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[Jmol-commits] SF.net SVN: jmol:[16253] branches/v12_2/Jmol/src/org/jmol
|
From: <ha...@us...> - 2011-10-04 18:37:21
|
Revision: 16253
http://jmol.svn.sourceforge.net/jmol/?rev=16253&view=rev
Author: hansonr
Date: 2011-10-04 18:37:11 +0000 (Tue, 04 Oct 2011)
Log Message:
-----------
version=12.2.1_dev
# CODE -- ?? Eclipse is refusing to set tabs to 2 spaces on this new project??
# bug fix: color isosurface {atomset} <color> does not work if isosurface has not already been mapped.
Modified Paths:
--------------
branches/v12_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v12_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v12_2/Jmol/src/org/jmol/shapesurface/Isosurface.java 2011-10-04 18:34:01 UTC (rev 16252)
+++ branches/v12_2/Jmol/src/org/jmol/shapesurface/Isosurface.java 2011-10-04 18:37:11 UTC (rev 16253)
@@ -198,416 +198,435 @@
//private boolean allowContourLines;
boolean allowMesh = true;
- @SuppressWarnings("unchecked")
- @Override
- public void setProperty(String propertyName, Object value, BitSet bs) {
+ @SuppressWarnings("unchecked")
+ @Override
+ public void setProperty(String propertyName, Object value, BitSet bs) {
- //System.out.println("isosurface testing " + propertyName + " " + value + (propertyName == "token" ? " " + Token.nameOf(((Integer)value).intValue()) : ""));
+ // System.out.println("isosurface testing " + propertyName + " " + value
+ // + (propertyName == "token" ? " " +
+ // Token.nameOf(((Integer)value).intValue()) : ""));
- //isosurface-only (no calculation required; no calc parameters to set)
+ // isosurface-only (no calculation required; no calc parameters to set)
- if ("navigate" == propertyName) {
- navigate(((Integer) value).intValue());
- return;
- }
- if ("delete" == propertyName) {
- setPropertySuper(propertyName, value, bs);
- if (!explicitID)
- nLCAO = nUnnamed = 0;
- currentMesh = thisMesh = null;
- return;
- }
+ if ("navigate" == propertyName) {
+ navigate(((Integer) value).intValue());
+ return;
+ }
+ if ("delete" == propertyName) {
+ setPropertySuper(propertyName, value, bs);
+ if (!explicitID)
+ nLCAO = nUnnamed = 0;
+ currentMesh = thisMesh = null;
+ return;
+ }
- if ("remapColor" == propertyName) {
- if (thisMesh != null) {
- thisMesh.remapColors((ColorEncoder) value, translucentLevel);
- }
- return;
- }
+ if ("remapColor" == propertyName) {
+ if (thisMesh != null) {
+ thisMesh.remapColors((ColorEncoder) value, translucentLevel);
+ }
+ return;
+ }
- if ("thisID" == propertyName) {
- if (actualID != null)
- value = actualID;
- setPropertySuper("thisID", value, null);
- return;
- }
+ if ("thisID" == propertyName) {
+ if (actualID != null)
+ value = actualID;
+ setPropertySuper("thisID", value, null);
+ return;
+ }
- if ("atomcolor" == propertyName) {
- if (thisMesh != null) {
- thisMesh.colorAtoms(Graphics3D.getColix(value), bs);
- }
- return;
- }
+ if ("atomcolor" == propertyName) {
+ if (thisMesh != null) {
+ if (thisMesh.vertexSource == null) {
+ short colix = (!thisMesh.isColorSolid ? 0 : thisMesh.colix);
+ setProperty("init", null, null);
+ setProperty("map", Boolean.FALSE, null);
+ setProperty("property", new float[viewer.getAtomCount()],
+ null);
+ if (colix != 0) {
+ thisMesh.colorCommand = "color isosurface "
+ + Graphics3D.getHexCode(colix);
+ setProperty("color", new Integer(Graphics3D
+ .getArgb(colix)), null);
+ }
+ }
+ thisMesh.colorAtoms(Graphics3D.getColix(value), bs);
+ }
+ return;
+ }
- if ("pointSize" == propertyName) {
- if (thisMesh != null) {
- thisMesh.volumeRenderPointSize = ((Float) value).floatValue();
- }
- return;
- }
+ if ("pointSize" == propertyName) {
+ if (thisMesh != null) {
+ thisMesh.volumeRenderPointSize = ((Float) value).floatValue();
+ }
+ return;
+ }
- if ("vertexcolor" == propertyName) {
- if (thisMesh != null) {
- thisMesh.colorVertices(Graphics3D.getColix(value), bs);
- }
- return;
- }
+ if ("vertexcolor" == propertyName) {
+ if (thisMesh != null) {
+ thisMesh.colorVertices(Graphics3D.getColix(value), bs);
+ }
+ return;
+ }
- if ("color" == propertyName) {
- if (thisMesh != null) {
- // thisMesh.vertexColixes = null;
- thisMesh.isColorSolid = true;
- thisMesh.polygonColixes = null;
- thisMesh.colorEncoder = null;
- thisMesh.vertexColorMap = null;
- } else if (!TextFormat.isWild(previousMeshID)) {
- for (int i = meshCount; --i >= 0;) {
- // isomeshes[i].vertexColixes = null;
- isomeshes[i].isColorSolid = true;
- isomeshes[i].polygonColixes = null;
- isomeshes[i].colorEncoder = null;
- isomeshes[i].vertexColorMap = null;
- }
- }
- setPropertySuper(propertyName, value, bs);
- return;
- }
+ if ("color" == propertyName) {
+ if (thisMesh != null) {
+ // thisMesh.vertexColixes = null;
+ thisMesh.isColorSolid = true;
+ thisMesh.polygonColixes = null;
+ thisMesh.colorEncoder = null;
+ thisMesh.vertexColorMap = null;
+ } else if (!TextFormat.isWild(previousMeshID)) {
+ for (int i = meshCount; --i >= 0;) {
+ // isomeshes[i].vertexColixes = null;
+ isomeshes[i].isColorSolid = true;
+ isomeshes[i].polygonColixes = null;
+ isomeshes[i].colorEncoder = null;
+ isomeshes[i].vertexColorMap = null;
+ }
+ }
+ setPropertySuper(propertyName, value, bs);
+ return;
+ }
- if ("nocontour" == propertyName) {
- // recontouring
- if (thisMesh != null) {
- thisMesh.deleteContours();
- }
- return;
- }
- if ("fixed" == propertyName) {
- isFixed = ((Boolean) value).booleanValue();
- setMesh();
- return;
- }
+ if ("nocontour" == propertyName) {
+ // recontouring
+ if (thisMesh != null) {
+ thisMesh.deleteContours();
+ }
+ return;
+ }
+ if ("fixed" == propertyName) {
+ isFixed = ((Boolean) value).booleanValue();
+ setMesh();
+ return;
+ }
- if ("newObject" == propertyName) {
- if (thisMesh != null)
- thisMesh.clear(thisMesh.meshType, false);
- return;
- }
+ if ("newObject" == propertyName) {
+ if (thisMesh != null)
+ thisMesh.clear(thisMesh.meshType, false);
+ return;
+ }
- if ("refreshTrajectories" == propertyName) {
- for (int i = meshCount; --i >= 0;)
- if (meshes[i].connections != null
- && meshes[i].modelIndex == ((Integer) ((Object[]) value)[0])
- .intValue())
- meshes[i].updateCoordinates((Matrix4f) ((Object[]) value)[2],
- (BitSet) ((Object[]) value)[1]);
- return;
- }
+ if ("refreshTrajectories" == propertyName) {
+ for (int i = meshCount; --i >= 0;)
+ if (meshes[i].connections != null
+ && meshes[i].modelIndex == ((Integer) ((Object[]) value)[0])
+ .intValue())
+ meshes[i].updateCoordinates(
+ (Matrix4f) ((Object[]) value)[2],
+ (BitSet) ((Object[]) value)[1]);
+ return;
+ }
- if ("modelIndex" == propertyName) {
- if (!iHaveModelIndex) {
- modelIndex = ((Integer) value).intValue();
- isFixed = (modelIndex < 0);
- sg.setModelIndex(Math.abs(modelIndex));
- }
- return;
- }
+ if ("modelIndex" == propertyName) {
+ if (!iHaveModelIndex) {
+ modelIndex = ((Integer) value).intValue();
+ isFixed = (modelIndex < 0);
+ sg.setModelIndex(Math.abs(modelIndex));
+ }
+ return;
+ }
- if ("lcaoCartoon" == propertyName || "lonePair" == propertyName
- || "radical" == propertyName) {
- // z x center rotationAxis (only one of x, y, or z is nonzero; in radians)
- Vector3f[] info = (Vector3f[]) value;
- if (!explicitID) {
- setPropertySuper("thisID", null, null);
- }
- // center (info[2]) is set in SurfaceGenerator
- if (!sg.setParameter("lcaoCartoonCenter", info[2]))
- drawLcaoCartoon(
- info[0],
- info[1],
- info[3],
- ("lonePair" == propertyName ? 2 : "radical" == propertyName ? 1 : 0));
- return;
- }
+ if ("lcaoCartoon" == propertyName || "lonePair" == propertyName
+ || "radical" == propertyName) {
+ // z x center rotationAxis (only one of x, y, or z is nonzero; in
+ // radians)
+ Vector3f[] info = (Vector3f[]) value;
+ if (!explicitID) {
+ setPropertySuper("thisID", null, null);
+ }
+ // center (info[2]) is set in SurfaceGenerator
+ if (!sg.setParameter("lcaoCartoonCenter", info[2]))
+ drawLcaoCartoon(info[0], info[1], info[3],
+ ("lonePair" == propertyName ? 2
+ : "radical" == propertyName ? 1 : 0));
+ return;
+ }
- if ("select" == propertyName) {
- if (iHaveBitSets)
- return;
- }
+ if ("select" == propertyName) {
+ if (iHaveBitSets)
+ return;
+ }
- if ("ignore" == propertyName) {
- if (iHaveBitSets)
- return;
- }
+ if ("ignore" == propertyName) {
+ if (iHaveBitSets)
+ return;
+ }
- if ("meshcolor" == propertyName) {
- int rgb = ((Integer) value).intValue();
- meshColix = Graphics3D.getColix(rgb);
- if (thisMesh != null)
- thisMesh.meshColix = meshColix;
- return;
- }
+ if ("meshcolor" == propertyName) {
+ int rgb = ((Integer) value).intValue();
+ meshColix = Graphics3D.getColix(rgb);
+ if (thisMesh != null)
+ thisMesh.meshColix = meshColix;
+ return;
+ }
- if ("offset" == propertyName) {
- offset = new Point3f((Point3f) value);
- if (offset.equals(JmolConstants.center))
- offset = null;
- if (thisMesh != null) {
- thisMesh.ptOffset = offset;
- thisMesh.altVertices = null;
- }
- return;
- }
+ if ("offset" == propertyName) {
+ offset = new Point3f((Point3f) value);
+ if (offset.equals(JmolConstants.center))
+ offset = null;
+ if (thisMesh != null) {
+ thisMesh.ptOffset = offset;
+ thisMesh.altVertices = null;
+ }
+ return;
+ }
- if ("rotate" == propertyName) {
- Point4f pt4 = (Point4f) value;
- if (thisMesh != null) {
- if (pt4 == null || thisMesh.q == null)
- thisMesh.q = new Quaternion();
- thisMesh.q = thisMesh.q.mul(new Quaternion(pt4));
- thisMesh.altVertices = null;
- }
- return;
- }
+ if ("rotate" == propertyName) {
+ Point4f pt4 = (Point4f) value;
+ if (thisMesh != null) {
+ if (pt4 == null || thisMesh.q == null)
+ thisMesh.q = new Quaternion();
+ thisMesh.q = thisMesh.q.mul(new Quaternion(pt4));
+ thisMesh.altVertices = null;
+ }
+ return;
+ }
- if ("bsDisplay" == propertyName) {
- bsDisplay = (BitSet) value;
- return;
- }
- if ("displayWithin" == propertyName) {
- Object[] o = (Object[]) value;
- displayWithinDistance2 = ((Float) o[0]).floatValue();
- isDisplayWithinNot = (displayWithinDistance2 < 0);
- displayWithinDistance2 *= displayWithinDistance2;
- displayWithinPoints = (List<Point3f>) o[3];
- if (displayWithinPoints.size() == 0)
- displayWithinPoints = viewer.getAtomPointVector((BitSet) o[2]);
- return;
- }
+ if ("bsDisplay" == propertyName) {
+ bsDisplay = (BitSet) value;
+ return;
+ }
+ if ("displayWithin" == propertyName) {
+ Object[] o = (Object[]) value;
+ displayWithinDistance2 = ((Float) o[0]).floatValue();
+ isDisplayWithinNot = (displayWithinDistance2 < 0);
+ displayWithinDistance2 *= displayWithinDistance2;
+ displayWithinPoints = (List<Point3f>) o[3];
+ if (displayWithinPoints.size() == 0)
+ displayWithinPoints = viewer.getAtomPointVector((BitSet) o[2]);
+ return;
+ }
- if ("finalize" == propertyName) {
- if (thisMesh != null) {
- String cmd = (String) value;
- if (cmd != null && !cmd.startsWith("; isosurface map")) {
- thisMesh.setDiscreteColixes(sg.getParams().contoursDiscrete, sg
- .getParams().contourColixes);
- setJvxlInfo();
- }
- setScriptInfo(cmd);
- }
- clearSg();
- return;
- }
+ if ("finalize" == propertyName) {
+ if (thisMesh != null) {
+ String cmd = (String) value;
+ if (cmd != null && !cmd.startsWith("; isosurface map")) {
+ thisMesh.setDiscreteColixes(
+ sg.getParams().contoursDiscrete,
+ sg.getParams().contourColixes);
+ setJvxlInfo();
+ }
+ setScriptInfo(cmd);
+ }
+ clearSg();
+ return;
+ }
- if ("privateKey" == propertyName) {
- this.privateKey = ((Double) value).doubleValue();
- return;
- }
+ if ("privateKey" == propertyName) {
+ this.privateKey = ((Double) value).doubleValue();
+ return;
+ }
- if ("connections" == propertyName) {
- if (currentMesh != null)
- connections = currentMesh.connections = (int[]) value;
- return;
- }
+ if ("connections" == propertyName) {
+ if (currentMesh != null)
+ connections = currentMesh.connections = (int[]) value;
+ return;
+ }
- if ("cutoffRange" == propertyName) {
- cutoffRange = (float[]) value;
- return;
- }
+ if ("cutoffRange" == propertyName) {
+ cutoffRange = (float[]) value;
+ return;
+ }
- // Isosurface / SurfaceGenerator both interested
+ // Isosurface / SurfaceGenerator both interested
- if ("slab" == propertyName) {
- if (value instanceof Integer) {
- if (thisMesh != null)
- thisMesh.jvxlData.slabValue = ((Integer) value).intValue();
- return;
- }
- if (thisMesh != null) {
- Object[] slabInfo = (Object[]) value;
- int tok = ((Integer) slabInfo[0]).intValue();
- switch (tok) {
- case Token.mesh:
- Object[] data = (Object[]) slabInfo[1];
- Mesh m = getMesh((String) data[1]);
- if (m == null)
- return;
- data[1] = m;
- break;
- }
- slabPolygons(slabInfo);
- return;
- }
- }
+ if ("slab" == propertyName) {
+ if (value instanceof Integer) {
+ if (thisMesh != null)
+ thisMesh.jvxlData.slabValue = ((Integer) value).intValue();
+ return;
+ }
+ if (thisMesh != null) {
+ Object[] slabInfo = (Object[]) value;
+ int tok = ((Integer) slabInfo[0]).intValue();
+ switch (tok) {
+ case Token.mesh:
+ Object[] data = (Object[]) slabInfo[1];
+ Mesh m = getMesh((String) data[1]);
+ if (m == null)
+ return;
+ data[1] = m;
+ break;
+ }
+ slabPolygons(slabInfo);
+ return;
+ }
+ }
- if ("cap" == propertyName) {
- // for lcaocartoons?
- if (thisMesh != null && thisMesh.polygonCount != 0) {
- thisMesh.slabPolygons((Object[]) value, true);
- thisMesh.initialize(thisMesh.lighting, null, null);
- return;
- }
- }
- if ("map" == propertyName) {
- setProperty("squareData", Boolean.FALSE, null);
- if (thisMesh == null || thisMesh.vertexCount == 0)
- return;
- }
+ if ("cap" == propertyName) {
+ // for lcaocartoons?
+ if (thisMesh != null && thisMesh.polygonCount != 0) {
+ thisMesh.slabPolygons((Object[]) value, true);
+ thisMesh.initialize(thisMesh.lighting, null, null);
+ return;
+ }
+ }
+ if ("map" == propertyName) {
+ setProperty("squareData", Boolean.FALSE, null);
+ if (thisMesh == null || thisMesh.vertexCount == 0)
+ return;
+ }
- if ("deleteVdw" == propertyName) {
- for (int i = meshCount; --i >= 0;)
- if (isomeshes[i].bsVdw != null
- && (bs == null || bs.intersects(isomeshes[i].bsVdw)))
- deleteMesh(i);
- currentMesh = thisMesh = null;
- return;
- }
- if ("mapColor" == propertyName || "readFile" == propertyName) {
- if (value == null) {
- // ScriptEvaluator has passed the filename to us as the value of the
- // "fileName" property. We retrieve that from the surfaceGenerator
- // and open a BufferedReader for it. Or not. But that would be
- // unlikely since we have just checked it in ScriptEvaluator
- value = viewer.getBufferedReaderOrErrorMessageFromName(
- sg.getFileName(), null, true);
- if (value instanceof String) {
- Logger.error("Isosurface: could not open file " + sg.getFileName()
- + " -- " + value);
- return;
- }
- try {
- value = new BufferedReader(new InputStreamReader((InputStream) value,
- "ISO-8859-1"));
- } catch (UnsupportedEncodingException e) {
- // ignore
- }
- }
- } else if ("atomIndex" == propertyName) {
- atomIndex = ((Integer) value).intValue();
- } else if ("center" == propertyName) {
- center.set((Point3f) value);
- } else if ("colorRGB" == propertyName) {
- int rgb = ((Integer) value).intValue();
- defaultColix = Graphics3D.getColix(rgb);
- } else if ("contour" == propertyName) {
- explicitContours = true;
- } else if ("functionXY" == propertyName) {
- //allowContourLines = false;
- if (sg.isStateDataRead())
- setScriptInfo(null); // for script DATA1
- } else if ("init" == propertyName) {
- newSg();
- } else if ("getSurfaceSets" == propertyName) {
- if (thisMesh != null) {
- thisMesh.thisSet = ((Integer) value).intValue();
- thisMesh.calculatedVolume = null;
- thisMesh.calculatedArea = null;
- }
- } else if ("localName" == propertyName) {
- value = viewer.getOutputStream((String) value, null);
- propertyName = "outputStream";
- } else if ("molecularOrbital" == propertyName) {
- if (value instanceof Integer) {
- moNumber = ((Integer) value).intValue();
- moLinearCombination = null;
- } else {
- moLinearCombination = (float[]) value;
- moNumber = 0;
- }
- if (!isColorExplicit)
- isPhaseColored = true;
- } else if ("phase" == propertyName) {
- isPhaseColored = true;
- } else if ("plane" == propertyName) {
- //allowContourLines = false;
- } else if ("pocket" == propertyName) {
- // Boolean pocket = (Boolean) value;
- // lighting = (pocket.booleanValue() ? JmolConstants.FULLYLIT
- // : JmolConstants.FRONTLIT);
- } else if ("scale3d" == propertyName) {
- scale3d = ((Float) value).floatValue();
- if (thisMesh != null) {
- thisMesh.scale3d = thisMesh.jvxlData.scale3d = scale3d;
- thisMesh.altVertices = null;
- }
- } else if ("title" == propertyName) {
- if (value instanceof String && "-".equals(value))
- value = null;
- setPropertySuper(propertyName, value, bs);
- value = title;
- } else if ("withinPoints" == propertyName) {
- Object[] o = (Object[]) value;
- withinDistance2 = ((Float) o[0]).floatValue();
- isWithinNot = (withinDistance2 < 0);
- withinDistance2 *= withinDistance2;
- withinPoints = (List<Point3f>) o[3];
- if (withinPoints.size() == 0)
- withinPoints = viewer.getAtomPointVector((BitSet) o[2]);
- } else if (("nci" == propertyName || "orbital" == propertyName)
- && sg != null) {
- sg.getParams().testFlags = (viewer.getTestFlag(2) ? 2 : 0);
- }
+ if ("deleteVdw" == propertyName) {
+ for (int i = meshCount; --i >= 0;)
+ if (isomeshes[i].bsVdw != null
+ && (bs == null || bs.intersects(isomeshes[i].bsVdw)))
+ deleteMesh(i);
+ currentMesh = thisMesh = null;
+ return;
+ }
+ if ("mapColor" == propertyName || "readFile" == propertyName) {
+ if (value == null) {
+ // ScriptEvaluator has passed the filename to us as the value of
+ // the
+ // "fileName" property. We retrieve that from the
+ // surfaceGenerator
+ // and open a BufferedReader for it. Or not. But that would be
+ // unlikely since we have just checked it in ScriptEvaluator
+ value = viewer.getBufferedReaderOrErrorMessageFromName(sg
+ .getFileName(), null, true);
+ if (value instanceof String) {
+ Logger.error("Isosurface: could not open file "
+ + sg.getFileName() + " -- " + value);
+ return;
+ }
+ try {
+ value = new BufferedReader(new InputStreamReader(
+ (InputStream) value, "ISO-8859-1"));
+ } catch (UnsupportedEncodingException e) {
+ // ignore
+ }
+ }
+ } else if ("atomIndex" == propertyName) {
+ atomIndex = ((Integer) value).intValue();
+ } else if ("center" == propertyName) {
+ center.set((Point3f) value);
+ } else if ("colorRGB" == propertyName) {
+ int rgb = ((Integer) value).intValue();
+ defaultColix = Graphics3D.getColix(rgb);
+ } else if ("contour" == propertyName) {
+ explicitContours = true;
+ } else if ("functionXY" == propertyName) {
+ // allowContourLines = false;
+ if (sg.isStateDataRead())
+ setScriptInfo(null); // for script DATA1
+ } else if ("init" == propertyName) {
+ newSg();
+ } else if ("getSurfaceSets" == propertyName) {
+ if (thisMesh != null) {
+ thisMesh.thisSet = ((Integer) value).intValue();
+ thisMesh.calculatedVolume = null;
+ thisMesh.calculatedArea = null;
+ }
+ } else if ("localName" == propertyName) {
+ value = viewer.getOutputStream((String) value, null);
+ propertyName = "outputStream";
+ } else if ("molecularOrbital" == propertyName) {
+ if (value instanceof Integer) {
+ moNumber = ((Integer) value).intValue();
+ moLinearCombination = null;
+ } else {
+ moLinearCombination = (float[]) value;
+ moNumber = 0;
+ }
+ if (!isColorExplicit)
+ isPhaseColored = true;
+ } else if ("phase" == propertyName) {
+ isPhaseColored = true;
+ } else if ("plane" == propertyName) {
+ // allowContourLines = false;
+ } else if ("pocket" == propertyName) {
+ // Boolean pocket = (Boolean) value;
+ // lighting = (pocket.booleanValue() ? JmolConstants.FULLYLIT
+ // : JmolConstants.FRONTLIT);
+ } else if ("scale3d" == propertyName) {
+ scale3d = ((Float) value).floatValue();
+ if (thisMesh != null) {
+ thisMesh.scale3d = thisMesh.jvxlData.scale3d = scale3d;
+ thisMesh.altVertices = null;
+ }
+ } else if ("title" == propertyName) {
+ if (value instanceof String && "-".equals(value))
+ value = null;
+ setPropertySuper(propertyName, value, bs);
+ value = title;
+ } else if ("withinPoints" == propertyName) {
+ Object[] o = (Object[]) value;
+ withinDistance2 = ((Float) o[0]).floatValue();
+ isWithinNot = (withinDistance2 < 0);
+ withinDistance2 *= withinDistance2;
+ withinPoints = (List<Point3f>) o[3];
+ if (withinPoints.size() == 0)
+ withinPoints = viewer.getAtomPointVector((BitSet) o[2]);
+ } else if (("nci" == propertyName || "orbital" == propertyName)
+ && sg != null) {
+ sg.getParams().testFlags = (viewer.getTestFlag(2) ? 2 : 0);
+ }
- // surface Export3D only (return TRUE) or shared (return FALSE)
+ // surface Export3D only (return TRUE) or shared (return FALSE)
- if (sg != null && sg.setParameter(propertyName, value, bs)) {
- if (sg.isValid())
- return;
- propertyName = "delete";
- }
+ if (sg != null && sg.setParameter(propertyName, value, bs)) {
+ if (sg.isValid())
+ return;
+ propertyName = "delete";
+ }
- // ///////////// isosurface LAST, shared
+ // ///////////// isosurface LAST, shared
- if ("init" == propertyName) {
- explicitID = false;
- scriptAppendix = "";
- String script = (value instanceof String ? (String) value : null);
- int pt = (script == null ? -1 : script.indexOf("# ID="));
- actualID = (pt >= 0 ? Parser.getNextQuotedString(script, pt) : null);
- setPropertySuper("thisID", MeshCollection.PREVIOUS_MESH_ID, null);
- if (script != null && !(iHaveBitSets = getScriptBitSets(script, null)))
- sg.setParameter("select", bs);
- initializeIsosurface();
- sg.setModelIndex(isFixed ? -1 : modelIndex);
- return;
- }
+ if ("init" == propertyName) {
+ explicitID = false;
+ scriptAppendix = "";
+ String script = (value instanceof String ? (String) value : null);
+ int pt = (script == null ? -1 : script.indexOf("# ID="));
+ actualID = (pt >= 0 ? Parser.getNextQuotedString(script, pt) : null);
+ setPropertySuper("thisID", MeshCollection.PREVIOUS_MESH_ID, null);
+ if (script != null
+ && !(iHaveBitSets = getScriptBitSets(script, null)))
+ sg.setParameter("select", bs);
+ initializeIsosurface();
+ sg.setModelIndex(isFixed ? -1 : modelIndex);
+ return;
+ }
- if ("clear" == propertyName) {
- discardTempData(true);
- return;
- }
+ if ("clear" == propertyName) {
+ discardTempData(true);
+ return;
+ }
- /*
- * if ("background" == propertyName) { boolean doHide = !((Boolean)
- * value).booleanValue(); if (thisMesh != null) thisMesh.hideBackground =
- * doHide; else { for (int i = meshCount; --i >= 0;)
- * meshes[i].hideBackground = doHide; } return; }
- */
+ /*
+ * if ("background" == propertyName) { boolean doHide = !((Boolean)
+ * value).booleanValue(); if (thisMesh != null) thisMesh.hideBackground
+ * = doHide; else { for (int i = meshCount; --i >= 0;)
+ * meshes[i].hideBackground = doHide; } return; }
+ */
- if (propertyName == "deleteModelAtoms") {
- int modelIndex = ((int[]) ((Object[]) value)[2])[0];
- int firstAtomDeleted = ((int[]) ((Object[]) value)[2])[1];
- int nAtomsDeleted = ((int[]) ((Object[]) value)[2])[2];
- for (int i = meshCount; --i >= 0;) {
- Mesh m = meshes[i];
- if (m == null)
- continue;
- if (m.modelIndex == modelIndex) {
- meshCount--;
- if (m == currentMesh)
- currentMesh = thisMesh = null;
- meshes = isomeshes = (IsosurfaceMesh[]) ArrayUtil.deleteElements(
- meshes, i, 1);
- } else if (m.modelIndex > modelIndex) {
- m.modelIndex--;
- if (m.atomIndex >= firstAtomDeleted)
- m.atomIndex -= nAtomsDeleted;
- }
- }
- return;
- }
+ if (propertyName == "deleteModelAtoms") {
+ int modelIndex = ((int[]) ((Object[]) value)[2])[0];
+ int firstAtomDeleted = ((int[]) ((Object[]) value)[2])[1];
+ int nAtomsDeleted = ((int[]) ((Object[]) value)[2])[2];
+ for (int i = meshCount; --i >= 0;) {
+ Mesh m = meshes[i];
+ if (m == null)
+ continue;
+ if (m.modelIndex == modelIndex) {
+ meshCount--;
+ if (m == currentMesh)
+ currentMesh = thisMesh = null;
+ meshes = isomeshes = (IsosurfaceMesh[]) ArrayUtil
+ .deleteElements(meshes, i, 1);
+ } else if (m.modelIndex > modelIndex) {
+ m.modelIndex--;
+ if (m.atomIndex >= firstAtomDeleted)
+ m.atomIndex -= nAtomsDeleted;
+ }
+ }
+ return;
+ }
- // processing by meshCollection:
- setPropertySuper(propertyName, value, bs);
- }
+ // processing by meshCollection:
+ setPropertySuper(propertyName, value, bs);
+ }
protected void slabPolygons(Object[] slabInfo) {
thisMesh.slabPolygons(slabInfo, false);
Modified: branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
===================================================================
--- branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2011-10-04 18:34:01 UTC (rev 16252)
+++ branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2011-10-04 18:37:11 UTC (rev 16253)
@@ -73,7 +73,7 @@
imesh = (IsosurfaceMesh) isosurface.meshes[i];
hasColorRange = false;
if (renderMesh(mySlabValue, slabValue)) {
- System.out.println("render isossurface " + i + " " + isosurface.meshCount);
+ //System.out.println("render isossurface " + i + " " + isosurface.meshCount);
if (!isExport)
renderInfo();
if (isExport && haveBsSlabGhost) {
Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2011-10-04 18:34:01 UTC (rev 16252)
+++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2011-10-04 18:37:11 UTC (rev 16253)
@@ -4,6 +4,9 @@
version=12.2.1_dev
+# CODE -- ?? Eclipse is refusing to set tabs to 2 spaces on this new project??
+
+# bug fix: color isosurface {atomset} <color> does not work if isosurface has not already been mapped.
# bug fix: PDB reader not reading Rasmol-style files with multiple bonding
# CONECT 1 2 2
# or
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