Revision: 20356
http://sourceforge.net/p/jmol/code/20356
Author: hansonr
Date: 2015-03-05 03:23:13 +0000 (Thu, 05 Mar 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.03.05b"
synchronized with 14.2.13_2015.03.05
bug fix: reading legacy mapped plane (2ptn-molecular_slice1.jvxl.txt) crashes
Jmol
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
trunk/Jmol/src/org/jmol/shape/Shape.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java 2015-03-05
03:22:19 UTC (rev 20355)
+++ trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java 2015-03-05
03:23:13 UTC (rev 20356)
@@ -113,6 +113,11 @@
void setValue(float value) {
this.value = value;
}
+
+ @Override
+ public String toString() {
+ return value + " " + x + " " + y + " " + z;
+ }
}
@@ -167,7 +172,6 @@
* @return 0
*/
public int addTriangle(int iA, int iB, int iC, int check, int iContour) {
- //System.out.println("addT " + iA + " " + iB + " " + iC);
if (triangleCount == triangles.length)
triangles = (Triangle[]) AU.doubleLength(triangles);
triangles[triangleCount++] = new Triangle(iA, iB, iC, check, iContour);
@@ -253,11 +257,12 @@
cutoff = (cutoff < 0 ? -zeroOffset : zeroOffset);
contourValuesUsed[i] = cutoff;
- Logger.info("#contour " + (i + 1)+ " " + cutoff);
+ Logger.info("#contour " + (i + 1)+ " " + cutoff + " " + triangleCount);
htPts.clear();
- for (int ii = triangleCount; --ii >= 0;)
+ for (int ii = triangleCount; --ii >= 0;) {
if (triangles[ii].isValid)
checkContour(triangles[ii], i, cutoff);
+ }
if (thisContour > 0) {
if (i + 1 == thisContour)
minCutoff = cutoff;
@@ -305,7 +310,6 @@
return htPts.get(key).intValue();
float valueA = contourVertexes[iA].value;
float valueB = contourVertexes[iB].value;
- //System.out.println(iA + " " + iB + " " + valueA + " " + value + " " +
valueB);
int iPt = -1;
if (valueA != valueB) {
float f = (value - valueA) / (valueB - valueA);
@@ -331,9 +335,6 @@
private void checkContour(Triangle t, int i, float value) {
if (thisContour > 0 && i + 1 != thisContour)
return;
- //System.out.println(" ms i=" + i + " " + contourVertexes[pts[0]].value +
" " + contourVertexes[pts[1]].value + " " + contourVertexes[pts[2]].value + " "
+ value);
- //System.out.println(pts[0] + " " + pts[1] + " " + pts[2]);
- //System.out.println(contourVertexes[pts[0]] + "\n" +
contourVertexes[pts[1]] + "\n" + contourVertexes[pts[2]]);
int ipt0 = intercept(t, 0, value);
int ipt1 = intercept(t, 1, value);
int ipt2 = intercept(t, 2, value);
@@ -377,7 +378,6 @@
for (int i = 0; i < triangleCount; i++)
if (triangles[i].isValid) {
Triangle t = triangles[i];
- //System.out.println(contourVertexes[t.pts[0]].value + " " +
contourVertexes[t.pts[1]].value + " " + contourVertexes[t.pts[2]].value + " "
);
surfaceReader.addTriangleCheck(t.pts[0], t.pts[1], t.pts[2], t.check,
t.contourIndex, false, -1);
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2015-03-05
03:22:19 UTC (rev 20355)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2015-03-05
03:23:13 UTC (rev 20356)
@@ -233,8 +233,8 @@
|| param3 < 0);
params.isBicolorMap = (param1 > 0 && param2 < 0);
jvxlDataIsColorMapped = (param3 != 0);
- if (jvxlDataIsColorMapped)
- jvxlData.colorScheme = "RGB"; // legacy
+ if (jvxlDataIsColorMapped && !params.isContoured)
+ jvxlData.colorScheme = "RGB"; // legacy; but can't remap contours
jvxlDataIs2dContour = (jvxlDataIsColorMapped && params.isContoured);
if (params.isBicolorMap || params.colorBySign)
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2015-03-05
03:22:19 UTC (rev 20355)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2015-03-05
03:23:13 UTC (rev 20356)
@@ -692,12 +692,13 @@
params.mappedDataMin = contourPlaneMinimumValue;
params.mappedDataMax = contourPlaneMaximumValue;
}
- if (jvxlData.colorScheme != null)
+ if (jvxlData.colorScheme != null) {
+ boolean setContourValue = (marchingSquares != null &&
params.isContoured);
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) {
+ if (setContourValue) {
marchingSquares.setContourData(i, value);
continue;
}
@@ -707,6 +708,7 @@
colixes[i] = C.getColixTranslucent3(colix, true,
jvxlData.translucency);
}
+ }
return jvxlColorDataRead + "\n";
}
Modified: trunk/Jmol/src/org/jmol/shape/Shape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Shape.java 2015-03-05 03:22:19 UTC (rev
20355)
+++ trunk/Jmol/src/org/jmol/shape/Shape.java 2015-03-05 03:23:13 UTC (rev
20356)
@@ -29,6 +29,7 @@
import javajs.awt.Font;
import javajs.util.Lst;
+import javajs.util.PT;
import javajs.util.SB;
import javajs.util.T3;
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2015-03-05
03:22:19 UTC (rev 20355)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2015-03-05
03:23:13 UTC (rev 20356)
@@ -798,6 +798,7 @@
// still, if the scheme is translucent, we don't want to color the
vertices translucent
isTranslucent = false;
}
+ vcs = AU.ensureLengthShort(vcs, vc); // when reading contour plane may be
remapped
for (int i = vc; --i >= mergeVertexCount0;)
vcs[i] = ce.getColorIndex(vvs[i]);
setTranslucent(isTranslucent, translucentLevel);
@@ -813,7 +814,6 @@
color[0] = C.getArgb(colix[0]);
}
}
- //TODO -- still not right.
if (contourValues != null) {
contourColixes = new short[contourValues.length];
for (int i = 0; i < contourValues.length; i++)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-05 03:22:19 UTC
(rev 20355)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-05 03:23:13 UTC
(rev 20356)
@@ -14,8 +14,15 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.12_2015.03.05"
+Jmol.___JmolVersion="14.3.12_2015.03.05b"
+synchronized with 14.2.13_2015.03.05
+bug fix: reading legacy mapped plane (2ptn-molecular_slice1.jvxl.txt) crashes
Jmol
+
+JmolVersion="14.3.12_2015.03.05"
+synchronized with 14.2.13_2015.03.05
+released
+
bug fix: (14.3 only) write VRML|MAYA|OBJ|POVRAY broken
JmolVersion="14.3.12_2015.03.01"
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
