From: <ha...@us...> - 2008-08-31 01:11:29
|
Revision: 9823 http://jmol.svn.sourceforge.net/jmol/?rev=9823&view=rev Author: hansonr Date: 2008-08-31 01:11:26 +0000 (Sun, 31 Aug 2008) Log Message: ----------- version=11.6.RC12 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx # bug fix: getProperty("modelinfo",{atom expression}) not working Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-31 01:08:03 UTC (rev 9822) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-31 01:11:26 UTC (rev 9823) @@ -2458,8 +2458,8 @@ return modelSet.getPDBHeader(repaintManager.currentModelIndex); } - public Hashtable getModelInfo() { - return modelSet.getModelInfo(); + public Hashtable getModelInfo(Object atomExpression) { + return modelSet.getModelInfo(getModelBitSet(getAtomBitSet(atomExpression))); } public Hashtable getAuxiliaryInfo() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-12-02 20:12:49
|
Revision: 10403 http://jmol.svn.sourceforge.net/jmol/?rev=10403&view=rev Author: hansonr Date: 2008-12-02 20:12:45 +0000 (Tue, 02 Dec 2008) Log Message: ----------- version=11.7.15_dev # code: better handling of OutOfMemoryError conditions (2) Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-02 20:04:37 UTC (rev 10402) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-02 20:12:45 UTC (rev 10403) @@ -3639,6 +3639,7 @@ if (isScriptFile && writeInfo != null) writeImage(writeInfo); } else { + scriptStatus(strErrorMessage); statusManager.setScriptStatus("Jmol script terminated", strErrorMessage, 1); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-12-03 05:45:43
|
Revision: 10421 http://jmol.svn.sourceforge.net/jmol/?rev=10421&view=rev Author: hansonr Date: 2008-12-03 05:45:41 +0000 (Wed, 03 Dec 2008) Log Message: ----------- version=11.7.16_dev # code: better handling of OutOfMemoryError conditions Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-03 05:31:51 UTC (rev 10420) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-03 05:45:41 UTC (rev 10421) @@ -3437,11 +3437,14 @@ * @return base64-encoded or binary version of the image */ public Object getJpeg(int quality, boolean asString) { + byte[] jpeg = null; Image eImage = getScreenImage(); - ByteArrayOutputStream os = new ByteArrayOutputStream(); - JpegEncoder jc = new JpegEncoder(eImage, quality, os); - jc.Compress(); - byte[] jpeg = os.toByteArray(); + if (eImage != null) { + ByteArrayOutputStream os = new ByteArrayOutputStream(); + JpegEncoder jc = new JpegEncoder(eImage, quality, os); + jc.Compress(); + jpeg = os.toByteArray(); + } releaseScreenImage(); if (asString) return Base64.getBase64(jpeg).toString(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-12-07 06:22:32
|
Revision: 10458 http://jmol.svn.sourceforge.net/jmol/?rev=10458&view=rev Author: hansonr Date: 2008-12-07 06:22:27 +0000 (Sun, 07 Dec 2008) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-07 06:21:19 UTC (rev 10457) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-07 06:22:27 UTC (rev 10458) @@ -3623,7 +3623,7 @@ if (!isQuiet) scriptStatus("Jmol script terminated", strErrorMessage, 1 + eval.getExecutionWalltime(), strErrorMessageUntranslated); - if (writeInfo != null) { + if (writeInfo != null) { // had "isScriptFile" writeImage(writeInfo); writeInfo = null; } @@ -3638,7 +3638,7 @@ else Logger.error("--script check error\n" + strErrorMessageUntranslated); } - if (autoExit) { + if (autoExit) { // had "isScriptFile" System.out.flush(); System.exit(0); } else if (checkScriptOnly) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-12-07 10:17:55
|
Revision: 10462 http://jmol.svn.sourceforge.net/jmol/?rev=10462&view=rev Author: nicove Date: 2008-12-07 10:17:45 +0000 (Sun, 07 Dec 2008) Log Message: ----------- UTF8 fix Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-07 10:16:59 UTC (rev 10461) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-12-07 10:17:45 UTC (rev 10462) @@ -4288,7 +4288,7 @@ * that can be parsed more easily, involving the atoms and measurement * with units, for example: * - * [Si #3, O #8, Si #7, 60.1 \xB0] + * [Si #3, O #8, Si #7, 60.1 ] * * Viewer.setStatusMeasuring * Measures.clear This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-03-31 23:31:16
|
Revision: 10756 http://jmol.svn.sourceforge.net/jmol/?rev=10756&view=rev Author: hansonr Date: 2009-03-31 23:31:13 +0000 (Tue, 31 Mar 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-03-31 23:22:32 UTC (rev 10755) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-03-31 23:31:13 UTC (rev 10756) @@ -3058,12 +3058,12 @@ BitSet bsFrameOffsets; Point3f[] frameOffsets; - void setFrameOffsets(BitSet bsAtoms) { + public void setFrameOffsets(BitSet bsAtoms) { bsFrameOffsets = bsAtoms; transformManager.setFrameOffsets(frameOffsets = modelSet.getFrameOffsets(bsFrameOffsets)); } - BitSet getFrameOffsets() { + public BitSet getFrameOffsets() { return bsFrameOffsets; } @@ -7240,7 +7240,7 @@ fileManager.addLoadScript("zap " + Escape.escape(bs)); setCurrentModelIndex(0, false); repaintManager.setAnimationOn(false); - BitSet bsDeleted = modelSet.deleteAtoms(bs, true); + BitSet bsDeleted = modelSet.deleteModels(bs); setAnimationRange(0, 0); eval.deleteAtomsInVariables(bsDeleted); repaintManager.clear(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-05-22 19:47:24
|
Revision: 10897 http://jmol.svn.sourceforge.net/jmol/?rev=10897&view=rev Author: hansonr Date: 2009-05-22 19:47:14 +0000 (Fri, 22 May 2009) Log Message: ----------- 11.7.37 VERSION # new feature: load VIBRATION "filename" n ....... # --all features of the load command, but only loads the vibrational information # --applies {within(loadAtomDataTolerance,xyzcoord)}.vxyz = vibcoord, so to all unit cells # --optional n is just as for any load -- optional nth model # --operates on previously selected atoms only # --allows embedded jmolscript, just as for any load # --sets _vibrationName from file's atom set collection name # new feature: loadAtomDataTolerance (see above) Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-05-22 19:35:02 UTC (rev 10896) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-05-22 19:47:14 UTC (rev 10897) @@ -4165,9 +4165,14 @@ int prevFrame = Integer.MIN_VALUE; void setStatusFrameChanged(int frameNo) { + int modelIndex = repaintManager.currentModelIndex; + if (frameNo == Integer.MIN_VALUE) { + // force reset (reading vibrations) + prevFrame = Integer.MIN_VALUE; + frameNo = modelIndex; + } transformManager.setVibrationPeriod(Float.NaN); - - int modelIndex = repaintManager.currentModelIndex; + int firstIndex = repaintManager.firstModelIndex; int lastIndex = repaintManager.lastModelIndex; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-06-24 15:36:21
|
Revision: 11107 http://jmol.svn.sourceforge.net/jmol/?rev=11107&view=rev Author: hansonr Date: 2009-06-24 15:36:20 +0000 (Wed, 24 Jun 2009) Log Message: ----------- version=11.7.45_dev # new feature: application console buttons: PAUSE, ?, STEP Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-06-24 15:35:00 UTC (rev 11106) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-06-24 15:36:20 UTC (rev 11107) @@ -3767,6 +3767,8 @@ // + " " + Thread.currentThread().getId()); if (checkResume(strScript)) return "script processing resumed"; // be very odd if this fired + if (checkStepping(strScript)) + return "script processing stepped"; if (checkHalt(strScript)) return "script execution halted"; if (strScript == null) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-07-01 00:05:01
|
Revision: 11161 http://jmol.svn.sourceforge.net/jmol/?rev=11161&view=rev Author: hansonr Date: 2009-07-01 00:04:39 +0000 (Wed, 01 Jul 2009) Log Message: ----------- debug comments out Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-07-01 00:02:02 UTC (rev 11160) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-07-01 00:04:39 UTC (rev 11161) @@ -2118,62 +2118,39 @@ } public void zap(boolean notify, boolean resetUndo) { -System.out.println("zap 1"); stopAnimationThreads(); - System.out.println("zap 2"); if (modelSet != null) { - System.out.println("zapping " + modelSet); clearModelDependentObjects(); - System.out.println("zap 11"); fileManager.clear(); - System.out.println("zap 12"); repaintManager.clear(); animationManager.clear(); - System.out.println("zap 13"); transformManager.clear(); - System.out.println("zap 14"); pickingManager.clear(); - System.out.println("zap 15"); selectionManager.clear(); - System.out.println("zap 16"); clearAllMeasurements(); - System.out.println("zap 17"); if (minimizer != null) minimizer.setProperty("clear", null); - System.out.println("zap 18"); modelSet = modelManager.clear(); - System.out.println("zap 19"); if (haveDisplay) { mouseManager.clear(); - System.out.println("zap 20"); } stateManager.clear(); - System.out.println("zap 21"); global.clear(); - System.out.println("zap 22"); tempManager.clear(); - System.out.println("zap 23"); colorManager.clear(); - System.out.println("zap 24"); definedAtomSets.clear(); - System.out.println("zap 25"); // setRefreshing(true); // refresh(0, "Viewer:clear()"); dataManager.clear(); System.gc(); } - System.out.println("zap 3"); modelSet = modelManager.zap(); - System.out.println("zap 4"); initializeModel(); - System.out.println("zap 5"); if (notify) setFileLoadStatus(FILE_STATUS_ZAPPED, null, (resetUndo ? "resetUndo" : null), null, null); - System.out.println("zap 6"); if (Logger.debugging) Logger.checkMemory(); - System.out.println("zap 7"); } private void zap(String msg) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-08-13 10:28:22
|
Revision: 11313 http://jmol.svn.sourceforge.net/jmol/?rev=11313&view=rev Author: hansonr Date: 2009-08-13 10:28:15 +0000 (Thu, 13 Aug 2009) Log Message: ----------- code comment cleanup Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-08-13 10:24:16 UTC (rev 11312) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-08-13 10:28:15 UTC (rev 11313) @@ -696,7 +696,6 @@ if (isJmolDataFrame()) return; transformManager.setCenterAt(relativeTo, pt); - // refresh(0, "Viewer:setCenter(" + relativeTo + ")"); } void setCenterBitSet(BitSet bsCenter, boolean doScale) { @@ -709,7 +708,6 @@ if (isJmolDataFrame()) return; transformManager.setNewRotationCenter(center, doScale); - // refresh(0, "Viewer:setCenterBitSet()"); } void setNewRotationCenter(Point3f center) { @@ -717,7 +715,6 @@ if (isJmolDataFrame()) return; transformManager.setNewRotationCenter(center, true); - // refresh(0, "Viewer:setCenterBitSet()"); } public Point3f getNavigationCenter() { @@ -1005,25 +1002,21 @@ void slabByPixels(int pixels) { // MouseManager.mouseSinglePressDrag transformManager.slabByPercentagePoints(pixels); - // refresh(0, "Viewer:slabByPixels()"); } void depthByPixels(int pixels) { // MouseManager.mouseDoublePressDrag transformManager.depthByPercentagePoints(pixels); - // refresh(0, "Viewer:depthByPixels()"); } void slabDepthByPixels(int pixels) { // MouseManager.mouseSinglePressDrag transformManager.slabDepthByPercentagePoints(pixels); - // refresh(0, "Viewer:slabDepthByPixels()"); } void slabToPercent(int percentSlab) { // Eval.slab transformManager.slabToPercent(percentSlab); - // refresh(0, "Viewer:slabToPercent()"); } void slabInternal(Point4f plane, boolean isDepth) { @@ -1033,7 +1026,6 @@ void depthToPercent(int percentDepth) { // Eval.depth transformManager.depthToPercent(percentDepth); - // refresh(0, "Viewer:depthToPercent()"); } void setSlabDepthInternal(boolean isDepth) { @@ -1244,7 +1236,6 @@ public void setVectorScale(float scale) { global.setParameterValue("vectorScale", scale); global.vectorScale = scale; - // refresh(0, "set vectorScale"); } public float getDefaultDrawArrowScale() { @@ -1254,7 +1245,6 @@ public void setDefaultDrawArrowScale(float scale) { global.setParameterValue("defaultDrawArrowScale", scale); global.defaultDrawArrowScale = scale; - // refresh(0, "set defaultDrawArrowScale"); } float getVibrationScale() { @@ -1536,7 +1526,6 @@ public void selectAll() { // initializeModel selectionManager.selectAll(false); - // refresh(0, "Viewer:selectAll()"); } private boolean noneSelected; @@ -1553,13 +1542,11 @@ // not used in this project; in jmolViewer interface, though selectionManager.clearSelection(false); global.setParameterValue("hideNotSelected", false); - // refresh(0, "Viewer:clearSelection()"); } public void setSelectionSet(BitSet set) { // not used in this project; in jmolViewer interface, though selectionManager.setSelectionSet(set); - // refresh(0, "Viewer:setSelectionSet()"); } void setSelectionSubset(BitSet subset) { @@ -2210,8 +2197,6 @@ tempManager.clear(); colorManager.clear(); definedAtomSets.clear(); - // setRefreshing(true); - // refresh(0, "Viewer:clear()"); dataManager.clear(); System.gc(); } @@ -2401,7 +2386,6 @@ void calcBoundBoxDimensions(BitSet bs) { modelSet.calcBoundBoxDimensions(bs); axesAreTainted = true; - // refresh(0, "set calcBoundBoxDimensions"); } BoxInfo getBoxInfo(BitSet bs) { @@ -3025,7 +3009,6 @@ void clearAllMeasurements() { // Eval only setShapeProperty(JmolConstants.SHAPE_MEASURES, "clear", null); - // refresh(0, "Viewer:clearAllMeasurements()"); } public void clearMeasurements() { @@ -3071,14 +3054,12 @@ // Eval setShapeProperty(JmolConstants.SHAPE_MEASURES, isON ? "show" : "hide", atomCountPlusIndices); - // refresh(0, "Viewer:showMeasurements()"); } void hideMeasurements(boolean isOFF) { // Eval setShapeProperty(JmolConstants.SHAPE_MEASURES, "hideAll", Boolean .valueOf(isOFF)); - // refresh(0, "hideMeasurements()"); } void toggleMeasurement(int[] atomCountPlusIndices, String strFormat) { @@ -3156,7 +3137,6 @@ return; } animationManager.resumeAnimation(); - // refresh(0, "Viewer:resumeAnimation()"); } void pauseAnimation() { @@ -3165,7 +3145,6 @@ return; } animationManager.pauseAnimation(); - // refresh(0, "Viewer:pauseAnimation()"); } void setAnimationRange(int modelIndex1, int modelIndex2) { @@ -3185,27 +3164,21 @@ void setAnimationNext() { // Eval animationManager.setAnimationNext(); - // if (animationManager.setAnimationNext()) - // refresh(0, "Viewer:setAnimationNext()"); } void setAnimationPrevious() { // Eval animationManager.setAnimationPrevious(); - // if (animationManager.setAnimationPrevious()) - // refresh(0, "Viewer:setAnimationPrevious()"); } void setAnimationLast() { // Eval animationManager.setAnimationLast(); - // refresh(0, "Viewer:setAnimationLast()"); } void rewindAnimation() { // Eval animationManager.rewindAnimation(); - // refresh(0, "Viewer:rewindAnimation()"); } void setCurrentModelIndex(int modelIndex) { @@ -3380,9 +3353,8 @@ */ public void refresh(int mode, String strWhy) { // refresh(2) indicates this is a mouse motion -- not going through Eval - // script // so we bypass Eval and mainline on the other viewer! - // refresh(-1) is used in stateManager to force no repaint) + // refresh(-1) is used in stateManager to force no repaint // refresh(3) is used by operations to ONLY do a repaint -- no syncing if (repaintManager == null || !refreshing) return; @@ -3966,7 +3938,6 @@ } public void pauseScriptExecution() { - // refresh(0, "pauseScriptExecution"); eval.pauseExecution(); } @@ -4078,7 +4049,6 @@ setShapeSize(JmolConstants.SHAPE_LABELS, 0, Float.NaN, bs); modelSet.setShapeProperty(JmolConstants.SHAPE_LABELS, "toggleLabel", null, bs); - // refresh(0, "Viewer:togglePickingLabel()"); } BitSet getBitSetSelection() { @@ -4112,7 +4082,6 @@ // Eval.connect() // several points in Viewer modelSet.setShapeSize(shapeID, size, fsize, bsAtoms); - // refresh(0, "Viewer:setShapeSize(" + shapeID + "," + size + ")"); } public void setShapeProperty(int shapeID, String propertyName, Object value) { @@ -4121,7 +4090,6 @@ return; // not applicable modelSet.setShapeProperty(shapeID, propertyName, value, selectionManager.bsSelection); - // refresh(0, "Viewer:setShapeProperty()"); } void setShapeProperty(int shapeID, String propertyName, Object value, @@ -4130,7 +4098,6 @@ if (shapeID < 0) return; // not applicable modelSet.setShapeProperty(shapeID, propertyName, value, bs); - // refresh(0, "Viewer:setShapeProperty()"); } void setShapePropertyArgb(int shapeID, String propertyName, int argb) { @@ -5291,7 +5258,6 @@ // 11.6.RC2// if (key.equalsIgnoreCase("dotDensity")) { global.dotDensity = value; - // refresh(0, "Viewer:setDotDensity"); break; } @@ -5710,12 +5676,10 @@ if (key.equalsIgnoreCase("slabEnabled")) { // Eval.slab transformManager.setSlabEnabled(value); // refresh? - // refresh(0, "Viewer:setSlabEnabled"); break; } if (key.equalsIgnoreCase("zoomEnabled")) { transformManager.setZoomEnabled(value); - // refresh(0, "Viewer:setZoomEnabled()"); break; } if (key.equalsIgnoreCase("highResolution")) { @@ -5769,12 +5733,10 @@ } if (key.equalsIgnoreCase("showMultipleBonds")) { global.showMultipleBonds = value; - // refresh(0, "Viewer:setShowMultipleBonds()"); break; } if (key.equalsIgnoreCase("showHiddenSelectionHalos")) { global.showHiddenSelectionHalos = value; - // refresh(0, "Viewer:setShowHiddenSelectionHalos()"); break; } if (key.equalsIgnoreCase("windowCentered")) { @@ -5817,7 +5779,6 @@ } if (key.equalsIgnoreCase("greyscaleRendering")) { g3d.setGreyscaleMode(global.greyscaleRendering = value); - // refresh(0, "Viewer:setGreyscaleRendering()"); break; } if (key.equalsIgnoreCase("measurementLabels")) { @@ -5960,7 +5921,6 @@ return false; if (doRepaint) { setTainted(true); - // refresh(0, "viewer.setBooleanProperty"); } return true; } @@ -6093,7 +6053,6 @@ // app preferences dialog global.setParameterValue("perspectiveDepth", perspectiveDepth); transformManager.setPerspectiveDepth(perspectiveDepth); - // refresh(0, "Viewer:setPerspectiveDepth()"); } public void setAxesOrientationRasmol(boolean TF) { @@ -6125,7 +6084,6 @@ void setAxesScale(float scale) { global.axesScale = scale; axesAreTainted = true; - // refresh(0, "set axesScale"); } public Point3f[] getAxisPoints() { @@ -6363,7 +6321,6 @@ modelSet.deleteAllBonds(); modelSet.autoBond(null, null, null, null); addStateScript("connect;", false, true); - // refresh(0, "Viewer:rebond()"); } void setPdbConectBonding(boolean isAuto) { @@ -6378,7 +6335,6 @@ return; } addStateScript("connect PDB;", false, true); - // refresh(0, "Viewer:setPdbConnectBonding()"); } // ////////////////////////////////////////////////////////////// @@ -6426,8 +6382,8 @@ /* * void setModeMultipleBond(byte modeMultipleBond) { //not implemented - * global.modeMultipleBond = modeMultipleBond; //refresh(0, - * "Viewer:setModeMultipleBond()"); } + * global.modeMultipleBond = modeMultipleBond; + * } */ public byte getModeMultipleBond() { @@ -6444,7 +6400,6 @@ // setBooleanProperty global.setParameterValue("showHydrogens", TF); global.showHydrogens = TF; - // refresh(0, "Viewer:setShowHydrogens()"); } public boolean getShowHydrogens() { @@ -6507,7 +6462,6 @@ // setbooleanProperty global.setParameterValue("showMeasurements", TF); global.showMeasurements = TF; - // refresh(0, "setShowMeasurements()"); } public boolean getShowMeasurements() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-08-13 10:36:27
|
Revision: 11314 http://jmol.svn.sourceforge.net/jmol/?rev=11314&view=rev Author: hansonr Date: 2009-08-13 10:36:15 +0000 (Thu, 13 Aug 2009) Log Message: ----------- code comment cleanup Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-08-13 10:28:15 UTC (rev 11313) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-08-13 10:36:15 UTC (rev 11314) @@ -243,11 +243,9 @@ stateManager = new StateManager(this); g3d = new Graphics3D(display); colorManager = new ColorManager(this, g3d); - // initialize(); statusManager = new StatusManager(this); scriptManager = new ScriptManager(this); transformManager = new TransformManager11(this); - // transformManager = new TransformManager10(this); selectionManager = new SelectionManager(this); pickingManager = new PickingManager(this); if (display != null) { @@ -505,7 +503,7 @@ axesAreTainted = true; transformManager.homePosition(); if (modelSet.setCrystallographicDefaults()) - stateManager.setCrystallographicDefaults();// modelSet.someModelsHavePeriodicOrigin); + stateManager.setCrystallographicDefaults(); else setAxesModeMolecular(false); prevFrame = Integer.MIN_VALUE; @@ -1384,7 +1382,6 @@ private static void setSpecular(boolean specular) { // Eval ColorManager.setSpecular(specular); - // global.specular = specular; } boolean getSpecular() { @@ -1394,19 +1391,16 @@ private static void setSpecularPower(int specularPower) { // Eval ColorManager.setSpecularPower(Math.abs(specularPower)); - // global.specularPower = specularPower; } private static void setSpecularExponent(int specularExponent) { // Eval ColorManager.setSpecularPower(-Math.abs(specularExponent)); - // global.specularExponent = specularExponent; } private static void setAmbientPercent(int ambientPercent) { // Eval ColorManager.setAmbientPercent(ambientPercent); - // global.ambientPercent = ambientPercent; } static int getAmbientPercent() { @@ -1416,7 +1410,6 @@ private static void setDiffusePercent(int diffusePercent) { // Eval ColorManager.setDiffusePercent(diffusePercent); - // global.diffusePercent = diffusePercent; } static int getDiffusePercent() { @@ -1426,7 +1419,6 @@ private static void setSpecularPercent(int specularPercent) { // Eval ColorManager.setSpecularPercent(specularPercent); - // global.specularPercent = specularPercent; } static int getSpecularPercent() { @@ -2908,9 +2900,6 @@ int autoHbond(BitSet bsBonds) { // Eval - // modelSet.addStateScript("select", null, selectionManager.bsSelection, - // null, - // "; calculate hbonds;", false); return autoHbond(selectionManager.bsSelection, selectionManager.bsSelection, bsBonds, 0, 0); } @@ -3278,10 +3267,8 @@ void setInMotion(boolean inMotion) { // MouseManager, TransformManager - // Logger.debug("viewer.setInMotion("+inMotion+")"); if (wasInMotion ^ inMotion) { animationManager.setInMotion(inMotion); - // resizeImage(0, 0, false, false, true); if (inMotion) { ++motionEventNumber; } else { @@ -3301,7 +3288,6 @@ } void pushHoldRepaint(String why) { - // System.out.println("Viewer pushHoldRepaint " + why); repaintManager.pushHoldRepaint(); } @@ -3310,7 +3296,6 @@ } void popHoldRepaint(String why) { - // System.out.println("Viewer popHoldRepaint " + why); repaintManager.popHoldRepaint(); } @@ -4989,8 +4974,6 @@ "ERROR: cannot set boolean flag to string value: {0}", key)); return; } - // Logger.warn(key + " -- string variable defined (" + value.length() - // + " bytes)"); } if (isJmol) global.setParameterValue(key, value); @@ -5085,7 +5068,6 @@ if (key.equalsIgnoreCase("ellipsoidAxisDiameter")) { if (isInt) value = value / 1000; - // ellipsoidAxisDiameter" just handled as getParameter() break; } @@ -5215,8 +5197,6 @@ "ERROR: cannot set boolean flag to numeric value: {0}", key)); return true; } - // Logger.warn("viewer.setFloatProperty(" + key + "," + value - // + ") - float variable defined"); } if (isJmol) global.setParameterValue(key, value); @@ -5397,8 +5377,6 @@ "ERROR: cannot set boolean flag to numeric value: {0}", key)); return; } - // Logger.info("viewer.setIntProperty(" + key + "," + value - // + ") - integer variable defined"); } if (!defineNew) return; @@ -5749,8 +5727,6 @@ } if (key.equalsIgnoreCase("testFlag1")) { global.testFlag1 = value; - - // fileManager.getFileAsBytes("C:/temp/test/n-butane1.spardir/M0001/Molecule"); break; } if (key.equalsIgnoreCase("testFlag2")) { @@ -6218,7 +6194,6 @@ transformManager.homePosition(); } transformManager.setNavigationMode(TF); - // refresh(1,"set navigationMode"); } public boolean getNavigationMode() { @@ -6307,8 +6282,6 @@ int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds) { // eval - // System.out.println((new Date()).getTime() + " connect" + minDistance + - // " " + maxDistance); clearModelDependentObjects(); clearAllMeasurements(); // necessary for serialization return modelSet.makeConnections(minDistance, maxDistance, order, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-08-31 04:46:14
|
Revision: 11414 http://jmol.svn.sourceforge.net/jmol/?rev=11414&view=rev Author: hansonr Date: 2009-08-31 04:46:03 +0000 (Mon, 31 Aug 2009) Log Message: ----------- version=11.9.2_dev # code: refactoring org.jmol.viewer.Script... into org.jmol.script # with the result that far more viewer methods are more publicly accessible Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-08-31 04:43:18 UTC (rev 11413) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-08-31 04:46:03 UTC (rev 11414) @@ -6618,6 +6618,11 @@ return modelSet.getAtomNumber(i); } + public Quaternion getAtomQuaternion(int i) { + return (i < 0 ? null + : modelSet.getQuaternion(i, getQuaternionFrame())); + } + float getAtomX(int i) { return modelSet.getAtomX(i); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-09-08 05:58:48
|
Revision: 11511 http://jmol.svn.sourceforge.net/jmol/?rev=11511&view=rev Author: hansonr Date: 2009-09-08 05:58:36 +0000 (Tue, 08 Sep 2009) Log Message: ----------- version=11.9.3_dev # new feature: symop("x,y,z") or symop(n) returns matrix4f for this operator # new feature: symop(n)*symop(m) returns matrix4f for the concatenated operation n*m (m first, then n) # new feature: symop(mat,...), where mat is a matrix4f variable same as symop("x,y,z",...) # new feature: draw symop @matrixVariable # thus we can have: # # draw symop @{symop(11)*symop(14)} # # or # # x = symop(11) * symop(14) # print symop(x,"description") # # new feature: symop(xxx,"[what]") where "[what]" is: # "xyz", "description", "translation", "center", "axispoint","axis", "angle", "matrix4f", # or anything else is a draw ID # # new feature: symop() returns array of information for symop(3,"array") or symop("x,y,z", "array") # * xyz (Jones-Faithful calculated from matrix) # * xyzOriginal (Provided by operation) # * description ("C2 axis", for example) # * translation vector (fractional) # * translation vector (cartesian) # * inversion point # * axis point # * axis vector # * angle of rotation # * matrix4f representation Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-09-08 05:45:23 UTC (rev 11510) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-09-08 05:58:36 UTC (rev 11511) @@ -1698,7 +1698,8 @@ if (!allowScript) fileName = fileName.substring(1); fileName = fileName.replace('\\', '/'); - String type = fileManager.getFileTypeName(fileName); + String type = (fileName.indexOf(".zip") >= 0 ? "zip" + : fileManager.getFileTypeName(fileName)); checkHalt("exit"); // assumes a Jmol script file if no other file type allowScript &= (type == null); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-09-20 02:36:46
|
Revision: 11536 http://jmol.svn.sourceforge.net/jmol/?rev=11536&view=rev Author: hansonr Date: 2009-09-20 02:36:40 +0000 (Sun, 20 Sep 2009) Log Message: ----------- # bug fix: getProperty("menu") does not work until a menu has been called up by user Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-09-20 00:06:15 UTC (rev 11535) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-09-20 02:36:40 UTC (rev 11536) @@ -4268,6 +4268,8 @@ } public String getMenu(String type) { + if (jmolpopup == null) + jmolpopup = JmolPopup.newJmolPopup(this, true, menuStructure, true); return (jmolpopup == null ? "" : jmolpopup.getMenu("Jmol version " + Viewer.getJmolVersion() + "|_GET_MENU|" + type)); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-09-20 17:28:05
|
Revision: 11547 http://jmol.svn.sourceforge.net/jmol/?rev=11547&view=rev Author: hansonr Date: 2009-09-20 17:27:55 +0000 (Sun, 20 Sep 2009) Log Message: ----------- version=11.9.5 # bug fix: initialize does not reset antialiasDisplay or set animation off Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-09-20 17:27:31 UTC (rev 11546) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-09-20 17:27:55 UTC (rev 11547) @@ -575,7 +575,8 @@ setSpecularExponent(global.specularExponent); setSpecularPower(global.specularPower); - animationManager.setAnimationOn(false); + if (modelSet != null) + animationManager.setAnimationOn(false); animationManager.setAnimationFps(global.animationFps); statusManager.setAllowStatusReporting(global.statusReporting); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-06 19:39:57
|
Revision: 11688 http://jmol.svn.sourceforge.net/jmol/?rev=11688&view=rev Author: hansonr Date: 2009-11-06 19:39:23 +0000 (Fri, 06 Nov 2009) Log Message: ----------- version=11.9.8_dev # abstract public String loadInline(Vector arrayData, boolean isAppend); # @param arrayData a Vector of models, where each model is either a String # or a String[] or a Vector<String> Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-06 19:31:12 UTC (rev 11687) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-06 19:39:23 UTC (rev 11688) @@ -5944,16 +5944,24 @@ } private void jmolTest() { + /* Vector v = new Vector(); + Vector m = new Vector(); + v.add(m); + m.add("MODEL 2"); + m.add("HETATM 1 H1 UNK 1 2.457 0.000 0.000 1.00 0.00 H "); + m.add("HETATM 2 C1 UNK 1 1.385 0.000 0.000 1.00 0.00 C "); + m.add("HETATM 3 C2 UNK 1 -1.385 -0.000 0.000 1.00 0.00 C "); v.add(new String[] { - "MODEL 2", - "HETATM 1 H1 UNK 1 2.457 0.000 0.000 1.00 0.00 H ", - "HETATM 2 C1 UNK 1 1.385 0.000 0.000 1.00 0.00 C ", - "HETATM 3 C2 UNK 1 -1.385 -0.000 0.000 1.00 0.00 C ", + "MODEL 2", + "HETATM 1 H1 UNK 1 2.457 0.000 0.000 1.00 0.00 H ", + "HETATM 2 C1 UNK 1 1.385 0.000 0.000 1.00 0.00 C ", + "HETATM 3 C2 UNK 1 -1.385 -0.000 0.000 1.00 0.00 C ", }); - //v.add(new String[] {"3","testing","C 0 0 0","O 0 1 0","N 0 0 1"} ); - //v.add("3\ntesting\nC 0 0 0\nO 0 1 0\nN 0 0 1\n"); + v.add(new String[] {"3","testing","C 0 0 0","O 0 1 0","N 0 0 1"} ); + v.add("3\ntesting\nC 0 0 0\nO 0 1 0\nN 0 0 1\n"); loadInline(v, false); + */ } public boolean getPdbLoadInfo(int type) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-23 16:16:29
|
Revision: 11780 http://jmol.svn.sourceforge.net/jmol/?rev=11780&view=rev Author: hansonr Date: 2009-11-23 16:16:22 +0000 (Mon, 23 Nov 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 13:54:08 UTC (rev 11779) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 16:16:22 UTC (rev 11780) @@ -2227,7 +2227,6 @@ clearAllMeasurements(); if (minimizer != null) minimizer.setProperty("clear", null); - //modelSet = modelManager.clear(); if (haveDisplay) { mouseManager.clear(); actionManager.clear(); @@ -2239,7 +2238,7 @@ definedAtomSets.clear(); dataManager.clear(); System.gc(); - } + } modelSet = modelManager.zap(); initializeModel(); if (notify) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-23 16:19:46
|
Revision: 11781 http://jmol.svn.sourceforge.net/jmol/?rev=11781&view=rev Author: hansonr Date: 2009-11-23 16:19:38 +0000 (Mon, 23 Nov 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 16:16:22 UTC (rev 11780) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 16:19:38 UTC (rev 11781) @@ -2227,6 +2227,7 @@ clearAllMeasurements(); if (minimizer != null) minimizer.setProperty("clear", null); + modelSet = modelManager.zap(); if (haveDisplay) { mouseManager.clear(); actionManager.clear(); @@ -2238,8 +2239,9 @@ definedAtomSets.clear(); dataManager.clear(); System.gc(); + } else { + modelSet = modelManager.zap(); } - modelSet = modelManager.zap(); initializeModel(); if (notify) setFileLoadStatus(FILE_STATUS_ZAPPED, null, (resetUndo ? "resetUndo" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-23 19:49:33
|
Revision: 11795 http://jmol.svn.sourceforge.net/jmol/?rev=11795&view=rev Author: hansonr Date: 2009-11-23 19:49:17 +0000 (Mon, 23 Nov 2009) Log Message: ----------- # code: JmolFrameExportJmolAdapter abandoned -- hasn't been implemented since 11.0 Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 19:48:05 UTC (rev 11794) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-23 19:49:17 UTC (rev 11795) @@ -2352,11 +2352,6 @@ return modelSet.getModelBitSet(atomList, allTrajectories); } - Object getClientFile() { - // DEPRECATED - use getExportJmolAdapter() - return null; - } - // this is a problem. SmarterJmolAdapter doesn't implement this; // it can only return null. @@ -2367,46 +2362,6 @@ .getClientAtomStringProperty(clientAtom, propertyName)); } - /* **************************************************************************** - * This is the method that was originally used to extract the model data from Jmol. - * It was never fully developed and has been abandoned. - * - * Much simpler is to use the public methods in JmolViewer and Viewer directly. - * - * See Jmol 11.8 for a version including FrameExportJmolAdapter.java if desired. - * - * LEGACY NOTES: - * - * Note that the API provided by JmolAdapter is used to import data into Jmol - * and to export data out of Jmol. - * - * When exporting, a few of the methods in JmolAdapter do not make sense. - * openBufferedReader(...) Others may be implemented in the future, but are - * not currently all pdb specific things Just pass in null for the methods - * that want a clientFile. The main methods to use are getFrameCount(null) -> - * currently always returns 1 getAtomCount(null, 0) getAtomIterator(null, 0) - * getBondIterator(null, 0) - * - * The AtomIterator and BondIterator return Objects as unique IDs to identify - * the atoms. atomIterator.getAtomUid() bondIterator.getAtomUid1() & - * bondIterator.getAtomUid2() The ExportJmolAdapter will return the 0-based - * atom index as a boxed Integer. That means that you can cast the results to - * get a zero-based atom index int atomIndex = - * ((Integer)atomIterator.getAtomUid()).intValue(); ... int bondedAtom1 = - * ((Integer)bondIterator.getAtomUid1()).intValue(); int bondedAtom2 = - * ((Integer)bondIterator.getAtomUid2()).intValue(); - * - * post questions to jmo...@li... - * - * @return A JmolAdapter - ****************************************************************************/ - - /* - JmolAdapter getExportJmolAdapter() { - return new FrameExportJmolAdapter(this, modelSet); - } - */ - public ModelSet getModelSet() { return modelSet; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-26 19:57:55
|
Revision: 11804 http://jmol.svn.sourceforge.net/jmol/?rev=11804&view=rev Author: hansonr Date: 2009-11-26 19:57:42 +0000 (Thu, 26 Nov 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-26 18:05:40 UTC (rev 11803) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-26 19:57:42 UTC (rev 11804) @@ -1619,9 +1619,7 @@ // applet is being destroyed clearScriptQueue(); haltScriptExecution(); - transformManager.setSpinOn(false); - transformManager.setNavOn(false); - transformManager.setVibrationPeriod(0); + stopAnimationThreads(); scriptManager.startCommandWatcher(false); scriptManager.interruptQueueThreads(); g3d.destroy(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-12-02 18:46:54
|
Revision: 11839 http://jmol.svn.sourceforge.net/jmol/?rev=11839&view=rev Author: hansonr Date: 2009-12-02 18:46:46 +0000 (Wed, 02 Dec 2009) Log Message: ----------- version=11.9.10_dev # new feature: double-click-drag translates model # new feature: multitouch gesture antiparallel strokes: rotate at point # new feature: multitouch gesture spread/pinch: zoom in/out at point # new feature: app command parameter [-M or --multitouch] "sparshui" or "sparshui-simulated" # applet jmolSetCallback("multiTouchSparshUI", "true") # applet jmolSetCallback("multiTouchSparshUI-simulated", "true") # with those variables set, Jmol will load the multitouch package and start # an integrated SparshUI server (if none is already started). In addition, # with the -simulated flag, Jmol simulates multitouch using CTRL-LEFT drag (twice) # This incorporation of SparshUI also demonstrates the on-the-fly loading # of a client gesture into the SparshUI system using an extension of the # SparshUI protocol that allows delivery of a class name rather than a SparshUI # gesture ordinal. # # code: ActionManagerMT - for multitouch # code: preliminary org.jmol.multitouch package # code: preliminary com.sparshui package (I've been assured this is LGPL # despite the GPL license in the direcory) # Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-12-02 18:35:46 UTC (rev 11838) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-12-02 18:46:46 UTC (rev 11839) @@ -7607,8 +7607,6 @@ translateXYBy(Parser.parseInt(tokens[2]), Parser.parseInt(tokens[3])); else if (key.equals("rotateMolecule")) rotateMolecule(Parser.parseInt(tokens[2]), Parser.parseInt(tokens[3])); - else if (key.equals("centerAt")) - centerAt(Parser.parseInt(tokens[2]), Parser.parseInt(tokens[3]), null); break; case 5: if (key.equals("spinXYBy")) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-12 23:28:00
|
Revision: 12106 http://jmol.svn.sourceforge.net/jmol/?rev=12106&view=rev Author: hansonr Date: 2010-01-12 23:27:53 +0000 (Tue, 12 Jan 2010) Log Message: ----------- version=11.9.18_dev # bug fix: connected(0, {carbon}) not working # new feature: set slabByMolecule # new feature: set zshadePower -- log_2(p) in f = [(zDepth - z) / (zDepth - zSlab)]^p # Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-01-12 23:23:11 UTC (rev 12105) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-01-12 23:27:53 UTC (rev 12106) @@ -5375,7 +5375,7 @@ break; } if (key.equalsIgnoreCase("zshadePower")) { - Graphics3D.setZShadePower(Math.min(value, 1)); + Graphics3D.setZShadePower(Math.max(value, 1)); break; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-02 16:08:31
|
Revision: 12736 http://jmol.svn.sourceforge.net/jmol/?rev=12736&view=rev Author: hansonr Date: 2010-04-02 16:08:24 +0000 (Fri, 02 Apr 2010) Log Message: ----------- version=12.0.RC1 # release candidate 1 for Jmol 12.0 # # new feature: calculate hbonds {....} {....} *introduced in 11.7.9, but not checked or documented Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-04-02 15:33:38 UTC (rev 12735) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-04-02 16:08:24 UTC (rev 12736) @@ -1629,14 +1629,18 @@ scriptManager.startCommandWatcher(false); scriptManager.interruptQueueThreads(); g3d.destroy(); - if (appConsole != null) { - appConsole.dispose(); - appConsole = null; + try { + if (appConsole != null) { + appConsole.dispose(); + appConsole = null; + } + if (scriptEditor != null) { + scriptEditor.dispose(); + scriptEditor = null; + } + } catch (Exception e) { + //ignore -- Disposal was interrupted only in Eclipse } - if (scriptEditor != null) { - scriptEditor.dispose(); - scriptEditor = null; - } } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-09 01:00:29
|
Revision: 13041 http://jmol.svn.sourceforge.net/jmol/?rev=13041&view=rev Author: hansonr Date: 2010-05-09 01:00:23 +0000 (Sun, 09 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-09 00:51:37 UTC (rev 13040) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-09 01:00:23 UTC (rev 13041) @@ -4885,9 +4885,13 @@ if (!haveDisplay) return; // Eval - if (appConsole == null) - getProperty("DATA_API", "getAppConsole", Boolean.TRUE); - appConsole.setVisible(showConsole); + try { + if (appConsole == null) + getProperty("DATA_API", "getAppConsole", Boolean.TRUE); + appConsole.setVisible(showConsole); + } catch (Exception e) { + // no console for this client... + } } public void clearConsole() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-13 15:39:58
|
Revision: 13087 http://jmol.svn.sourceforge.net/jmol/?rev=13087&view=rev Author: hansonr Date: 2010-05-13 15:39:51 +0000 (Thu, 13 May 2010) Log Message: ----------- better JME-->addHydrogens-->minimize sequence Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-13 15:01:49 UTC (rev 13086) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-13 15:39:51 UTC (rev 13087) @@ -2101,8 +2101,12 @@ BitSet bsNew = new BitSet(); modelSet = modelManager.createModelSet(fullPathName, fileName, atomSetCollection, bsNew, isAppend); - if (bsNew.cardinality() > 0) + if (bsNew.cardinality() > 0) { + String jmolScript = (String) modelSet.getModelSetAuxiliaryInfo("jmolscript"); minimize(Integer.MAX_VALUE, 0, bsNew, true, true, false); + if (jmolScript != null) + modelSet.getModelSetAuxiliaryInfo().put("jmolscript", jmolScript); + } //but we need to NOT save H atom positions, either! if (!isAppend) initializeModel(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |