+bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx
INTERSECT yyy)
+ -- needs revision to create DATA option; can be huge and very long to
process state file
+
+
TODO: PyMOL uniqueAtomSettings for transparency
-- will require by-vertex translucent option
+
code: color/translucent/opaque clean up in ScriptEvaluator
bug fix: load :2-butanone fails
bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different
data structure
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