From: <ha...@us...> - 2009-11-13 23:15:06
|
Revision: 11739 http://jmol.svn.sourceforge.net/jmol/?rev=11739&view=rev Author: hansonr Date: 2009-11-13 23:14:55 +0000 (Fri, 13 Nov 2009) Log Message: ----------- version=11.8.10_dev # bug fix: zoom/rotateXY modes not properly isolated Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-13 20:45:37 UTC (rev 11738) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-13 23:14:55 UTC (rev 11739) @@ -4,6 +4,7 @@ version=11.8.10_dev +# bug fix: zoom/rotateXY modes not properly isolated # bug fix: moveto with {0 0 0 0} uses instead {0 0 1 0} # bug fix: zoomto fights with user over orientation # bug fix: AIMS files with empty lines preceding keyword lines are now recognized Modified: branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager.java 2009-11-13 20:45:37 UTC (rev 11738) +++ branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager.java 2009-11-13 23:14:55 UTC (rev 11739) @@ -628,14 +628,15 @@ } // fall through case MIDDLE: - // if (deltaY < 0 && deltaX > deltaY || deltaY > 0 && deltaX < deltaY) - if (Math.abs(deltaY) > 5 * Math.abs(deltaX)) + if (Math.abs(deltaY) > 5 * Math.abs(deltaX)) { + // if (deltaY < 0 && deltaX > deltaY || deltaY > 0 && deltaX < deltaY) checkMotion(); - viewer.zoomBy(deltaY); - // if (deltaX < 0 && deltaY > deltaX || deltaX > 0 && deltaY < deltaX) - if (Math.abs(deltaX) > 5 * Math.abs(deltaY)) + viewer.zoomBy(deltaY); + } else if (Math.abs(deltaX) > 5 * Math.abs(deltaY)) { + // if (deltaX < 0 && deltaY > deltaX || deltaX > 0 && deltaY < deltaX) checkMotion(); - viewer.rotateZBy(-deltaX); + viewer.rotateZBy(-deltaX); + } return; case SHIFT_RIGHT: // the one-button Mac folks won't get this gesture checkMotion(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-18 19:30:24
|
Revision: 11754 http://jmol.svn.sourceforge.net/jmol/?rev=11754&view=rev Author: hansonr Date: 2009-11-18 19:30:16 +0000 (Wed, 18 Nov 2009) Log Message: ----------- version=11.8.10_dev # bug fix: MSIE mouse-wheel malfunction due to Jmol not consuming the wheel motion Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager14.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-18 18:42:30 UTC (rev 11753) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-18 19:30:16 UTC (rev 11754) @@ -4,6 +4,7 @@ version=11.8.10_dev +# bug fix: MSIE mouse-wheel malfunction due to Jmol not consuming the wheel motion # bug fix: isosurface xxx lcaocartoon ... does not always honor xxx as isosurface name # bug fix: Hall name translator can incorrectly assign matrix for F m -3 m group # bug fix: Gaussian '09 reader not reading " Atom AN" properly in frequency lists Modified: branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager14.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager14.java 2009-11-18 18:42:30 UTC (rev 11753) +++ branches/v11_8/Jmol/src/org/jmol/viewer/MouseManager14.java 2009-11-18 19:30:16 UTC (rev 11754) @@ -44,7 +44,8 @@ viewer.getDisplay().removeMouseWheelListener(this); } - public void mouseWheelMoved(MouseWheelEvent e) { + public void mouseWheelMoved(MouseWheelEvent e) { + e.consume(); mouseWheel(e.getWhen(), e.getWheelRotation(), e.getModifiers()); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-23 19:20:36
|
Revision: 11786 http://jmol.svn.sourceforge.net/jmol/?rev=11786&view=rev Author: hansonr Date: 2009-11-23 19:20:28 +0000 (Mon, 23 Nov 2009) Log Message: ----------- version=11.8.11_dev # bug fix: zshade not resetting properly; now reset off with reset() or load of model Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-23 17:32:07 UTC (rev 11785) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-23 19:20:28 UTC (rev 11786) @@ -4,6 +4,7 @@ version=11.8.11_dev +# bug fix: zshade not resetting properly; now reset off with reset() or load of model # bug fix: occasional null pointer error during ZAP due to continued rendering by # previous graphic painting thread @@ -64,7 +65,7 @@ # bug fix: write VAR for string array does not work. # bug fix: GAMESS reader vibrations use wrong atom coordinates # bug fix: PQR reader not adaptive -# bug fix: zshade now working correctly +# bug fix: zshade now working correctly (almost -- see 11.8.11) # bug fix: setting spacefill to a large user-defined VDW radius incorrect # bug fix: Gaussian 09 LOG file reader upgrade for MOs # bug fix: unitcell offset {1 1 1}; select UNITCELL Modified: branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java 2009-11-23 17:32:07 UTC (rev 11785) +++ branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java 2009-11-23 19:20:28 UTC (rev 11786) @@ -553,7 +553,7 @@ + ";minimizationsteps;minimizationrefresh;minimizationcriterion;navigationmode;" + ";perspectivedepth;visualrange;perspectivemodel;refreshing;rotationradius" + ";showaxes;showaxis1;showaxis2;showaxis3;showboundbox;showfrank;showunitcell" - + ";slabenabled;specular;specularexponent;specularpercent;specularpower;stateversion" + + ";slabenabled;zshade;specular;specularexponent;specularpercent;specularpower;stateversion" + ";statusreporting;stereo;stereostate" + ";unitcellcolor;windowcentered;zerobasedxyzrasmol;zoomenabled" + @@ -739,7 +739,6 @@ boolean showKeyStrokes = true; boolean showMeasurements = true; boolean zoomLarge = true; //false would be like Chime - boolean zShade = false; String backgroundImageFileName; //atoms and bonds @@ -1189,7 +1188,7 @@ disablePopupMenu = g.disablePopupMenu; defaultDirectory = g.defaultDirectory; messageStyleChime = g.messageStyleChime; - zShade = g.zShade; + //zShade = g.zShade; } resetParameterStringValue("animFrameCallback", g); @@ -1400,7 +1399,7 @@ setParameterValue("wireframeRotation", wireframeRotation); setParameterValue("zoomEnabled", true); setParameterValue("zoomLarge", zoomLarge); - setParameterValue("zShade", zShade); + setParameterValue("zShade", false); setParameterValue("zeroBasedXyzRasmol", zeroBasedXyzRasmol); } Modified: branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java 2009-11-23 17:32:07 UTC (rev 11785) +++ branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java 2009-11-23 19:20:28 UTC (rev 11786) @@ -187,6 +187,8 @@ commands.append(" slab ").append(slabPercentSetting).append(";depth ") .append(depthPercentSetting).append( slabEnabled && !isNavigationMode ? ";slab on" : "").append(";\n"); + if (zShadeEnabled) + commands.append(" set zShade;\n"); if (slabPlane != null) commands.append(" slab plane ").append(Escape.escape(slabPlane)).append( ";\n"); @@ -738,6 +740,7 @@ boolean slabEnabled = false; boolean internalSlab = false; + boolean zShadeEnabled = false; int slabPercentSetting; int depthPercentSetting; @@ -752,12 +755,18 @@ viewer.getGlobalSettings().setParameterValue("slabEnabled", slabEnabled); } + void setZShadeEnabled(boolean zShadeEnabled) { + this.zShadeEnabled = zShadeEnabled; + viewer.getGlobalSettings().setParameterValue("zShade", zShadeEnabled); + } + void slabReset() { slabToPercent(100); depthToPercent(0); depthPlane = null; slabPlane = null; setSlabEnabled(false); + setZShadeEnabled(false); } int getSlabPercentSetting() { @@ -1078,24 +1087,15 @@ height = (antialias ? screenHeight * 2 : screenHeight); scaleFitToScreen(false, useZoomLarge, resetSlab, resetZoom); finalizeTransformParameters(); - //System.out.println("transformManager setScreenParameters sppa=" + scalePixelsPerAngstrom - // + " screenWidth,Height, useZoomLarge, antialias, resetSlab, resetZoom " - //+ useZoomLarge + ","+antialias + "," + resetSlab + "," + resetZoom); } void setAntialias(boolean TF) { - //System.out.println("setAntialias antialias=" + antialias + " TF=" + TF - // + " width=" + width + " height=" + height + " screenWidth/height" + - // screenWidth + "," + screenHeight); - boolean isNew = (antialias != TF); antialias = TF; width = (antialias ? screenWidth * 2 : screenWidth); height = (antialias ? screenHeight * 2 : screenHeight); if (isNew) scaleFitToScreen(false, useZoomLarge, false, false); - //System.out.println("setAntialias2 " + TF + "width=" + width + " height=" + height - // + " screenWidth/height" + screenWidth + "," + screenHeight); } private float defaultScaleToScreen(float radius) { @@ -1115,17 +1115,11 @@ } void scaleFitToScreen(boolean andCenter) { - //System.out.println("transformManager scaleFitToSreen " + andCenter); scaleFitToScreen(andCenter, viewer.getZoomLarge(), true, true); } void scaleFitToScreen(boolean andCenter, boolean zoomLarge, boolean resetSlab, boolean resetZoom) { - //System.out.println("transformManager scaleFitToScreen andcenter " + andCenter - // + " screenWidth,Height, " + screenWidth + "," + screenHeight + - // " zoomLarge, antialias, resetSlab, resetZoom width/height " - // + zoomLarge + ","+antialias + "," + resetSlab + "," + resetZoom - // + " " + width + "/" + height); if (width == 0 || height == 0) { screenPixelCount = 1; } else { @@ -1270,8 +1264,6 @@ // cale to screen coordinates matrixTemp.setZero(); matrixTemp.set(scalePixelsPerAngstrom); - - //System.out.println("calcTransMatrix scalepixelsperangstrom=" + scalePixelsPerAngstrom); // negate y (for screen) and z (for zbuf) matrixTemp.m11 = matrixTemp.m22 = -scalePixelsPerAngstrom; @@ -1281,9 +1273,6 @@ // note that the image is still centered at 0, 0 in the xy plane - // System.out.println("modelCenterOffset + matrixTransform: " + modelCenterOffset - // + matrixTransform); - } void rotatePoint(Point3f pt, Point3f ptRot) { @@ -1382,7 +1371,6 @@ void unTransformPoint(Point3f screenPt, Point3f coordPt) { //draw move2D pointT.set(screenPt); - //System.out.println("unTransformPt screenpt " + pointT + " " + fixedRotationOffset); if (isNavigationMode) { pointT.x -= navigationOffset.x; pointT.y -= navigationOffset.y; @@ -1400,7 +1388,6 @@ pointT.y += navigationShiftXY.y; } matrixUnTransform(pointT, coordPt); - //System.out.println("unTransformPt pointT " + pointT); } protected void matrixUnTransform(Point3f screen, Point3f angstroms) { Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 17:32:07 UTC (rev 11785) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 19:20:28 UTC (rev 11786) @@ -1052,7 +1052,7 @@ transformManager.finalizeTransformParameters(); g3d.setSlabAndDepthValues(transformManager.slabValue, - transformManager.depthValue, global.zShade, + transformManager.depthValue, transformManager.zShadeEnabled, transformManager.zSlabValue, transformManager.zDepthValue); } @@ -1434,10 +1434,6 @@ return ColorManager.getSpecularPercent(); } - boolean getZShade() { - return global.zShade; - } - public short getColixAtomPalette(Atom atom, byte pid) { return colorManager.getColixAtomPalette(atom, pid); } @@ -5619,7 +5615,7 @@ break; } if (key.equalsIgnoreCase("zShade")) { - global.zShade = value; + transformManager.setZShadeEnabled(value); break; } if (key.equalsIgnoreCase("drawHover")) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-24 20:49:58
|
Revision: 11796 http://jmol.svn.sourceforge.net/jmol/?rev=11796&view=rev Author: hansonr Date: 2009-11-24 20:49:50 +0000 (Tue, 24 Nov 2009) Log Message: ----------- version=11.8.11_dev # bug fix: zShade/navigation mode incompatibility # bug fix: navigate TRACE broken in 11.7.47 Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager11.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-23 19:49:17 UTC (rev 11795) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-24 20:49:50 UTC (rev 11796) @@ -4,6 +4,8 @@ version=11.8.11_dev +# bug fix: zShade/navigation mode incompatibility +# bug fix: navigate TRACE broken in 11.7.47 # code: JmolFrameExportJmolAdapter abandoned -- hasn't been implemented since 11.0 # bug fix: zshade not resetting properly; now reset off with reset() or load of model Modified: branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java 2009-11-23 19:49:17 UTC (rev 11795) +++ branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager.java 2009-11-24 20:49:50 UTC (rev 11796) @@ -1593,12 +1593,14 @@ if (navCenter != null && isNavigationMode) { Point3f pt = new Point3f(navigationCenter); pt.add(aaStepNavCenter); + navigating = true; navigate(0, pt); if (!Float.isNaN(xNav) && !Float.isNaN(yNav)) navTranslatePercent(0, xNavTransStart + xNavTransDelta * fStep, yNavTransStart + yNavTransDelta * fStep); if (!Float.isNaN(navDepth)) setNavigationDepthPercent(0, navDepthStart + navDepthDelta * fStep); + navigating = false; } targetTime += frameTimeMillis; if (System.currentTimeMillis() < targetTime) { Modified: branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager11.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager11.java 2009-11-23 19:49:17 UTC (rev 11795) +++ branches/v11_8/Jmol/src/org/jmol/viewer/TransformManager11.java 2009-11-24 20:49:50 UTC (rev 11796) @@ -25,7 +25,7 @@ import org.jmol.util.Escape; import org.jmol.util.Logger; -import org.jmol.viewer.StateManager.Orientation; +//import org.jmol.viewer.StateManager.Orientation; import javax.vecmath.Point3f; import javax.vecmath.Vector3f; @@ -316,8 +316,8 @@ depthValue = Integer.MAX_VALUE; if (!slabEnabled) return; - slabValue = (isNavigationMode ? 10 : (int) (referencePlaneOffset - navigationSlabOffset)); - depthValue = zValueFromPercent(depthPercentSetting); + zSlabValue = slabValue = (isNavigationMode ? -100 : 0) + (int) (referencePlaneOffset - navigationSlabOffset); + zDepthValue = depthValue = zValueFromPercent(depthPercentSetting); viewer.getGlobalSettings().setParameterValue("navigationDepth",getNavigationDepthPercent()); viewer.getGlobalSettings().setParameterValue("navigationSlab",getNavigationSlabOffsetPercent()); @@ -622,8 +622,10 @@ private void navigateTo(float floatSecondsTotal, Vector3f axis, float degrees, Point3f center, float depthPercent, float xTrans, float yTrans) { - +/* Orientation o = viewer.getOrientation(); + System.out.println("BEG " + getOrientationText(0)); + if (!Float.isNaN(degrees) && degrees != 0) navigate(0, axis, degrees); if (center != null) { @@ -634,8 +636,86 @@ if (!Float.isNaN(depthPercent)) setNavigationDepthPercent(depthPercent); Orientation o1 = viewer.getOrientation(); + System.out.println("END1 " + getOrientationText(0)); o.restore(0, true); o1.restore(floatSecondsTotal, true); + System.out.println("END2 " + getOrientationText(0)); + */ + + Point3f ptMoveToCenter = (center == null ? navigationCenter : center); + int fps = 30; + int totalSteps = (int) (floatSecondsTotal * fps); + if (floatSecondsTotal > 0) + viewer.setInMotion(true); + if (degrees == 0) + degrees = Float.NaN; + if (totalSteps > 1) { + int frameTimeMillis = 1000 / fps; + long targetTime = System.currentTimeMillis(); + float depthStart = getNavigationDepthPercent(); + float depthDelta = depthPercent - depthStart; + float xTransStart = navigationOffset.x; + float xTransDelta = xTrans - xTransStart; + float yTransStart = navigationOffset.y; + float yTransDelta = yTrans - yTransStart; + float degreeStep = degrees / totalSteps; + aaStepCenter.set(ptMoveToCenter); + aaStepCenter.sub(navigationCenter); + aaStepCenter.scale(1f / totalSteps); + Point3f centerStart = new Point3f(navigationCenter); + for (int iStep = 1; iStep < totalSteps; ++iStep) { + navigating = true; + float fStep = iStep / (totalSteps - 1f); + if (!Float.isNaN(degrees)) + navigate(0, axis, degreeStep); + if (center != null) { + centerStart.add(aaStepCenter); + navigate(0, centerStart); + } + if (!Float.isNaN(xTrans) || !Float.isNaN(yTrans)) { + float x = Float.NaN; + float y = Float.NaN; + if (!Float.isNaN(xTrans)) + x = xTransStart + xTransDelta * fStep; + if (!Float.isNaN(yTrans)) + y = yTransStart + yTransDelta * fStep; + navTranslatePercent(-1, x, y); + } + + if (!Float.isNaN(depthPercent)) { + setNavigationDepthPercent(depthStart + depthDelta * fStep); + } + navigating = false; + targetTime += frameTimeMillis; + if (System.currentTimeMillis() < targetTime) { + viewer.requestRepaintAndWait(); + if (!viewer.isScriptExecuting()) + break; + int sleepTime = (int) (targetTime - System.currentTimeMillis()); + if (sleepTime > 0) { + try { + Thread.sleep(sleepTime); + } catch (InterruptedException ie) { + } + } + } + } + } else { + int sleepTime = (int) (floatSecondsTotal * 1000) - 30; + if (sleepTime > 0) { + try { + Thread.sleep(sleepTime); + } catch (InterruptedException ie) { + } + } + } + //if (center != null) + //navigate(0, center); + if (!Float.isNaN(xTrans) || !Float.isNaN(yTrans)) + navTranslatePercent(-1, xTrans, yTrans); + if (!Float.isNaN(depthPercent)) + setNavigationDepthPercent(depthPercent); + viewer.setInMotion(false); } void navigate(float seconds, Point3f[][] pathGuide) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-26 14:46:51
|
Revision: 11798 http://jmol.svn.sourceforge.net/jmol/?rev=11798&view=rev Author: hansonr Date: 2009-11-26 14:46:36 +0000 (Thu, 26 Nov 2009) Log Message: ----------- version=11.8.11_dev # bug fix: console command recall (up arrow) does not always return full command line Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-24 20:50:42 UTC (rev 11797) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-26 14:46:36 UTC (rev 11798) @@ -4,13 +4,13 @@ version=11.8.11_dev +# bug fix: console command recall (up arrow) does not always return full command line # bug fix: zShade/navigation mode incompatibility # bug fix: navigate TRACE broken in 11.7.47 -# code: JmolFrameExportJmolAdapter abandoned -- hasn't been implemented since 11.0 - # bug fix: zshade not resetting properly; now reset off with reset() or load of model # bug fix: occasional null pointer error during ZAP due to continued rendering by # previous graphic painting thread +# code: JmolFrameExportJmolAdapter abandoned -- hasn't been implemented since 11.0 # ----------------------------------------------------------------------------- Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2009-11-24 20:50:42 UTC (rev 11797) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2009-11-26 14:46:36 UTC (rev 11798) @@ -1100,6 +1100,7 @@ vBraces.add(theToken); iBrace++; isEndOfCommand = true; + ichEnd = ichToken + 1; return CONTINUE; } } @@ -1270,6 +1271,7 @@ case Token.whilecmd: if (nTokens > 2 && braceCount == 0 && parenCount == 0) { isEndOfCommand = true; + ichEnd = ichToken + 1; flowContext.setLine(); } break; @@ -1277,6 +1279,7 @@ case Token.ifcmd: if (nTokens > 2 && braceCount == 0 && parenCount == 0) { isEndOfCommand = true; + ichEnd = ichToken + 1; flowContext.setLine(); } break; @@ -1290,6 +1293,7 @@ addContextVariable(ident); } else if (braceCount == 0 && parenCount == 0) { isEndOfCommand = true; + ichEnd = ichToken + 1; flowContext.setLine(); } break; Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2009-11-24 20:50:42 UTC (rev 11797) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2009-11-26 14:46:36 UTC (rev 11798) @@ -384,14 +384,19 @@ if (pc >= lineIndices.length) return ""; if (allThisLine) { - StringBuffer sb = new StringBuffer(); + int pt0 = -1; + int pt1 = script.length(); for (int i = 0; i < lineNumbers.length; i++) - if (lineNumbers[i] == lineNumbers[pc]) - sb.append(getCommand(i, false, false)); - else if (lineNumbers[i] == 0 || lineNumbers[i] > lineNumbers[pc]) { + if (lineNumbers[i] == lineNumbers[pc]) { + if (pt0 < 0) + pt0 = lineIndices[i][0]; + pt1 = lineIndices[i][1]; + } else if (lineNumbers[i] == 0 || lineNumbers[i] > lineNumbers[pc]) { break; } - return sb.toString(); + if (pt1 == script.length() - 1 && script.endsWith("}")) + pt1++; + return script.substring(Math.max(pt0, 0), Math.min(script.length(), pt1)); } int ichBegin = lineIndices[pc][0]; int ichEnd = lineIndices[pc][1]; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-26 14:49:53
|
Revision: 11799 http://jmol.svn.sourceforge.net/jmol/?rev=11799&view=rev Author: hansonr Date: 2009-11-26 14:49:41 +0000 (Thu, 26 Nov 2009) Log Message: ----------- version=11.8.11_dev # bug fix: navigation key release causing unnecessary refresh Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-26 14:46:36 UTC (rev 11798) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-26 14:49:41 UTC (rev 11799) @@ -4,6 +4,7 @@ version=11.8.11_dev +# bug fix: navigation key release causing unnecessary refresh # bug fix: console command recall (up arrow) does not always return full command line # bug fix: zShade/navigation mode incompatibility # bug fix: navigate TRACE broken in 11.7.47 Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-26 14:46:36 UTC (rev 11798) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-26 14:49:41 UTC (rev 11799) @@ -735,7 +735,7 @@ if (isJmolDataFrame()) return; transformManager.navigate(keyWhere, modifiers); - if (!transformManager.vibrationOn) + if (!transformManager.vibrationOn && keyWhere != 0) refresh(1, "Viewer:navigate()"); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-28 00:58:44
|
Revision: 11805 http://jmol.svn.sourceforge.net/jmol/?rev=11805&view=rev Author: hansonr Date: 2009-11-28 00:58:36 +0000 (Sat, 28 Nov 2009) Log Message: ----------- version=11.8.11_dev # bug fix: select *.CD not accepted. (not a problem in 11.9.10) Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java branches/v11_8/Jmol/src/org/jmol/viewer/Token.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-26 19:57:42 UTC (rev 11804) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-28 00:58:36 UTC (rev 11805) @@ -4,6 +4,7 @@ version=11.8.11_dev +# bug fix: select *.CD not accepted. # bug fix: navigation key release causing unnecessary refresh # bug fix: console command recall (up arrow) does not always return full command line # bug fix: zShade/navigation mode incompatibility Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java 2009-11-26 19:57:42 UTC (rev 11804) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java 2009-11-28 00:58:36 UTC (rev 11805) @@ -1036,6 +1036,7 @@ case Token.times: return true; case Token.opIf: + case Token.cd: case Token.identifier: break; default: Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Token.java 2009-11-26 19:57:42 UTC (rev 11804) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Token.java 2009-11-28 00:58:36 UTC (rev 11805) @@ -256,7 +256,7 @@ //final static int boundbox see mathproperty final static int calculate = command | 6; final static int cartoon = command | 7 | defaultON; - final static int cd = command | 7 | implicitStringCommand; + final static int cd = command | 7 | implicitStringCommand | expression; final static int centerAt = command | 8; //final static int color see intproperty final static int configuration = command | 9; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-04 04:38:51
|
Revision: 11853 http://jmol.svn.sourceforge.net/jmol/?rev=11853&view=rev Author: hansonr Date: 2009-12-04 04:38:43 +0000 (Fri, 04 Dec 2009) Log Message: ----------- version=11.8.12_dev # bug fix: dot product miscalculation Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-03 20:15:19 UTC (rev 11852) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-04 04:38:43 UTC (rev 11853) @@ -4,6 +4,7 @@ version=11.8.12_dev +# bug fix: dot product miscalculation # bug fix: NWChem reader not reading files with lower-case-only atom names # bug fix: code - viewer.getDisplayModelIndex() not used properly when background model is present # bug fix: rear mesh lines not visible on isosurface when surface also drawn Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java 2009-12-03 20:15:19 UTC (rev 11852) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java 2009-12-04 04:38:43 UTC (rev 11853) @@ -800,7 +800,7 @@ // point.dot(plane) if (plane2 != null) pt2 = new Point3f(plane2.x, plane2.y, plane2.z); - return addX(pt1.x * pt2.x + pt1.y * pt2.y + pt2.z * pt2.z); + return addX(pt1.x * pt2.x + pt1.y * pt2.y + pt1.z * pt2.z); } if (plane1 == null) @@ -810,6 +810,7 @@ } private Point3f ptValue(ScriptVariable x) throws ScriptException { + Object pt; if (isSyntaxCheck) return new Point3f(); switch (x.tok) { @@ -819,8 +820,12 @@ return (Point3f) eval.getBitsetProperty(ScriptVariable.bsSelect(x), Token.xyz, null, null, x.value, null, false, Integer.MAX_VALUE); case Token.string: + pt = Escape.unescapePoint(ScriptVariable.sValue(x)); + if (pt instanceof Point3f) + return (Point3f) pt; + break; case Token.list: - Object pt = Escape.unescapePoint(ScriptVariable.sValue(x)); + pt = Escape.unescapePoint("{" + ScriptVariable.sValue(x) + "}"); if (pt instanceof Point3f) return (Point3f) pt; break; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-05 07:09:01
|
Revision: 11857 http://jmol.svn.sourceforge.net/jmol/?rev=11857&view=rev Author: hansonr Date: 2009-12-05 07:08:53 +0000 (Sat, 05 Dec 2009) Log Message: ----------- version=11.8.12_dev # bug fix: zoom/zoomTo does not refresh transform parameters Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-04 21:07:16 UTC (rev 11856) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-05 07:08:53 UTC (rev 11857) @@ -4,6 +4,7 @@ version=11.8.12_dev +# bug fix: zoom/zoomTo does not refresh transform parameters # bug fix: dot product miscalculation # bug fix: NWChem reader not reading files with lower-case-only atom names # bug fix: code - viewer.getDisplayModelIndex() not used properly when background model is present Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java 2009-12-04 21:07:16 UTC (rev 11856) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java 2009-12-05 07:08:53 UTC (rev 11857) @@ -2115,6 +2115,7 @@ // q%-4 Matrix column 1 // q%-5 Matrix column 2 // q%-6 AxisAngle format + // q%-9 Matrix format case 0: return addX(q.w); case 1: Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-12-04 21:07:16 UTC (rev 11856) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-12-05 07:08:53 UTC (rev 11857) @@ -770,6 +770,7 @@ transformManager.moveTo(floatSecondsTotal, center, rotAxis, degrees, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth); moveUpdate(floatSecondsTotal); + finalizeTransformParameters(); } void moveTo(float floatSecondsTotal, Point3f center, Matrix3f rotationMatrix, @@ -779,6 +780,7 @@ transformManager.moveTo(floatSecondsTotal, center, rotationMatrix, zoom, xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth); moveUpdate(floatSecondsTotal); + finalizeTransformParameters(); } private void moveUpdate(float floatSecondsTotal) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-06 17:19:53
|
Revision: 11871 http://jmol.svn.sourceforge.net/jmol/?rev=11871&view=rev Author: hansonr Date: 2009-12-06 17:19:39 +0000 (Sun, 06 Dec 2009) Log Message: ----------- version=11.8.13_dev # bug fix: {xxx}.xxx = syntax immediately following "for ( ) {...}" causes compilation error Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-06 17:19:23 UTC (rev 11870) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-06 17:19:39 UTC (rev 11871) @@ -4,6 +4,7 @@ version=11.8.13_dev +# bug fix: {xxx}.xxx = syntax immediately following "for ( ) {...}" causes compilation error # bug fix: draw: when only some models are visible, does not properly assign models to drawn object # code: draw: dmesh.modelFlags not properly implemented (reset in setModelVisibility) # bug fix: zoomTo out not functioning Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2009-12-06 17:19:23 UTC (rev 11870) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2009-12-06 17:19:39 UTC (rev 11871) @@ -634,6 +634,7 @@ // check for end of all brace work tokenCommand = Token.tokenAll; tokCommand = 1; + theTok = Token.nada; switch (checkFlowEndBrace()) { case ERROR: return ERROR; @@ -1418,6 +1419,10 @@ // time to execute end vBraces.remove(--iBrace); Token token = (Token) vBraces.remove(--iBrace); + if (theTok == Token.leftbrace) { + braceCount--; + parenCount--; + } return forceFlowEnd(token); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-15 14:37:58
|
Revision: 11915 http://jmol.svn.sourceforge.net/jmol/?rev=11915&view=rev Author: hansonr Date: 2009-12-15 14:37:51 +0000 (Tue, 15 Dec 2009) Log Message: ----------- version=11.8.14_dev # bug fix: _width and _height lost after initialize Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-15 04:49:55 UTC (rev 11914) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-15 14:37:51 UTC (rev 11915) @@ -4,6 +4,8 @@ version=11.8.14_dev +# bug fix: _width and _height lost after initialize + # ----------------------------------------------------------------------------- #version=11.8.13 Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-12-15 04:49:55 UTC (rev 11914) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2009-12-15 14:37:51 UTC (rev 11915) @@ -554,6 +554,8 @@ setBooleanProperty("_applet", isApplet); setBooleanProperty("_signedApplet", isSignedApplet); setBooleanProperty("_useCommandThread", useCommandThread); + global.setParameterValue("_width", dimScreen.width); + global.setParameterValue("_height", dimScreen.height); colorManager.resetElementColors(); setObjectColor("background", "black"); setObjectColor("axis1", "red"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-21 17:22:22
|
Revision: 11963 http://jmol.svn.sourceforge.net/jmol/?rev=11963&view=rev Author: hansonr Date: 2009-12-21 17:22:14 +0000 (Mon, 21 Dec 2009) Log Message: ----------- 11.8.14 VERSION # bug fix: _width and _height lost after initialize # bug fix: Jmol 11.8.10-11.8.13 will not read state orientation correctly Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-21 16:59:57 UTC (rev 11962) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-21 17:22:14 UTC (rev 11963) @@ -2,9 +2,10 @@ # NOTE: Generally only bug fixes should be entered here. # NOTE: New features should be introduced in the trunk version 11.9.x -version=11.8.14_dev +version=11.8.14 # bug fix: _width and _height lost after initialize +# bug fix: Jmol 11.8.10-11.8.13 will not read state orientation correctly # ----------------------------------------------------------------------------- Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2009-12-21 16:59:57 UTC (rev 11962) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2009-12-21 17:22:14 UTC (rev 11963) @@ -4973,6 +4973,7 @@ Point4f pt4 = getPoint4f(i); i = iToken + 1; axis.set(pt4.x, pt4.y, pt4.z); + degrees = (pt4.x == 0 && pt4.y == 0 && pt4.z == 0 ? Float.NaN : pt4.w); } break; case Token.front: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-23 18:45:05
|
Revision: 11991 http://jmol.svn.sourceforge.net/jmol/?rev=11991&view=rev Author: hansonr Date: 2009-12-23 18:44:56 +0000 (Wed, 23 Dec 2009) Log Message: ----------- version=11.8.15_dev # bug fix: older format %{...} not recognized by script compiler Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-23 18:41:55 UTC (rev 11990) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-12-23 18:44:56 UTC (rev 11991) @@ -4,6 +4,7 @@ version=11.8.15_dev +# bug fix: older format %{...} not recognized by script compiler # bug fix: long scripts in setEcho being chopped when saved in state # bug fix: "color background xxxx" clears background image as well # bug fix: labels given text after containing an image have incorrect y-displacement Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2009-12-23 18:41:55 UTC (rev 11990) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2009-12-23 18:44:56 UTC (rev 11991) @@ -1728,11 +1728,10 @@ } /** - * An "implied string" is a parameter that is not quoted - * but because of its position in a command is implied to - * be a string. First we must exclude @xxxx. Then we consume - * the entire math syntax @{......} or any set of characters - * not involving white space. + * An "implied string" is a parameter that is not quoted but because of its + * position in a command is implied to be a string. First we must exclude + * @xxxx. Then we consume the entire math syntax @{......} or any set of + * characters not involving white space. * * @return true or false */ @@ -1743,15 +1742,17 @@ while (ichT < cchScript && !eol(ch = script.charAt(ichT)) && ch != '}') ++ichT; boolean isMath = false; - // if we have @{ then this is not an implied string look ahead to \n, \r, terminal ;, or } - if (ichT > ichToken && script.charAt(ichToken) == '@' + // if we have @{ then this is not an implied string look ahead to \n, \r, + // terminal ;, or } + if (ichT > ichToken + && (script.charAt(ichToken) == '@' || script.charAt(ichToken) == '%') && (ichT <= ichToken + 1 || !(isMath = script.charAt(ichToken + 1) == '{'))) return false; if (isMath) { ichT = ichMathTerminator(script, ichToken + 1, cchScript); if (ichT == cchScript) return false; - return ((cchToken = ichT + 1 - ichToken) > 0); + return ((cchToken = ichT + 1 - ichToken) > 0); } while (--ichT > ichToken && Character.isWhitespace(script.charAt(ichT))) { } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-03 02:41:20
|
Revision: 12021 http://jmol.svn.sourceforge.net/jmol/?rev=12021&view=rev Author: hansonr Date: 2010-01-03 02:41:14 +0000 (Sun, 03 Jan 2010) Log Message: ----------- version=11.8.16_dev # bug fix: select within(0.3, hkl, {1 2 3}) requires quotes: "hkl" Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java branches/v11_8/Jmol/src/org/jmol/viewer/Token.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-03 02:40:34 UTC (rev 12020) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-03 02:41:14 UTC (rev 12021) @@ -4,6 +4,8 @@ version=11.8.16_dev +# bug fix: select within(0.3, hkl, {1 2 3}) requires quotes: "hkl" + # ----------------------------------------------------------------------------- #version=11.8.15 Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java 2010-01-03 02:40:34 UTC (rev 12020) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java 2010-01-03 02:41:14 UTC (rev 12021) @@ -496,13 +496,15 @@ return true; } - // within ( plane, ....) - // within ( distance, plane, planeExpression) - // within ( hkl, .... - // within ( distance, orClause) - // within ( group, ....) - private boolean clauseWithin() { + private boolean clauseWithin() { + + // within ( distance, plane, planeExpression) + // within ( distance, hkl, hklExpression) + // within ( distance, coord, point) + // within ( distance, orClause) + // within ( group|branch|etc, ....) + addNextToken(); if (!addNextTokenIf(Token.leftparen)) return false; @@ -534,10 +536,8 @@ case Token.element: case Token.group: case Token.helix: - case Token.hkl: case Token.model: case Token.molecule: - case Token.plane: case Token.site: case Token.structure: case Token.string: @@ -565,21 +565,15 @@ tok = tokPeek(); } boolean isCoordOrPlane = false; - if (key == null) { - if (tok == Token.identifier) { - //distance was specified, but to what? - getToken(); - key = ((String) theValue).toLowerCase(); - if (key.equals("hkl")) { - isCoordOrPlane = true; - addTokenToPostfix(Token.string, key); - } else { - returnToken(); - } - } else if (tok == Token.coord || tok == Token.plane) { + if (key == null) { + switch(tok) { + case Token.hkl: + case Token.coord: + case Token.plane: isCoordOrPlane = true; addNextToken(); - } else if (tok == Token.leftbrace) { + break; + case Token.leftbrace: returnToken(); isCoordOrPlane = true; addTokenToPostfix(Token Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2010-01-03 02:40:34 UTC (rev 12020) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2010-01-03 02:41:14 UTC (rev 12021) @@ -2872,6 +2872,11 @@ case Token.define: rpn.addX(getAtomBitSet(this, (String) value)); break; + case Token.hkl: + rpn.addX(new ScriptVariable(instruction)); + rpn.addX(new ScriptVariable(Token.point4f, hklParameter(pc + 2))); + pc = iToken; + break; case Token.plane: rpn.addX(new ScriptVariable(instruction)); rpn.addX(new ScriptVariable(Token.point4f, planeParameter(pc + 2))); Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Token.java 2010-01-03 02:40:34 UTC (rev 12020) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Token.java 2010-01-03 02:41:14 UTC (rev 12021) @@ -675,7 +675,7 @@ final public static int frontlit = misc | 19; final public static int frontonly = misc | 20; final public static int fullylit = misc | 21; - final static int hkl = misc | 120; + final static int hkl = misc | 120 | expression; final static int image = misc | 121; //11.5.53 final public static int info = misc | 122; final static int jmol = misc | 23; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-05 01:48:27
|
Revision: 12038 http://jmol.svn.sourceforge.net/jmol/?rev=12038&view=rev Author: hansonr Date: 2010-01-05 01:48:19 +0000 (Tue, 05 Jan 2010) Log Message: ----------- version=11.8.16_dev # bug fix: write to clipboard not working Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-05 00:56:45 UTC (rev 12037) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-05 01:48:19 UTC (rev 12038) @@ -4,6 +4,7 @@ version=11.8.16_dev +# bug fix: write to clipboard not working # bug fix: label %i not working # bug fix: select within(0.3, hkl, {1 2 3}) requires quotes: "hkl" Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-01-05 00:56:45 UTC (rev 12037) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-01-05 01:48:19 UTC (rev 12038) @@ -7255,7 +7255,7 @@ JmolImageCreatorInterface c; try { c = (JmolImageCreatorInterface) Interface - .getOptionInterface("util.ImageCreator"); + .getOptionInterface("export.image.ImageCreator"); c.setViewer(this); return c.clipImage(text); } catch (Error er) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-11 15:57:12
|
Revision: 12092 http://jmol.svn.sourceforge.net/jmol/?rev=12092&view=rev Author: hansonr Date: 2010-01-11 15:56:52 +0000 (Mon, 11 Jan 2010) Log Message: ----------- version=11.8.16_dev # bug fix: obscure compiler PDB bug for polyhedra, structure, frame commmands # utilizing user-defined functions of the form @{xxx({n})} Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-11 14:14:36 UTC (rev 12091) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-11 15:56:52 UTC (rev 12092) @@ -4,6 +4,8 @@ version=11.8.16_dev +# bug fix: obscure compiler PDB bug for polyhedra, structure, frame commmands +# utilizing user-defined functions of the form @{xxx({n})} # bug fix: polyhedra colors not deleted when polyhedra deleted # bug fix: polyhedra can be lost if only a subset are colored # bug fix: write to clipboard not working Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java 2010-01-11 14:14:36 UTC (rev 12091) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompilationTokenParser.java 2010-01-11 15:56:52 UTC (rev 12092) @@ -78,7 +78,7 @@ protected int itokenInfix; protected boolean isSetBrace; - protected boolean isImplicitExpression; + protected boolean isMathExpressionCommand; protected boolean isSetOrDefine; private Vector ltokenPostfix; @@ -153,12 +153,12 @@ return false; continue; } - if (!isImplicitExpression) + if (!isMathExpressionCommand) addTokenToPostfix(tokenBegin = new Token(Token.expressionBegin, "implicitExpressionBegin")); - if (!clauseOr(isCommaAsOrAllowed || !isImplicitExpression + if (!clauseOr(isCommaAsOrAllowed || !isMathExpressionCommand && tokPeek(Token.leftparen))) return false; - if (!isImplicitExpression + if (!isMathExpressionCommand && !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd)) { addTokenToPostfix(Token.tokenExpressionEnd); } @@ -171,7 +171,7 @@ tokenBegin.intValue = 0; tokCommand = Token.nada; isEmbeddedExpression = true; - isImplicitExpression = true; + isMathExpressionCommand = true; isCommaAsOrAllowed = false; } } @@ -182,7 +182,7 @@ } private boolean isExpressionNext() { - return tokPeek(Token.leftbrace) || !isImplicitExpression && tokPeek(Token.leftparen); + return tokPeek(Token.leftbrace) || !isMathExpressionCommand && tokPeek(Token.leftparen); } protected static boolean tokenAttr(Token token, int tok) { @@ -419,7 +419,7 @@ return error(ERROR_tokenExpected, ")"); return checkForItemSelector(); case Token.leftbrace: - return checkForCoordinate(isImplicitExpression); + return checkForCoordinate(isMathExpressionCommand); } return error(ERROR_unrecognizedExpressionToken, "" + valuePeek()); } Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2010-01-11 14:14:36 UTC (rev 12091) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2010-01-11 15:56:52 UTC (rev 12092) @@ -37,7 +37,7 @@ class ScriptCompiler extends ScriptCompilationTokenParser { /** - * The Compiler clas is really two parts -- + * The Compiler class is really two parts -- * * Compiler.class going from characters to tokens * CompilationTokenParser further syntax checking and modifications @@ -660,8 +660,8 @@ tokenCommand = (Token) ltoken.firstElement(); tokCommand = tokenCommand.tok; - isImplicitExpression = Token.tokAttr(tokCommand, - Token.mathExpressionCommand); + isMathExpressionCommand = (tokCommand == Token.identifier + || Token.tokAttr(tokCommand, Token.mathExpressionCommand)); isSetOrDefine = (tokCommand == Token.set || tokCommand == Token.define); isCommaAsOrAllowed = Token.tokAttr(tokCommand, Token.atomExpressionCommand); int size = ltoken.size(); @@ -951,13 +951,8 @@ addTokenToPrefix(new Token(Token.integer, val, intString)); return CONTINUE; } - if (tokCommand == Token.structure && nTokens == 2 - || tokCommand == Token.frame && nTokens == 2 - || tokCommand == Token.polyhedra - || lastToken.tok == Token.select - || lastToken.tok == Token.within - || !(lastToken.tok == Token.identifier || tokenAttr(lastToken, - Token.mathfunc))) { + if (!isMathExpressionCommand && parenCount == 0 + || lastToken.tok != Token.identifier && !tokenAttr(lastToken, Token.mathfunc)) { // here if: // select ({...}) // within({...}) @@ -1146,6 +1141,8 @@ ichCurrentCommand = ichEnd = ichToken; tokenCommand = theToken; tokCommand = theTok; + isMathExpressionCommand = (tokCommand == Token.identifier + || Token.tokAttr(tokCommand, Token.mathExpressionCommand)); // checking first here for a flow command because // if (......) {.....} ELSE if (Token.tokAttr(tokCommand, Token.flowCommand)) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-13 20:18:15
|
Revision: 12120 http://jmol.svn.sourceforge.net/jmol/?rev=12120&view=rev Author: hansonr Date: 2010-01-13 20:18:07 +0000 (Wed, 13 Jan 2010) Log Message: ----------- version=11.8.17_dev # bug fix: applet cannot load inline Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-13 20:16:36 UTC (rev 12119) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-13 20:18:07 UTC (rev 12120) @@ -4,6 +4,7 @@ version=11.8.17_dev +# bug fix: applet cannot load inline # ----------------------------------------------------------------------------- #version=11.8.16 Modified: branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java 2010-01-13 20:16:36 UTC (rev 12119) +++ branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java 2010-01-13 20:18:07 UTC (rev 12120) @@ -85,7 +85,7 @@ } synchronized void cancelRendering() { - if (!repaintPending || repaintInterrupted) + if (!repaintPending || repaintInterrupted || holdRepaint > 0) return; repaintInterrupted = true; try { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-30 22:58:23
|
Revision: 12269 http://jmol.svn.sourceforge.net/jmol/?rev=12269&view=rev Author: hansonr Date: 2010-01-30 22:58:17 +0000 (Sat, 30 Jan 2010) Log Message: ----------- 11.8.18_dev # bug fix: within molecule was using undocumented "visible" Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-30 22:29:34 UTC (rev 12268) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-30 22:58:17 UTC (rev 12269) @@ -4,6 +4,7 @@ version=11.8.18_dev +# bug fix: within molecule was using undocumented "visible" # bug fix: frame *;draw {atomno=1} {atomno=5} not working properly # bug fix: pdb reader as trajectory error # bug fix: MO export to cartesian exporters (VRML/X3D/Maya) should not do front-only Modified: branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java 2010-01-30 22:29:34 UTC (rev 12268) +++ branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java 2010-01-30 22:58:17 UTC (rev 12269) @@ -117,17 +117,18 @@ viewer.clearClickCount(); return; case JmolConstants.PICKING_SELECT_MOLECULE: - applyMouseStyle("visible and within(molecule, " + spec +")", shiftKey, alternateKey, isDoubleClick); + applyMouseStyle("within(molecule, " + spec +")", shiftKey, alternateKey, isDoubleClick); viewer.clearClickCount(); return; + case JmolConstants.PICKING_SELECT_MODEL: + applyMouseStyle("within(model, " + spec +")", shiftKey, alternateKey, isDoubleClick); + viewer.clearClickCount(); + return; + // only the next two use VISIBLE (as per the documentation) case JmolConstants.PICKING_SELECT_SITE: applyMouseStyle("visible and within(site, " + spec +")", shiftKey, alternateKey, isDoubleClick); viewer.clearClickCount(); return; - case JmolConstants.PICKING_SELECT_MODEL: - applyMouseStyle("within(model, " + spec +")", shiftKey, alternateKey, isDoubleClick); - viewer.clearClickCount(); - return; case JmolConstants.PICKING_SELECT_ELEMENT: applyMouseStyle("visible and within(element, " + spec +")", shiftKey, alternateKey, isDoubleClick); viewer.clearClickCount(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-06 00:34:52
|
Revision: 12314 http://jmol.svn.sourceforge.net/jmol/?rev=12314&view=rev Author: hansonr Date: 2010-02-06 00:34:03 +0000 (Sat, 06 Feb 2010) Log Message: ----------- version=11.8.18_dev # bug fix: drawHover status not reported properly after zap/new model loaded Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java branches/v11_8/Jmol/src/org/jmol/viewer/Token.java branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-06 00:26:57 UTC (rev 12313) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-06 00:34:03 UTC (rev 12314) @@ -4,6 +4,7 @@ version=11.8.18_dev +# bug fix: drawHover status not reported properly after zap/new model loaded # code: model properties atomCount, bondCount should be private # bug fix: bitsets not properly handled in model deletion # bug fix: bfactor min/max was ignoring first atom Modified: branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java 2010-02-06 00:26:57 UTC (rev 12313) +++ branches/v11_8/Jmol/src/org/jmol/viewer/PickingManager.java 2010-02-06 00:34:03 UTC (rev 12314) @@ -40,7 +40,6 @@ private int pickingStyleSelect = JmolConstants.PICKINGSTYLE_SELECT_JMOL; private int pickingStyleMeasure = JmolConstants.PICKINGSTYLE_MEASURE_OFF; - private boolean drawHover; private int pickingStyle; private MeasurementPending measurementQueued; @@ -52,7 +51,7 @@ void clear() { pickingMode = JmolConstants.PICKING_IDENT; - drawHover = false; + pickingStyle = pickingStyleSelect; } void setPickingMode(int pickingMode) { @@ -82,14 +81,6 @@ return pickingStyle; } - void setDrawHover(boolean TF) { - drawHover = TF; - } - - boolean getDrawHover() { - return drawHover; - } - void atomsPicked(BitSet bs, int modifiers) { if (BitSetUtil.firstSetBit(bs) < 0) return; Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java 2010-02-06 00:26:57 UTC (rev 12313) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptMathProcessor.java 2010-02-06 00:34:03 UTC (rev 12314) @@ -24,6 +24,7 @@ package org.jmol.viewer; import java.util.BitSet; +import java.util.Date; import java.util.Vector; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -603,6 +604,7 @@ return evaluateArray(args); case Token.abs: case Token.acos: + case Token.now: case Token.cos: case Token.sin: case Token.sqrt: @@ -1371,6 +1373,12 @@ q = new Quaternion(p4); return addX(q.toPoint4f()); } + if (tok == Token.now) { + if (args.length == 1 && args[0].tok == Token.string) + return addX((new Date()) + "\t" + ScriptVariable.sValue(args[0])); + return addX(((int) System.currentTimeMillis() & 0x7FFFFFFF) + - (args.length == 0 ? 0 : ScriptVariable.iValue(args[0]))); + } if (args.length != 1) return false; if (isSyntaxCheck) Modified: branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java 2010-02-06 00:26:57 UTC (rev 12313) +++ branches/v11_8/Jmol/src/org/jmol/viewer/StateManager.java 2010-02-06 00:34:03 UTC (rev 12314) @@ -126,6 +126,7 @@ viewer.setShowAxes(false); viewer.setShowBbcage(false); viewer.setShowUnitCell(false); + viewer.setBooleanProperty("drawHover", false); } void setCrystallographicDefaults() { @@ -783,6 +784,7 @@ int delayMaximumMs = 0; float dipoleScale = 1.0f; boolean disablePopupMenu = false; + boolean drawHover = false; boolean drawPicking = false; boolean bondPicking = false; boolean atomPicking = true; @@ -1271,7 +1273,7 @@ setParameterValue("dotsSelectedOnly", dotsSelectedOnly); setParameterValue("dotSurface", dotSurface); setParameterValue("dragSelected", false); - setParameterValue("drawHover", false); + setParameterValue("drawHover", drawHover); setParameterValue("drawPicking", drawPicking); setParameterValue("dynamicMeasurements", dynamicMeasurements); setParameterValue("ellipsoidArcs", ellipsoidArcs); Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Token.java 2010-02-06 00:26:57 UTC (rev 12313) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Token.java 2010-02-06 00:34:03 UTC (rev 12314) @@ -565,6 +565,7 @@ final static int function = 4 | 0 << 9 | mathfunc | flowCommand | noeval; final static int getproperty = 5 | 0 << 9 | mathfunc | command; final static int write = 6 | 0 << 9 | mathfunc | command; + final static int now = 16 | 0 << 9 | mathfunc; // xxx(a) @@ -631,12 +632,13 @@ final static int quaternion = 6 | 4 << 9 | mathfunc | command; final static int axisangle = 7 | 4 << 9 | mathfunc; + // xxx(a,b,c,d,e) final static int within = 1 | 5 << 9 | mathfunc; final public static int connected = 2 | 5 << 9 | mathfunc; - // more SET parameters +// more SET parameters final public static int ambient = setparam | 1; final static int bondmode = setparam | 2; @@ -857,6 +859,7 @@ "moveto", new Token(moveto), "navigate", new Token(navigate), "navigation", null, + "now", new Token(now), "pause", new Token(pause), "wait", null, "pmesh", new Token(pmesh), Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-02-06 00:26:57 UTC (rev 12313) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-02-06 00:34:03 UTC (rev 12314) @@ -4180,7 +4180,7 @@ } public boolean getDrawHover() { - return pickingManager.getDrawHover(); + return haveDisplay && global.drawHover; } public String getAtomInfo(int atomIndex) { @@ -5582,7 +5582,7 @@ break; } if (key.equalsIgnoreCase("drawHover")) { - pickingManager.setDrawHover(value); + global.drawHover = value; break; } if (key.equalsIgnoreCase("navigationMode")) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-07 16:45:35
|
Revision: 12324 http://jmol.svn.sourceforge.net/jmol/?rev=12324&view=rev Author: hansonr Date: 2010-02-07 16:45:29 +0000 (Sun, 07 Feb 2010) Log Message: ----------- version=11.8.19_dev # bug fix: refresh after echo @{...} causes Jmol to hang. Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-07 16:44:15 UTC (rev 12323) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-07 16:45:29 UTC (rev 12324) @@ -4,6 +4,8 @@ version=11.8.19_dev +# bug fix: refresh after echo @{...} causes Jmol to hang. + # ----------------------------------------------------------------------------- #version=11.8.18 Modified: branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java 2010-02-07 16:44:15 UTC (rev 12323) +++ branches/v11_8/Jmol/src/org/jmol/viewer/RepaintManager.java 2010-02-07 16:45:29 UTC (rev 12324) @@ -30,7 +30,6 @@ import org.jmol.shape.ShapeRenderer; import org.jmol.util.Logger; -import java.awt.Component; import java.awt.Rectangle; class RepaintManager { @@ -69,7 +68,11 @@ synchronized void requestRepaintAndWait() { repaintDisplay(); try { - wait(); + wait(1000); + if (repaintPending) { + System.out.println("repaintManager-11.8 requestRepaintAndWait Thread " + Thread.currentThread().getName()); + repaintDone(); + } } catch (InterruptedException e) { } } @@ -78,25 +81,9 @@ holdRepaint = 0; repaintPending = true; repaintInterrupted = false; - Component display = viewer.getDisplay(); - if (display == null) - return; - display.repaint(); + viewer.repaint(); } - synchronized void cancelRendering() { - if (!repaintPending || repaintInterrupted || holdRepaint > 0) - return; - repaintInterrupted = true; - try { - //System.out.println("repaintManager waiting for rendering to complete"); - wait(); - } catch (InterruptedException e) { - } - repaintInterrupted = false; - //System.out.println("repaintManager continuing"); - } - synchronized void repaintDone() { repaintPending = false; notify(); // to cancel any wait in requestRepaintAndWait() Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-02-07 16:44:15 UTC (rev 12323) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-02-07 16:45:29 UTC (rev 12324) @@ -6959,7 +6959,7 @@ return (String) evaluateExpression(exp); } - public synchronized Object evaluateExpression(Object stringOrTokens) { + public Object evaluateExpression(Object stringOrTokens) { return ScriptEvaluator.evaluateExpression(this, stringOrTokens); } @@ -7762,4 +7762,10 @@ return repaintManager.repaintPending; } + void repaint() { + if (display == null) + return; + display.repaint(); + } + } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-08 12:59:32
|
Revision: 12331 http://jmol.svn.sourceforge.net/jmol/?rev=12331&view=rev Author: hansonr Date: 2010-02-08 12:59:13 +0000 (Mon, 08 Feb 2010) Log Message: ----------- version=11.8.19_dev # bug fix: write frame typed in application can hang Jmol. Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-08 12:56:01 UTC (rev 12330) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-08 12:59:13 UTC (rev 12331) @@ -4,6 +4,7 @@ version=11.8.19_dev +# bug fix: write frame typed in application can hang Jmol. # bug fix: refresh after echo @{...} causes Jmol to hang. # ----------------------------------------------------------------------------- Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2010-02-08 12:56:01 UTC (rev 12330) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2010-02-08 12:59:13 UTC (rev 12331) @@ -10562,7 +10562,9 @@ if (tok == Token.image) { pt++; } else if (tok == Token.frame) { - if (args[++pt].tok == Token.expressionBegin + if (++pt == args.length) + return ""; + if (args[pt].tok == Token.expressionBegin || args[pt].tok == Token.bitset) { bsFrames = expression(args, pt, 0, true, false, true, true); pt = iToken + 1; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-14 19:01:27
|
Revision: 12392 http://jmol.svn.sourceforge.net/jmol/?rev=12392&view=rev Author: hansonr Date: 2010-02-14 19:01:20 +0000 (Sun, 14 Feb 2010) Log Message: ----------- # bug fix: [state] button in app console not showing state Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-14 18:59:04 UTC (rev 12391) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-14 19:01:20 UTC (rev 12392) @@ -4,6 +4,7 @@ version=11.8.19_dev +# bug fix: [state] button in app console not showing state # bug fix: load sometimes not properly accounting for unique axis information # bug fix: write frame typed in application can hang Jmol. # bug fix: refresh after echo @{...} causes Jmol to hang. Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-02-14 18:59:04 UTC (rev 12391) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Viewer.java 2010-02-14 19:01:20 UTC (rev 12392) @@ -6794,8 +6794,8 @@ file_text = new String[] { null, null }; if (file_text[1] == null) file_text[1] = "<no data>"; - String filename = file_text[1]; - String msg = file_text[0]; + String filename = file_text[0]; + String msg = file_text[1]; JmolScriptEditorInterface scriptEditor = (JmolScriptEditorInterface) getProperty( "DATA_API", "getScriptEditor", Boolean.TRUE); if (msg != null) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-24 21:50:14
|
Revision: 12469 http://jmol.svn.sourceforge.net/jmol/?rev=12469&view=rev Author: hansonr Date: 2010-02-24 21:50:07 +0000 (Wed, 24 Feb 2010) Log Message: ----------- version=11.8.19_dev # bug fix: select 1:3.* Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-24 19:48:46 UTC (rev 12468) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-24 21:50:07 UTC (rev 12469) @@ -4,6 +4,7 @@ version=11.8.19_dev +# bug fix: select 1:3.* # bug fix: [state] button in app console not showing state # bug fix: load sometimes not properly accounting for unique axis information # bug fix: write frame typed in application can hang Jmol. Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2010-02-24 19:48:46 UTC (rev 12468) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptCompiler.java 2010-02-24 21:50:07 UTC (rev 12469) @@ -1866,7 +1866,7 @@ // to determine if it is an alpha char ch1; if (ichT < cchScript && !eol(ch1 = script.charAt(ichT))) { - if (Character.isLetter(ch1) || ch1 == '?') + if (Character.isLetter(ch1) || ch1 == '?' || ch1 == '*') return false; //well, guess what? we also have to look for 86.1Na, so... //watch out for moveto..... 56.;refresh... This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-26 22:39:09
|
Revision: 12486 http://jmol.svn.sourceforge.net/jmol/?rev=12486&view=rev Author: hansonr Date: 2010-02-26 22:39:03 +0000 (Fri, 26 Feb 2010) Log Message: ----------- version=11.8.19_dev # bug fix: load models {(.....)} not preserved in state Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-26 21:53:31 UTC (rev 12485) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-26 22:39:03 UTC (rev 12486) @@ -4,6 +4,7 @@ version=11.8.19_dev +# bug fix: load models {(.....)} not preserved in state # bug fix: structure HELIX {3-4} will cause 5-... to lose structure type # bug fix: select 1:3.* # bug fix: [state] button in app console not showing state Modified: branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2010-02-26 21:53:31 UTC (rev 12485) +++ branches/v11_8/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2010-02-26 22:39:03 UTC (rev 12486) @@ -6513,7 +6513,9 @@ (int) pt.z }); loadScript.append(" " + Escape.escape(pt)); } else if (tokAt(i) == Token.bitset) { - htParams.put("bsModels", (BitSet) getToken(i++).value); + BitSet bsModels = (BitSet) getToken(i++).value; + htParams.put("bsModels", bsModels); + loadScript.append(" " + Escape.escape(bsModels)); } else { htParams.put("firstLastStep", new int[] { 0, -1, 1 }); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-27 15:18:26
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Revision: 12494 http://jmol.svn.sourceforge.net/jmol/?rev=12494&view=rev Author: hansonr Date: 2010-02-27 15:18:18 +0000 (Sat, 27 Feb 2010) Log Message: ----------- version=11.8.19_dev # bug fix: select IONS broken (left broken in 11.6) Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_8/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-27 15:14:37 UTC (rev 12493) +++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2010-02-27 15:18:18 UTC (rev 12494) @@ -4,6 +4,7 @@ version=11.8.19_dev +# bug fix: select IONS broken (left broken in 11.6) # bug fix: load models {(.....)} not preserved in state # bug fix: structure HELIX {3-4} will cause 5-... to lose structure type # bug fix: select 1:3.* Modified: branches/v11_8/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/viewer/JmolConstants.java 2010-02-27 15:14:37 UTC (rev 12493) +++ branches/v11_8/Jmol/src/org/jmol/viewer/JmolConstants.java 2010-02-27 15:18:18 UTC (rev 12494) @@ -2701,7 +2701,7 @@ // solvent // "@solvent _g>="+GROUPID_WATER+" & _g<="+GROUPID_SULPHATE, // water or ions - "@ions _g>="+(GROUPID_WATER+3)+",_g<="+GROUPID_SULPHATE, + "@ions _g="+(GROUPID_SULPHATE - 1)+",_g="+GROUPID_SULPHATE, // // structure related This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |