Revision: 18568
http://sourceforge.net/p/jmol/code/18568
Author: hansonr
Date: 2013-08-14 13:27:57 +0000 (Wed, 14 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.14"
FEATURE CHANGE: set wireframeRotation expanded to include bioshapes and
isosurfaces
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/render/MeshRenderer.java
trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
trunk/Jmol/src/org/jmol/renderbio/MeshRibbonRenderer.java
trunk/Jmol/src/org/jmol/renderbio/RibbonsRenderer.java
trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java
trunk/Jmol/src/org/jmol/renderbio/StrandsRenderer.java
trunk/Jmol/src/org/jmol/renderbio/TraceRenderer.java
trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.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 2013-08-14 11:48:10 UTC
(rev 18567)
+++ trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2013-08-14 13:27:57 UTC
(rev 18568)
@@ -134,7 +134,8 @@
private boolean doRender;
protected boolean volumeRender;
protected BS bsPolygons;
- protected boolean isTranslucentInherit;
+ protected boolean isTranslucentInherit;
+ protected boolean wireframeOnly;
private boolean setVariables() {
if (mesh.visibilityFlags == 0)
@@ -170,7 +171,8 @@
bsPolygons = (isGhostPass ? mesh.bsSlabGhost
: selectedPolyOnly ? mesh.bsSlabDisplay : null);
- frontOnly = !viewer.getSlabEnabled() && mesh.frontOnly
+ wireframeOnly = (!isExport && viewer.getBoolean(T.wireframerotation) &&
viewer.getInMotion(true));
+ frontOnly = wireframeOnly || !viewer.getSlabEnabled() && mesh.frontOnly
&& !mesh.isTwoSided && !selectedPolyOnly;
screens = viewer.allocTempScreens(vertexCount);
if (frontOnly)
@@ -214,10 +216,10 @@
if (!g3d.setColix(isGhostPass ? mesh.slabColix : colix))
return;
if (mesh.showPoints || mesh.polygonCount == 0)
- renderPoints();
- if (isGhostPass ? mesh.slabMeshType == T.mesh : mesh.drawTriangles)
+ renderPoints();
+ if (wireframeOnly || (isGhostPass ? mesh.slabMeshType == T.mesh :
mesh.drawTriangles))
renderTriangles(false, mesh.showTriangles, false);
- if (isGhostPass ? mesh.slabMeshType == T.fill : mesh.fillTriangles)
+ if (!wireframeOnly && (isGhostPass ? mesh.slabMeshType == T.fill :
mesh.fillTriangles))
renderTriangles(true, mesh.showTriangles, generateSet);
}
@@ -360,24 +362,25 @@
exportSurface(colix);
}
- protected void drawTriangle(P3i screenA, short colixA,
- P3i screenB, short colixB,
- P3i screenC, short colixC, int check, int diam) {
- if (antialias || diam != 1) {
- if (antialias)
- diam <<= 1;
- if ((check & 1) == 1)
- g3d.fillCylinderXYZ(colixA, colixB, GData.ENDCAPS_OPEN, diam,
- screenA.x, screenA.y, screenA.z, screenB.x, screenB.y, screenB.z);
- if ((check & 2) == 2)
- g3d.fillCylinderXYZ(colixB, colixC, GData.ENDCAPS_OPEN, diam,
- screenB.x, screenB.y, screenB.z, screenC.x, screenC.y, screenC.z);
- if ((check & 4) == 4)
- g3d.fillCylinderXYZ(colixA, colixC, GData.ENDCAPS_OPEN, diam,
- screenA.x, screenA.y, screenA.z, screenC.x, screenC.y, screenC.z);
- } else {
- g3d.drawTriangle3C(screenA, colixA, screenB, colixB, screenC, colixC,
check);
+ protected void drawTriangle(P3i screenA, short colixA, P3i screenB,
+ short colixB, P3i screenC, short colixC,
+ int check, int diam) {
+ if (wireframeOnly || !antialias && diam == 1) {
+ g3d.drawTriangle3C(screenA, colixA, screenB, colixB, screenC, colixC,
+ check);
+ return;
}
+ if (antialias)
+ diam <<= 1;
+ if ((check & 1) == 1)
+ g3d.fillCylinderXYZ(colixA, colixB, GData.ENDCAPS_OPEN, diam, screenA.x,
+ screenA.y, screenA.z, screenB.x, screenB.y, screenB.z);
+ if ((check & 2) == 2)
+ g3d.fillCylinderXYZ(colixB, colixC, GData.ENDCAPS_OPEN, diam, screenB.x,
+ screenB.y, screenB.z, screenC.x, screenC.y, screenC.z);
+ if ((check & 4) == 4)
+ g3d.fillCylinderXYZ(colixA, colixC, GData.ENDCAPS_OPEN, diam, screenA.x,
+ screenA.y, screenA.z, screenC.x, screenC.y, screenC.z);
}
protected int checkNormals(short nA, short nB, short nC) {
Modified: trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -110,7 +110,6 @@
needTranslucent = false;
boolean TF = (!isExport && viewer.getBoolean(T.wireframerotation) &&
viewer.getInMotion(true));
- System.out.println(viewer.getBoolean(T.wireframerotation) + " bioshaperend
" + viewer.getInMotion(true));
if (TF != wireframeOnly)
invalidateMesh = true;
wireframeOnly = TF;
Modified: trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -42,8 +42,15 @@
@Override
protected void renderBioShape(BioShape bioShape) {
+ if (wireframeOnly) {
+ if (wingVectors == null || isCarbohydrate)
+ renderTrace();
+ else
+ renderMeshRibbon();
+ return;
+ }
newRockets = true;
- if (bioShape.wingVectors == null || isCarbohydrate)
+ if (wingVectors == null || isCarbohydrate)
return;
getScreenControlPoints();
if (isNucleic) {
@@ -67,7 +74,7 @@
calcScreenControlPoints(cordMidPoints);
controlPoints = cordMidPoints;
}
- render1();
+ renderRockets();
viewer.freeTempPoints(cordMidPoints);
viewer.freeTempScreens(ribbonTopScreens);
viewer.freeTempScreens(ribbonBottomScreens);
@@ -101,7 +108,7 @@
}
@Override
- protected void render1() {
+ protected void renderRockets() {
boolean lastWasSheet = false;
boolean lastWasHelix = false;
ProteinStructure previousStructure = null;
@@ -143,10 +150,10 @@
lastWasHelix = isHelix;
}
if (renderAsRockets || !renderArrowHeads)
- renderRockets();
+ renderCartoonRockets();
}
- private void renderRockets() {
+ private void renderCartoonRockets() {
// doing the cylinders separately because we want to connect them if we
can.
// Key structures that must render properly
Modified: trunk/Jmol/src/org/jmol/renderbio/MeshRibbonRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/MeshRibbonRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/MeshRibbonRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -30,11 +30,15 @@
@Override
protected void renderBioShape(BioShape bioShape) {
+ renderMeshRibbon();
+ }
+
+ protected void renderMeshRibbon() {
if (!setStrandCount())
return;
- float offset = ((strandCount >> 1) * strandSeparation) + baseOffset;
+ float offset = ((strandCount >> 1) * strandSeparation) + baseStrandOffset;
render2Strand(false, offset, offset);
- render1();
+ renderStrands();
}
protected void render2Strand(boolean doFill, float offsetTop, float
offsetBottom) {
Modified: trunk/Jmol/src/org/jmol/renderbio/RibbonsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/RibbonsRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/RibbonsRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -33,6 +33,10 @@
protected void renderBioShape(BioShape bioShape) {
if (wingVectors == null)
return;
+ if (wireframeOnly) {
+ renderMeshRibbon();
+ return;
+ }
render2Strand(true, isNucleic ? 1f : 0.5f, isNucleic ? 0f : 0.5f);
}
}
Modified: trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/RocketsRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -37,7 +37,7 @@
import org.jmol.util.V3;
-public class RocketsRenderer extends BioShapeRenderer {
+public class RocketsRenderer extends MeshRibbonRenderer {
//private final static float MIN_CONE_HEIGHT = 0.05f;
@@ -48,6 +48,10 @@
protected void renderBioShape(BioShape bioShape) {
if (!(bioShape.bioPolymer instanceof AlphaPolymer))
return;
+ if (wireframeOnly) {
+ renderMeshRibbon();
+ return;
+ }
boolean val = !viewer.getBoolean(T.rocketbarrels);
if (renderArrowHeads != val) {
bioShape.falsifyMesh();
@@ -56,7 +60,7 @@
calcRopeMidPoints(newRockets);
calcScreenControlPoints(cordMidPoints);
controlPoints = cordMidPoints;
- render1();
+ renderRockets();
viewer.freeTempPoints(cordMidPoints);
}
@@ -99,7 +103,7 @@
}
}
- protected void render1() {
+ protected void renderRockets() {
tPending = false;
for (int i = bsVisible.nextSetBit(0); i >= 0; i = bsVisible
.nextSetBit(i + 1)) {
Modified: trunk/Jmol/src/org/jmol/renderbio/StrandsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/StrandsRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/StrandsRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -29,48 +29,52 @@
import org.jmol.shapebio.Strands;
import org.jmol.util.P3i;
-public class StrandsRenderer extends BioShapeRenderer {
+public class StrandsRenderer extends TraceRenderer {
protected int strandCount;
protected float strandSeparation;
- protected float baseOffset;
+ protected float baseStrandOffset;
@Override
protected void renderBioShape(BioShape bioShape) {
+ renderStrandShape();
+ }
+
+ protected void renderStrandShape() {
if (!setStrandCount())
return;
- render1();
+ renderStrands();
}
-
+
protected boolean setStrandCount() {
if (wingVectors == null)
return false;
- strandCount = viewer.getStrandCount(((Strands) shape).shapeID);
+ strandCount = (shape instanceof Strands ? viewer.getStrandCount(((Strands)
shape).shapeID) : 10);
strandSeparation = (strandCount <= 1) ? 0 : 1f / (strandCount - 1);
- baseOffset = ((strandCount & 1) == 0 ? strandSeparation / 2
+ baseStrandOffset = ((strandCount & 1) == 0 ? strandSeparation / 2
: strandSeparation);
return true;
}
- protected void render1() {
+ protected void renderStrands() {
P3i[] screens;
for (int i = strandCount >> 1; --i >= 0;) {
- float f = (i * strandSeparation) + baseOffset;
+ float f = (i * strandSeparation) + baseStrandOffset;
screens = calcScreens(f);
- render1Strand(screens);
+ renderStrand(screens);
viewer.freeTempScreens(screens);
screens = calcScreens(-f);
- render1Strand(screens);
+ renderStrand(screens);
viewer.freeTempScreens(screens);
}
if (strandCount % 2 == 1) {
screens = calcScreens(0f);
- render1Strand(screens);
+ renderStrand(screens);
viewer.freeTempScreens(screens);
}
}
- private void render1Strand(P3i[] screens) {
+ private void renderStrand(P3i[] screens) {
for (int i = bsVisible.nextSetBit(0); i >= 0; i = bsVisible.nextSetBit(i +
1))
renderHermiteCylinder(screens, i);
}
Modified: trunk/Jmol/src/org/jmol/renderbio/TraceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/TraceRenderer.java 2013-08-14
11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/renderbio/TraceRenderer.java 2013-08-14
13:27:57 UTC (rev 18568)
@@ -31,6 +31,10 @@
@Override
protected void renderBioShape(BioShape bioShape) {
+ renderTrace();
+ }
+
+ protected void renderTrace() {
getScreenControlPoints();
for (int i = bsVisible.nextSetBit(0); i >= 0; i = bsVisible.nextSetBit(i +
1))
renderHermiteConic(i, false);
Modified: trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-08-14 11:48:10 UTC (rev 18567)
+++ trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-08-14 13:27:57 UTC (rev 18568)
@@ -52,7 +52,8 @@
private Boolean showKey;
private boolean hasColorRange;
private int meshScale = -1;
-
+ private int mySlabValue;
+ private int globalSlabValue;
@Override
protected boolean render() {
@@ -60,32 +61,20 @@
}
protected boolean renderIso() {
- needTranslucent = false;
- iShowNormals = viewer.getTestFlag(4);
- showNumbers = viewer.getTestFlag(3);
- isosurface = (Isosurface) shape;
- // 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();
- showKey = (viewer.getBoolean(T.isosurfacekey) ? Boolean.TRUE : null);
- if (isNavigationMode)
- mySlabValue = (int) viewer.getNavigationOffset().z;
- isosurface.keyXy = null;
- meshScale = -1;
+
+ setGlobals();
+
for (int i = isosurface.meshCount; --i >= 0;) {
imesh = (IsosurfaceMesh) isosurface.meshes[i];
if (imesh.connections != null &&
!viewer.getModelSet().atoms[imesh.connections[0]].isVisible(0))
continue;
hasColorRange = false;
- if (renderMeshSlab(mySlabValue, slabValue)) {
+ if (renderMeshSlab()) {
if (!isExport)
renderInfo();
if (isExport && isGhostPass) {
exportPass = 1;
- renderMeshSlab(mySlabValue, slabValue);
+ renderMeshSlab();
exportPass = 2;
}
}
@@ -93,6 +82,22 @@
return needTranslucent;
}
+ private void setGlobals() {
+ needTranslucent = false;
+ iShowNormals = viewer.getTestFlag(4);
+ showNumbers = viewer.getTestFlag(3);
+ isosurface = (Isosurface) shape;
+ // 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);
+ showKey = (viewer.getBoolean(T.isosurfacekey) ? Boolean.TRUE : null);
+ isosurface.keyXy = null;
+ meshScale = -1;
+ globalSlabValue = g3d.getSlab();
+ mySlabValue = (isNavigationMode ? (int) viewer.getNavigationOffset().z :
Integer.MAX_VALUE);
+ }
+
protected void renderInfo() {
if (hasColorRange && imesh.colorEncoder != null && Boolean.TRUE == showKey)
showKey();
@@ -150,8 +155,9 @@
isosurface.keyXy[1] = (y + dy) / factor;
}
- private boolean renderMeshSlab(int mySlabValue, int slabValue) {
+ private boolean renderMeshSlab() {
volumeRender = (imesh.jvxlData.colorDensity &&
imesh.jvxlData.allowVolumeRender);
+ int thisSlabValue = mySlabValue;
if (!isNavigationMode) {
int meshSlabValue = imesh.jvxlData.slabValue;
if (meshSlabValue != Integer.MIN_VALUE
@@ -162,7 +168,7 @@
pt2f.scale(0.5f); // center
viewer.transformPt3f(pt2f, pt2f);
float r = viewer.scaleToScreen((int)pt2f.z,
Math.round(points[0].distance(points[1]) * 500f));
- mySlabValue = Math.round(pt2f.z + r * (1 - meshSlabValue / 50f));
+ thisSlabValue = Math.round(pt2f.z + r * (1 - meshSlabValue / 50f));
}
}
boolean tcover = g3d.getTranslucentCoverOnly();
@@ -170,10 +176,10 @@
thePlane = imesh.jvxlData.jvxlPlane;
vertexValues = imesh.vertexValues;
boolean isOK;
- if (mySlabValue != Integer.MAX_VALUE && imesh.jvxlData.isSlabbable) {
- g3d.setSlab(mySlabValue);
+ if (thisSlabValue != Integer.MAX_VALUE && imesh.jvxlData.isSlabbable) {
+ g3d.setSlab(thisSlabValue);
isOK = renderMesh(imesh);
- g3d.setSlab(slabValue);
+ g3d.setSlab(globalSlabValue);
} else {
isOK = renderMesh(imesh);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-14 11:48:10 UTC
(rev 18567)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-14 13:27:57 UTC
(rev 18568)
@@ -13,6 +13,8 @@
___JmolVersion="13.3.4_dev_2013.08.14"
+FEATURE CHANGE: set wireframeRotation expanded to include bioshapes and
isosurfaces
+bug fix: isosurface slab not allowing two different slabs for two diffrent
isosurfaces
bug fix: set wireframeRotation not working ("inMotion" flag not properly read
in Viewer).
bug fix: screen repaints were being requested far too frequently
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