Revision: 20923
http://sourceforge.net/p/jmol/code/20923
Author: hansonr
Date: 2016-01-06 12:26:15 +0000 (Wed, 06 Jan 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.1_2016.01.06"
bug fix: labels, echos, and measurements disappear when z-shaded
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/api/JmolRendererInterface.java
branches/v14_4/Jmol/src/org/jmol/export/Export3D.java
branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java
branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java
branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorT.java
branches/v14_4/Jmol/src/org/jmol/g3d/TextRenderer.java
branches/v14_4/Jmol/src/org/jmol/render/EchoRenderer.java
branches/v14_4/Jmol/src/org/jmol/render/LabelsRenderer.java
branches/v14_4/Jmol/src/org/jmol/render/MeasuresRenderer.java
branches/v14_4/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/g3d/Pixelator.java
trunk/Jmol/src/org/jmol/g3d/PixelatorT.java
trunk/Jmol/src/org/jmol/g3d/TextRenderer.java
trunk/Jmol/src/org/jmol/render/EchoRenderer.java
trunk/Jmol/src/org/jmol/render/LabelsRenderer.java
trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/api/JmolRendererInterface.java
2016-01-05 03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/api/JmolRendererInterface.java
2016-01-06 12:26:15 UTC (rev 20923)
@@ -260,7 +260,7 @@
double privateKey,
Map<String, Object> params);
- public abstract void plotImagePixel(int argb, int x, int y, int z, int
shade, int bgargb, int width, int height, int[] zbuf, Object pixel, int
transpLog);
+ public abstract void plotImagePixel(int argb, int x, int y, int z, byte
shade, int bgargb, int width, int height, int[] zbuf, Object pixel, int
transpLog);
public abstract void plotPixelClippedP3i(P3i a);
Modified: branches/v14_4/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/export/Export3D.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/export/Export3D.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -789,7 +789,7 @@
}
@Override
- public void plotImagePixel(int argb, int x, int y, int z, int shade,
+ public void plotImagePixel(int argb, int x, int y, int z, byte shade,
int bgargb, int width, int height, int[] pbuf,
Object p, int transpLog) {
// from Text3D
if (isWebGL)
Modified: branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -432,7 +432,7 @@
if (pbuf != null) {
if (isPass2 && pbufT != null)
for (int offset = pbufT.length; --offset >= 0;)
- mergeBufferPixel(pbuf, offset, pbufT[offset], bgcolor);
+ pbuf[offset] = mergeBufferPixel(pbuf[offset], pbufT[offset],
bgcolor);
if (pixel == pixelShaded && pixelShaded.zShadePower == 0)
pixelShaded.showZBuffer();
@@ -455,13 +455,10 @@
currentlyRendering = isPass2 = false;
}
- public static void mergeBufferPixel(int[] pbuf, int offset, int argbB,
+ public static int mergeBufferPixel(int argbA, int argbB,
int bgcolor) {
- if (argbB == 0)
- return;
- int argbA = pbuf[offset];
- if (argbA == argbB)
- return;
+ if (argbB == 0 || argbA == argbB)
+ return argbA;
if (argbA == 0)
argbA = bgcolor;
int rbA = (argbA & 0x00FF00FF);
@@ -510,7 +507,7 @@
gA = (((gA << 2) + (gA << 1) + gA + gB) >> 3) & 0x0000FF00;
break;
}
- pbuf[offset] = 0xFF000000 | rbA | gA;
+ return 0xFF000000 | rbA | gA;
}
@Override
@@ -1193,7 +1190,7 @@
for (int j = 0; j < imageWidth; j++) {
int b = buffer[offset++];
if ((b & 0xFF000000) == (0xFF000000 & 0xFF000000))
- jmolRenderer.plotImagePixel(b, x + j, y + i, z, 8, bg, w,
+ jmolRenderer.plotImagePixel(b, x + j, y + i, z, (byte) 8, bg, w,
h, zb, p, t);
}
}
@@ -1608,24 +1605,13 @@
}
@Override
- public void plotImagePixel(int argb, int x, int y, int z, int shade,
+ public void plotImagePixel(int argb, int x, int y, int z, byte shade,
int bgargb, int width, int height, int[] zbuf,
Object p, int transpLog) {
// drawString via text3d.plotClipped; overridden in Export
if (x < 0 || x >= width || y < 0 || y >= height)
return;
- int offset = y * width + x;
- if (z < zbuf[offset]) {
- if (shade == 8)
- ((Pixelator) p).addPixel(offset, z, argb);
- else {
- // shade is a log of translucency, so adding two is equivalent to
- // multiplying them. Works like a charm! - BH
- shade += transpLog;
- if (shade <= 7)
- shadeTextPixel(offset, z, argb, bgargb, shade, zbuf);
- }
- }
+ ((Pixelator)p).addImagePixel(shade, transpLog, y * width + x, z, argb,
bgargb);
}
void plotPixelsClippedRaster(int count, int x, int y, int zAtLeft,
@@ -2046,12 +2032,4 @@
return false;
}
- void shadeTextPixel(int offset, int z, int argb, int bgargb, int shade,
- int[] zbuf) {
- if (bgargb != 0)
- mergeBufferPixel(pbuf, offset, bgargb, bgcolor);
- mergeBufferPixel(pbuf, offset, (argb & 0xFFFFFF) | shade << 24, bgcolor);
- zbuf[offset] = z;
- }
-
}
Modified: branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-05 03:07:48 UTC
(rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-06 12:26:15 UTC
(rev 20923)
@@ -60,4 +60,29 @@
pb[offset] = p;
}
+ public void addImagePixel(byte shade, int tLog, int offset, int z, int argb,
+ int bgargb) {
+ if (z < zb[offset]) {
+ switch (shade) {
+ case 0:
+ return;
+ case 8:
+ addPixel(offset, z, argb);
+ return;
+ default:
+ // shade is a log of translucency, so adding two is equivalent to
+ // multiplying them. Works like a charm! - BH
+ shade += tLog;
+ if (shade <= 7) {
+ int p = pb[offset];
+ if (bgargb != 0)
+ p = Graphics3D.mergeBufferPixel(p, bgargb, bgargb);
+ p = Graphics3D.mergeBufferPixel(p, (argb & 0xFFFFFF)
+ | (shade << 24), bgargb);
+ addPixel(offset, z, p);
+ }
+ }
+ }
+ }
+
}
\ No newline at end of file
Modified: branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorT.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorT.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorT.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -54,13 +54,13 @@
// if (zT != Integer.MAX_VALUE)
int argb = g.pbufT[offset];
if (!g.translucentCoverOnly && argb != 0 && zT - z > g.zMargin)
- Graphics3D.mergeBufferPixel(g.pbuf, offset, argb, g.bgcolor);
+ pb[offset] = Graphics3D.mergeBufferPixel(pb[offset], argb, g.bgcolor);
g.zbufT[offset] = z;
g.pbufT[offset] = p & g.translucencyMask;
} else if (z == zT) {
} else if (!g.translucentCoverOnly && z - zT > g.zMargin) {
// oops-out of order
- Graphics3D.mergeBufferPixel(g.pbuf, offset, p & g.translucencyMask,
g.bgcolor);
+ pb[offset] = Graphics3D.mergeBufferPixel(pb[offset], p &
g.translucencyMask, g.bgcolor);
}
}
}
\ No newline at end of file
Modified: branches/v14_4/Jmol/src/org/jmol/g3d/TextRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/g3d/TextRenderer.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/g3d/TextRenderer.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -125,26 +125,11 @@
if (shade != 0)
jr.plotImagePixel(argb, x + j, y + i, z, shade, bgargb, width,
height, zbuf, p, tLog);
}
- }
-
+ }
} else {
- int pbufOffset = y * width + x;
- for (int i = 0, off = 0; i < textHeight; i++) {
- for (int j = 0; j < textWidth; j++) {
- byte shade = tmap[off++];
- if (shade != 0 && z < zbuf[pbufOffset]) {
- if (shade == 8) {
- p.addPixel(pbufOffset, z, argb);
- } else {
- shade += tLog;
- if (shade <= 7)
- g3d.shadeTextPixel(pbufOffset, z, argb, bgargb, shade, zbuf);
- }
- }
- pbufOffset++;
- }
- pbufOffset += (width - textWidth);
- }
+ for (int i = 0, off = 0, pbufOffset = y * width + x; i < textHeight;
i++, pbufOffset += (width - textWidth))
+ for (int j = 0; j < textWidth; j++)
+ p.addImagePixel(tmap[off++], tLog, pbufOffset++, z, argb, bgargb);
}
return text3d.width;
}
Modified: branches/v14_4/Jmol/src/org/jmol/render/EchoRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/EchoRenderer.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/render/EchoRenderer.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -42,7 +42,6 @@
.getScalePixelsPerAngstrom(true) * 10000 : 0);
imageFontScaling = vwr.imageFontScaling;
boolean haveTranslucent = false;
- setZcutoff();
for (Text t : echo.objects.values()) {
if (!t.visible || t.hidden) {
continue;
@@ -61,8 +60,6 @@
z = pt0i.z - vwr.tm.zValueFromPercent(0) + z;
t.setZs(z, z);
}
- if (t.zSlab >= zCutoff)
- continue;
if (t.pointerPt == null) {
t.pointer = JC.LABEL_POINTER_NONE;
} else {
Modified: branches/v14_4/Jmol/src/org/jmol/render/LabelsRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/LabelsRenderer.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/render/LabelsRenderer.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -69,8 +69,6 @@
protected int zSlab = Integer.MIN_VALUE;
- protected int zCutoff;
-
private int zBox;
private float[] boxXY;
@@ -87,7 +85,6 @@
int[] offsets = labels.offsets;
if (labelStrings == null)
return false;
- setZcutoff();
Atom[] atoms = ms.at;
short backgroundColixContrast = vwr.cm.colixBackgroundContrast;
int backgroundColor = vwr.getBackgroundArgb();
@@ -119,8 +116,6 @@
isAbsolute = JC.isOffsetAbsolute(offset);
pointer = JC.getPointer(offset);
zSlab = atom.sZ - atom.sD / 2 - 3;
- if (zSlab > zCutoff)
- continue;
if (zSlab < 1)
zSlab = 1;
zBox = zSlab;
@@ -155,10 +150,6 @@
return false;
}
- protected void setZcutoff() {
- zCutoff = (tm.zShadeEnabled ? tm.zSlabValue : Integer.MAX_VALUE);
- }
-
protected Text renderLabelOrMeasure(Text text, String label) {
boolean newText = false;
if (text != null) {
Modified: branches/v14_4/Jmol/src/org/jmol/render/MeasuresRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/MeasuresRenderer.java
2016-01-05 03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/render/MeasuresRenderer.java
2016-01-06 12:26:15 UTC (rev 20923)
@@ -96,7 +96,6 @@
return false;
boolean showMeasurementLabels = vwr.getBoolean(T.measurementlabels);
measures.setVisibilityInfo();
- setZcutoff();
for (int i = measures.measurementCount; --i >= 0;) {
m = measures.measurements.get(i);
if (!m.isVisible || !m.isValid || (count = m.count) == 1 && m.traceX ==
Integer.MIN_VALUE)
@@ -214,7 +213,7 @@
int zB = b.sZ - b.sD - 10;
int radius = drawLine(a.sX, a.sY, zA, b.sX,
b.sY, zB, mad);
- if (s == null || zB >= zCutoff)
+ if (s == null)
return;
if (mad > 0)
radius <<= 1;
@@ -245,7 +244,7 @@
b.sY, zB, mad);
radius += drawLine(b.sX, b.sY, zB, c.sX,
c.sY, zC, mad);
- if (s == null || zB >= zCutoff)
+ if (s == null)
return;
radius = (radius + 1) / 2;
if (m.value > 175) {
@@ -321,7 +320,7 @@
radius += drawLine(c.sX, c.sY, zC, d.sX,
d.sY, zD, mad);
int zLabel = (zA + zB + zC + zD) / 4;
- if (s == null || zLabel >= zCutoff)
+ if (s == null)
return;
radius /= 3;
if (m.text == null) {
Modified: branches/v14_4/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2016-01-05 03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2016-01-06 12:26:15 UTC (rev 20923)
@@ -640,20 +640,13 @@
* just sets the color command for this isosurface.
*/
void setColorCommand() {
- if (colorEncoder == null)
+ if (colorEncoder == null || (colorCommand = colorEncoder.getColorScheme())
== null)
return;
- colorCommand = colorEncoder.getColorScheme();
if (colorCommand.equals("inherit")) {
colorCommand = "#inherit;";
return;
}
- if (colorCommand == null)
- return;
- colorCommand = "color $"
- + (PT.isLetter(thisID.charAt(0)) && thisID.indexOf(" ") < 0 ? thisID :
"\"" + thisID + "\"")
- + " \""
- + colorCommand
- + "\" range "
+ colorCommand = "color $" + PT.esc(thisID) + PT.esc(colorCommand) + "
range "
+ (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue + " "
+ jvxlData.valueMappedToRed : jvxlData.valueMappedToRed + " "
+ jvxlData.valueMappedToBlue);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-05
03:07:48 UTC (rev 20922)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-06
12:26:15 UTC (rev 20923)
@@ -7,8 +7,13 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.1_2016.01.04"
+Jmol.___JmolVersion="14.4.1_2016.01.06"
+bug fix: labels, echos, and measurements disappear when z-shaded
+
+JmolVersion="14.4.1_2016.01.04"
+released
+
bug fix: (JvxlReader) Jmol 12 mapped isosurface jvxl files do not show mapped
color
bug fix: setting cartoons on for phosphorus-only polymers fails
bug fix: setting default label properties using select none;.... fails
Modified: trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -260,7 +260,7 @@
double privateKey,
Map<String, Object> params);
- public abstract void plotImagePixel(int argb, int x, int y, int z, int
shade, int bgargb, int width, int height, int[] zbuf, Object pixel, int
transpLog);
+ public abstract void plotImagePixel(int argb, int x, int y, int z, byte
shade, int bgargb, int width, int height, int[] zbuf, Object pixel, int
transpLog);
public abstract void plotPixelClippedP3i(P3i a);
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2016-01-05 03:07:48 UTC
(rev 20922)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2016-01-06 12:26:15 UTC
(rev 20923)
@@ -789,7 +789,7 @@
}
@Override
- public void plotImagePixel(int argb, int x, int y, int z, int shade,
+ public void plotImagePixel(int argb, int x, int y, int z, byte shade,
int bgargb, int width, int height, int[] pbuf,
Object p, int transpLog) {
// from Text3D
if (isWebGL)
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-05 03:07:48 UTC (rev
20922)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-06 12:26:15 UTC (rev
20923)
@@ -432,7 +432,7 @@
if (pbuf != null) {
if (isPass2 && pbufT != null)
for (int offset = pbufT.length; --offset >= 0;)
- mergeBufferPixel(pbuf, offset, pbufT[offset], bgcolor);
+ pbuf[offset] = mergeBufferPixel(pbuf[offset], pbufT[offset],
bgcolor);
if (pixel == pixelShaded && pixelShaded.zShadePower == 0)
pixelShaded.showZBuffer();
@@ -455,13 +455,10 @@
currentlyRendering = isPass2 = false;
}
- public static void mergeBufferPixel(int[] pbuf, int offset, int argbB,
+ public static int mergeBufferPixel(int argbA, int argbB,
int bgcolor) {
- if (argbB == 0)
- return;
- int argbA = pbuf[offset];
- if (argbA == argbB)
- return;
+ if (argbB == 0 || argbA == argbB)
+ return argbA;
if (argbA == 0)
argbA = bgcolor;
int rbA = (argbA & 0x00FF00FF);
@@ -510,7 +507,7 @@
gA = (((gA << 2) + (gA << 1) + gA + gB) >> 3) & 0x0000FF00;
break;
}
- pbuf[offset] = 0xFF000000 | rbA | gA;
+ return 0xFF000000 | rbA | gA;
}
@Override
@@ -1193,7 +1190,7 @@
for (int j = 0; j < imageWidth; j++) {
int b = buffer[offset++];
if ((b & 0xFF000000) == (0xFF000000 & 0xFF000000))
- jmolRenderer.plotImagePixel(b, x + j, y + i, z, 8, bg, w,
+ jmolRenderer.plotImagePixel(b, x + j, y + i, z, (byte) 8, bg, w,
h, zb, p, t);
}
}
@@ -1608,24 +1605,13 @@
}
@Override
- public void plotImagePixel(int argb, int x, int y, int z, int shade,
+ public void plotImagePixel(int argb, int x, int y, int z, byte shade,
int bgargb, int width, int height, int[] zbuf,
Object p, int transpLog) {
// drawString via text3d.plotClipped; overridden in Export
if (x < 0 || x >= width || y < 0 || y >= height)
return;
- int offset = y * width + x;
- if (z < zbuf[offset]) {
- if (shade == 8)
- ((Pixelator) p).addPixel(offset, z, argb);
- else {
- // shade is a log of translucency, so adding two is equivalent to
- // multiplying them. Works like a charm! - BH
- shade += transpLog;
- if (shade <= 7)
- shadeTextPixel(offset, z, argb, bgargb, shade, zbuf);
- }
- }
+ ((Pixelator)p).addImagePixel(shade, transpLog, y * width + x, z, argb,
bgargb);
}
void plotPixelsClippedRaster(int count, int x, int y, int zAtLeft,
@@ -2046,12 +2032,4 @@
return false;
}
- void shadeTextPixel(int offset, int z, int argb, int bgargb, int shade,
- int[] zbuf) {
- if (bgargb != 0)
- mergeBufferPixel(pbuf, offset, bgargb, bgcolor);
- mergeBufferPixel(pbuf, offset, (argb & 0xFFFFFF) | shade << 24, bgcolor);
- zbuf[offset] = z;
- }
-
}
Modified: trunk/Jmol/src/org/jmol/g3d/Pixelator.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-05 03:07:48 UTC (rev
20922)
+++ trunk/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-06 12:26:15 UTC (rev
20923)
@@ -60,4 +60,29 @@
pb[offset] = p;
}
+ public void addImagePixel(byte shade, int tLog, int offset, int z, int argb,
+ int bgargb) {
+ if (z < zb[offset]) {
+ switch (shade) {
+ case 0:
+ return;
+ case 8:
+ addPixel(offset, z, argb);
+ return;
+ default:
+ // shade is a log of translucency, so adding two is equivalent to
+ // multiplying them. Works like a charm! - BH
+ shade += tLog;
+ if (shade <= 7) {
+ int p = pb[offset];
+ if (bgargb != 0)
+ p = Graphics3D.mergeBufferPixel(p, bgargb, bgargb);
+ p = Graphics3D.mergeBufferPixel(p, (argb & 0xFFFFFF)
+ | (shade << 24), bgargb);
+ addPixel(offset, z, p);
+ }
+ }
+ }
+ }
+
}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/g3d/PixelatorT.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/PixelatorT.java 2016-01-05 03:07:48 UTC (rev
20922)
+++ trunk/Jmol/src/org/jmol/g3d/PixelatorT.java 2016-01-06 12:26:15 UTC (rev
20923)
@@ -54,13 +54,13 @@
// if (zT != Integer.MAX_VALUE)
int argb = g.pbufT[offset];
if (!g.translucentCoverOnly && argb != 0 && zT - z > g.zMargin)
- Graphics3D.mergeBufferPixel(g.pbuf, offset, argb, g.bgcolor);
+ pb[offset] = Graphics3D.mergeBufferPixel(pb[offset], argb, g.bgcolor);
g.zbufT[offset] = z;
g.pbufT[offset] = p & g.translucencyMask;
} else if (z == zT) {
} else if (!g.translucentCoverOnly && z - zT > g.zMargin) {
// oops-out of order
- Graphics3D.mergeBufferPixel(g.pbuf, offset, p & g.translucencyMask,
g.bgcolor);
+ pb[offset] = Graphics3D.mergeBufferPixel(pb[offset], p &
g.translucencyMask, g.bgcolor);
}
}
}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/g3d/TextRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/TextRenderer.java 2016-01-05 03:07:48 UTC
(rev 20922)
+++ trunk/Jmol/src/org/jmol/g3d/TextRenderer.java 2016-01-06 12:26:15 UTC
(rev 20923)
@@ -125,26 +125,11 @@
if (shade != 0)
jr.plotImagePixel(argb, x + j, y + i, z, shade, bgargb, width,
height, zbuf, p, tLog);
}
- }
-
+ }
} else {
- int pbufOffset = y * width + x;
- for (int i = 0, off = 0; i < textHeight; i++) {
- for (int j = 0; j < textWidth; j++) {
- byte shade = tmap[off++];
- if (shade != 0 && z < zbuf[pbufOffset]) {
- if (shade == 8) {
- p.addPixel(pbufOffset, z, argb);
- } else {
- shade += tLog;
- if (shade <= 7)
- g3d.shadeTextPixel(pbufOffset, z, argb, bgargb, shade, zbuf);
- }
- }
- pbufOffset++;
- }
- pbufOffset += (width - textWidth);
- }
+ for (int i = 0, off = 0, pbufOffset = y * width + x; i < textHeight;
i++, pbufOffset += (width - textWidth))
+ for (int j = 0; j < textWidth; j++)
+ p.addImagePixel(tmap[off++], tLog, pbufOffset++, z, argb, bgargb);
}
return text3d.width;
}
Modified: trunk/Jmol/src/org/jmol/render/EchoRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/EchoRenderer.java 2016-01-05 03:07:48 UTC
(rev 20922)
+++ trunk/Jmol/src/org/jmol/render/EchoRenderer.java 2016-01-06 12:26:15 UTC
(rev 20923)
@@ -42,7 +42,6 @@
.getScalePixelsPerAngstrom(true) * 10000 : 0);
imageFontScaling = vwr.imageFontScaling;
boolean haveTranslucent = false;
- setZcutoff();
for (Text t : echo.objects.values()) {
if (!t.visible || t.hidden) {
continue;
@@ -61,8 +60,6 @@
z = pt0i.z - vwr.tm.zValueFromPercent(0) + z;
t.setZs(z, z);
}
- if (t.zSlab >= zCutoff)
- continue;
if (t.pointerPt == null) {
t.pointer = JC.LABEL_POINTER_NONE;
} else {
Modified: trunk/Jmol/src/org/jmol/render/LabelsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/LabelsRenderer.java 2016-01-05 03:07:48 UTC
(rev 20922)
+++ trunk/Jmol/src/org/jmol/render/LabelsRenderer.java 2016-01-06 12:26:15 UTC
(rev 20923)
@@ -69,8 +69,6 @@
protected int zSlab = Integer.MIN_VALUE;
- protected int zCutoff;
-
private int zBox;
private float[] boxXY;
@@ -87,7 +85,6 @@
int[] offsets = labels.offsets;
if (labelStrings == null)
return false;
- setZcutoff();
Atom[] atoms = ms.at;
short backgroundColixContrast = vwr.cm.colixBackgroundContrast;
int backgroundColor = vwr.getBackgroundArgb();
@@ -119,8 +116,6 @@
isAbsolute = JC.isOffsetAbsolute(offset);
pointer = JC.getPointer(offset);
zSlab = atom.sZ - atom.sD / 2 - 3;
- if (zSlab > zCutoff)
- continue;
if (zSlab < 1)
zSlab = 1;
zBox = zSlab;
@@ -155,10 +150,6 @@
return false;
}
- protected void setZcutoff() {
- zCutoff = (tm.zShadeEnabled ? tm.zSlabValue : Integer.MAX_VALUE);
- }
-
protected Text renderLabelOrMeasure(Text text, String label) {
boolean newText = false;
if (text != null) {
Modified: trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ trunk/Jmol/src/org/jmol/render/MeasuresRenderer.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -96,7 +96,6 @@
return false;
boolean showMeasurementLabels = vwr.getBoolean(T.measurementlabels);
measures.setVisibilityInfo();
- setZcutoff();
for (int i = measures.measurementCount; --i >= 0;) {
m = measures.measurements.get(i);
if (!m.isVisible || !m.isValid || (count = m.count) == 1 && m.traceX ==
Integer.MIN_VALUE)
@@ -214,7 +213,7 @@
int zB = b.sZ - b.sD - 10;
int radius = drawLine(a.sX, a.sY, zA, b.sX,
b.sY, zB, mad);
- if (s == null || zB >= zCutoff)
+ if (s == null)
return;
if (mad > 0)
radius <<= 1;
@@ -245,7 +244,7 @@
b.sY, zB, mad);
radius += drawLine(b.sX, b.sY, zB, c.sX,
c.sY, zC, mad);
- if (s == null || zB >= zCutoff)
+ if (s == null)
return;
radius = (radius + 1) / 2;
if (m.value > 175) {
@@ -320,9 +319,9 @@
c.sY, zC, mad);
radius += drawLine(c.sX, c.sY, zC, d.sX,
d.sY, zD, mad);
+ if (s == null)
+ return;
int zLabel = (zA + zB + zC + zD) / 4;
- if (s == null || zLabel >= zCutoff)
- return;
radius /= 3;
if (m.text == null) {
g3d.setC(labelColix);
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2016-01-05
03:07:48 UTC (rev 20922)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2016-01-06
12:26:15 UTC (rev 20923)
@@ -640,25 +640,19 @@
* just sets the color command for this isosurface.
*/
void setColorCommand() {
- if (colorEncoder == null)
+ if (colorEncoder == null || (colorCommand = colorEncoder.getColorScheme())
== null)
return;
- colorCommand = colorEncoder.getColorScheme();
if (colorCommand.equals("inherit")) {
colorCommand = "#inherit;";
return;
}
- if (colorCommand == null)
- return;
- colorCommand = "color $"
- + (PT.isLetter(thisID.charAt(0)) && thisID.indexOf(" ") < 0 ? thisID :
"\"" + thisID + "\"")
- + " \""
- + colorCommand
- + "\" range "
+ colorCommand = "color $" + PT.esc(thisID) + PT.esc(colorCommand) + "
range "
+ (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue + " "
+ jvxlData.valueMappedToRed : jvxlData.valueMappedToRed + " "
+ jvxlData.valueMappedToBlue);
}
+
/**
* from Isosurface.notifySurfaceGenerationCompleted()
*
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-05 03:07:48 UTC
(rev 20922)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-06 12:26:15 UTC
(rev 20923)
@@ -63,8 +63,12 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.1_2016.01.04"
+Jmol.___JmolVersion="14.5.1_2016.01.06"
+bug fix: labels, echos, and measurements disappear when z-shaded
+
+JmolVersion="14.5.1_2016.01.04"
+
bug fix: (JvxlReader) Jmol 12 mapped isosurface jvxl files do not show mapped
color
bug fix: setting default label properties using select none;.... fails
bug fix: setting cartoons on for phosphorus-only polymers fails
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