Revision: 20839
http://sourceforge.net/p/jmol/code/20839
Author: hansonr
Date: 2015-10-20 22:40:08 +0000 (Tue, 20 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.10.20"
bug fix: set platformSpeed 1 for pmesh fails
bug fix: polyhedron EDGES fails
bug fix: @{ {"hash":{0.1 0.1 0.1},...} } fails (attempts to turn "," into "OR")
-- solution is to not allow "," for OR within associative arrays
JmolVersion="14.4.0_2015.10.18"
bug fix: Polyhedra can have missing triangle for hexagonal faces
bug fix: calculate symmetry can break Jmol if unit cell has been changed
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java
branches/v14_4/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptTokenParser.java
branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java
branches/v14_4/Jmol/src/org/jmol/util/MeshCapper.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java 2015-10-19
06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java 2015-10-20
22:40:08 UTC (rev 20839)
@@ -290,7 +290,7 @@
protected void renderPoints() {
if (!mesh.isTriangleSet || mesh.pc < 0) {
for (int i = vertexCount; --i >= 0;)
- if (!frontOnly || normixes == null ||
transformedVectors[normixes[i]].z >= 0)
+ if (!frontOnly || normixes == null || isVisibleNormix(normixes[i]))
drawPoint(i, false);
return;
}
@@ -304,7 +304,7 @@
if (!isPolygonDisplayable(i))
continue;
int[] p = polygonIndexes[i];
- if (frontOnly && transformedVectors[normixes[i]].z < 0)
+ if (frontOnly && !isVisibleNormix(normixes[i]))
continue;
for (int j = p.length - 1; --j >= 0;) {
int pt = p[j];
@@ -370,7 +370,7 @@
int check;
if (mesh.isTriangleSet) {
short normix = normixes[i];
- if (!vwr.gdata.isDirectedTowardsCamera(normix))
+ if (frontOnly && !isVisibleNormix(normix))
continue;
if (fill) {
if (isPrecision)
@@ -458,6 +458,10 @@
exportSurface(colix);
}
+ private boolean isVisibleNormix(short normix) {
+ return (normix < 0 || transformedVectors[normix].z > 0);
+ }
+
private void drawTriangleBits(P3 screenA, short colixA, P3 screenB, short
colixB,
P3 screenC, short colixC, int check, int diam)
{
if (!antialias && diam == 1) {
Modified: branches/v14_4/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-19 06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-20 22:40:08 UTC (rev 20839)
@@ -114,14 +114,13 @@
if (!needTranslucent || g3d.setC(colix))
for (int i = planes.length; --i >= 0;) {
int[] pl = planes[i];
- //if (i != m)continue;
try {
g3d.fillTriangleTwoSided(normixes[i], sc[pl[0]], sc[pl[1]],
sc[pl[2]]);
} catch (Exception e) {
- System.out.println("heorhe");
+ System.out.println("PolyhedraRendererError");
}
- if (pl[3] >= 0)
- g3d.fillTriangleTwoSided(normixes[i], sc[pl[2]], sc[pl[3]],
sc[pl[0]]);
+// if (pl[3] >= 0)
+ // g3d.fillTriangleTwoSided(normixes[i], sc[pl[2]], sc[pl[3]],
sc[pl[0]]);
}
// edges are not drawn translucently ever
if (bsSelected != null && bsSelected.get(iAtom))
@@ -131,13 +130,7 @@
if (g3d.setC(C.getColixTranslucent3(colix, false, 0)))
for (int i = planes.length; --i >= 0;) {
int[] pl = planes[i];
- if (pl[3] < 0) {
drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], -pl[3]);
- } else {
- drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], 3);
- drawFace(normixes[i], sc[pl[0]], sc[pl[2]], sc[pl[3]], 6);
- }
-
}
return needTranslucent;
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptTokenParser.java
2015-10-19 06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptTokenParser.java
2015-10-20 22:40:08 UTC (rev 20839)
@@ -422,7 +422,7 @@
boolean haveString;
- private boolean clauseOr(boolean allowComma) {
+ private boolean clauseOr(boolean allowCommaAsOr) {
haveString = false;
if (!clauseAnd())
return false;
@@ -433,14 +433,14 @@
//OrNot: First OR, but if that makes no change, then NOT (special toggle)
int tok;
while ((tok = tokPeek())== T.opOr || tok == T.opXor
- || tok==T.opToggle|| allowComma && tok == T.comma) {
+ || tok==T.opToggle|| allowCommaAsOr && tok == T.comma) {
if (tok == T.comma && !haveString)
addSubstituteTokenIf(T.comma, T.tokenOr);
else
addNextToken();
if (!clauseAnd())
return false;
- if (allowComma && (lastToken.tok == T.rightbrace || lastToken.tok ==
T.bitset))
+ if (allowCommaAsOr && (lastToken.tok == T.rightbrace || lastToken.tok ==
T.bitset))
haveString = true;
}
return true;
@@ -596,7 +596,7 @@
if (isExpressionNext()) {
addTokenToPostfixToken(T.o(T.expressionBegin,
"implicitExpressionBegin"));
- if (!clauseOr(true))
+ if (!clauseOr(false))
return false;
if (lastToken != T.tokenCoordinateEnd) {
addTokenToPostfixToken(T.tokenExpressionEnd);
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-19
06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-20
22:40:08 UTC (rev 20839)
@@ -3330,7 +3330,7 @@
if (edgeParameterSeen)
error(ScriptError.ERROR_incompatibleArguments);
edgeParameterSeen = true;
- propertyName = T.nameOf(eval.iToken);
+ propertyName = T.nameOf(eval.theTok);
break;
case T.triangles:
case T.notriangles:
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2015-10-19 06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2015-10-20 22:40:08 UTC (rev 20839)
@@ -867,6 +867,8 @@
} else {
// set mask to exclude both of these.
int[] p10 = (int[]) ((Object[]) o)[0];
+ if (p10 == null)
+ return false;
int i0 = ((Integer) ((Object[]) o)[1]).intValue();
p10[3] = -((-p10[3]) ^ (1 << i0));
p1[3] = -((-p1[3]) ^ (1 << i));
@@ -879,6 +881,8 @@
}
}
// not supported for JavaScript faceList.removeObj(b);
+ htEdgeMap.put(edge, new Object[] { null });
+ htEdgeMap.put(edge0, new Object[] { null });
}
return true;
}
Modified: branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-19
06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-20
22:40:08 UTC (rev 20839)
@@ -318,12 +318,12 @@
@Override
public int[] getCellRange() {
- return symmetryInfo.cellRange;
+ return symmetryInfo == null ? null : symmetryInfo.cellRange;
}
@Override
public String getSymmetryInfoStr() {
- return symmetryInfo.infoStr;
+ return symmetryInfo == null ? "" : symmetryInfo.infoStr;
}
@Override
Modified: branches/v14_4/Jmol/src/org/jmol/util/MeshCapper.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/MeshCapper.java 2015-10-19
06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/util/MeshCapper.java 2015-10-20
22:40:08 UTC (rev 20839)
@@ -85,6 +85,8 @@
private Lst<int[]> lstTriangles;
+ private int nPoints;
+
/////////////// initialization //////////////////
/**
@@ -107,21 +109,22 @@
* generic entry for a polygon
*
* @param points
- * @return int[][i j k 7]
+ * @return int[][i j k mask]
*/
public int[][] triangulatePolygon(P3[] points) {
clear();
-
- int n = points.length;
+ // this is winding backward
+ nPoints = points.length;
CapVertex v0 = null;
- for (int i = 0; i < n; i++) {
+ for (int i = 0; i < nPoints; i++) {
CapVertex v = new CapVertex(points[i], i);
vertices.addLast(v);
- if (v0 != null)
- v.link(v0);
+ if (v0 != null) {
+ v0.link(v);
+ }
v0 = v;
}
- vertices.get(0).link(v0);
+ v0.link(vertices.get(0));
lstTriangles = new Lst<int[]>();
createCap(null);
int[][] a = AU.newInt2(lstTriangles.size());
@@ -188,12 +191,24 @@
* @param ipt3
*/
private void outputTriangle(int ipt1, int ipt2, int ipt3) {
- if (slicer == null)
- lstTriangles.addLast(new int[] { ipt1, ipt2, ipt3, 7 });
- else
+ if (slicer == null) {
+ int mask = 0;
+ if (isEdge(ipt1, ipt2))
+ mask |= 1;
+ if (isEdge(ipt2, ipt3))
+ mask |= 2;
+ if (isEdge(ipt3, ipt1))
+ mask |= 4;
+ lstTriangles.addLast(new int[] { ipt1, ipt2, ipt3, mask });
+ } else {
slicer.addTriangle(ipt1, ipt2, ipt3);
}
+ }
+ private boolean isEdge(int i, int j) {
+ return (j == (i + 1) % nPoints);
+ }
+
private CapVertex[] test(CapVertex[] vs) {
// dumping = testing = true;
// int n = 0;
@@ -242,7 +257,7 @@
V3 vab = V3.newVsub(vertices.get(0), vertices.get(1));
V3 vac;
if (norm == null) {
- vac = V3.newVsub(vertices.get(vertices.size() - 1), vertices.get(0));
+ vac = V3.newVsub(vertices.get(0), vertices.get(vertices.size() - 1));
} else {
vac = V3.newV(norm);
vac.cross(vac, vab);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-19
06:30:19 UTC (rev 20838)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-20
22:40:08 UTC (rev 20839)
@@ -7,8 +7,20 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.10.17"
+Jmol.___JmolVersion="14.4.0_2015.10.20"
+bug fix: set platformSpeed 1 for pmesh fails
+bug fix: polyhedron EDGES fails
+bug fix: @{ {"hash":{0.1 0.1 0.1},...} } fails (attempts to turn "," into "OR")
+ -- solution is to not allow "," for OR within associative arrays
+
+JmolVersion="14.4.0_2015.10.18"
+
+bug fix: Polyhedra can have missing triangle for hexagonal faces
+bug fix: calculate symmetry can break Jmol if unit cell has been changed
+
+JmolVersion="14.4.0_2015.10.17"
+
bug fix: if (...) \n { .... not working
bug fix: CIF reader will read empty second model for IUCr files with terminal
data_global block
bug fix: polyhedra bonds unitcell can cause error in HTML5
@@ -337,7 +349,6 @@
that are within distance of point.
bug fix: MRC surface reader: new version of EMAN2 leaves out alpha,beta,gamma;
does not load properly
-
bug fix: for (a in {*}) with no VAR fails if a has already been defined as an
integer
bug fix: better error reporting
@@ -6647,7 +6658,7 @@
bug fix: getProperty extractModel not honoring subset
bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350
bug fix: getProperty("JSON",....) should wrap value in {value:...}
-bug fix: MO persistent translucency broken in 11.x
+bug fix: MO per sistent translucency broken in 11.x
bug fix: show MENU write MENU load MENU all broken in 12.2
bug fix: {*}[n] should be empty if nAtoms <=n
bug fix: abinit reader was nonfunctional
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