From: <ha...@us...> - 2013-03-12 02:59:12
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Revision: 17969 http://sourceforge.net/p/jmol/code/17969 Author: hansonr Date: 2013-03-12 02:59:05 +0000 (Tue, 12 Mar 2013) Log Message: ----------- JmolList back to List/ArrayList for nonessential methods; fixes bug in file drop. Modified Paths: -------------- trunk/Jmol/src/org/jmol/export/JmolFileDropper.java trunk/Jmol/src/org/jmol/io/JmolBinary.java trunk/Jmol/src/org/jmol/util/TextFormat.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Viewer.java trunk/Jmol/src/org/openscience/chimetojmol/ChimePanel.java trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceToolGUI.java trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java Modified: trunk/Jmol/src/org/jmol/export/JmolFileDropper.java =================================================================== --- trunk/Jmol/src/org/jmol/export/JmolFileDropper.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/jmol/export/JmolFileDropper.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -39,13 +39,13 @@ import java.beans.PropertyChangeSupport; import java.io.File; +import java.util.List; import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; import org.jmol.util.Escape; -import org.jmol.util.JmolList; import org.jmol.util.Logger; @@ -106,7 +106,7 @@ viewer.openFileAsyncPDB(fname, true); } - private void loadFiles(JmolList<File> fileList) { + private void loadFiles(List<File> fileList) { StringBuilder sb = new StringBuilder(); for (int i = 0; i < fileList.size(); ++ i) { File f = fileList.get(i); @@ -167,8 +167,8 @@ Logger.error("transfer failed"); } // if o is still null we had an exception - if (o instanceof JmolList) { - JmolList<File> fileList = (JmolList<File>) o; + if (o instanceof List) { + List<File> fileList = (List<File>) o; final int length = fileList.size(); if (length == 1) { String fileName = fileList.get(0).getAbsolutePath().trim(); Modified: trunk/Jmol/src/org/jmol/io/JmolBinary.java =================================================================== --- trunk/Jmol/src/org/jmol/io/JmolBinary.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/jmol/io/JmolBinary.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -33,6 +33,7 @@ import java.io.StringReader; import java.io.UnsupportedEncodingException; +import java.util.List; import java.util.Map; import org.jmol.api.Interface; @@ -521,7 +522,7 @@ return getJzu().spartanFileList(name, zipDirectory); } - public static void getFileReferences(String script, JmolList<String> fileList) { + public static void getFileReferences(String script, List<String> fileList) { for (int ipt = 0; ipt < FileManager.scriptFilePrefixes.length; ipt++) { String tag = FileManager.scriptFilePrefixes[ipt]; int i = -1; @@ -529,7 +530,7 @@ String s = Parser.getQuotedStringAt(script, i); if (s.indexOf("::") >= 0) s = TextFormat.splitChars(s, "::")[1]; - fileList.addLast(s); + fileList.add(s); } } } Modified: trunk/Jmol/src/org/jmol/util/TextFormat.java =================================================================== --- trunk/Jmol/src/org/jmol/util/TextFormat.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/jmol/util/TextFormat.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -25,8 +25,10 @@ package org.jmol.util; +import java.util.List; + //import java.text.DecimalFormat; @@ -700,8 +702,8 @@ return sb.toString(); } - public static String replaceQuotedStrings(String s, JmolList<String> list, - JmolList<String> newList) { + public static String replaceQuotedStrings(String s, List<String> list, + List<String> newList) { int n = list.size(); for (int i = 0; i < n; i++) { String name = list.get(i); @@ -713,8 +715,8 @@ return s; } - public static String replaceStrings(String s, JmolList<String> list, - JmolList<String> newList) { + public static String replaceStrings(String s, List<String> list, + List<String> newList) { int n = list.size(); for (int i = 0; i < n; i++) { String name = list.get(i); Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-12 02:59:05 UTC (rev 17969) @@ -11,6 +11,7 @@ ___JmolVersion="13.1.14_dev" +bug fix: FileDropper broken bug fix: LcaoCartoon "-sp3d" not working bug fix: PyMOL PSE files not accessible by Jmol app File...Open or drag/drop bug fix: incorrect calculation of RMSD for COMPARE and SMILES Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -9025,7 +9025,8 @@ setCursor(JC.CURSOR_DEFAULT); setBooleanProperty("refreshing", true); fileManager.setPathForAllFiles(""); - Logger.error("viewer handling error condition: " + er); + Logger.error("viewer handling error condition: " + er + " "); + //er.printStackTrace(); notifyError("Error", "doClear=" + doClear + "; " + er, "" + er); } catch (Throwable e1) { try { Modified: trunk/Jmol/src/org/openscience/chimetojmol/ChimePanel.java =================================================================== --- trunk/Jmol/src/org/openscience/chimetojmol/ChimePanel.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/chimetojmol/ChimePanel.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -18,7 +18,8 @@ import java.io.InputStream; import java.io.OutputStream; import java.net.URL; -import org.jmol.util.JmolList; +import java.util.ArrayList; +import java.util.List; import java.util.regex.Pattern; @@ -39,7 +40,7 @@ private JScrollPane logScrollPane; private JFileChooser chooser; private File oldDir; - private JmolList<File> pages; + private List<File> pages; private int nDir; private int nFiles; //private int nControls; @@ -140,7 +141,7 @@ void getFileList() { logArea.setText(""); - pages = new JmolList<File>(); + pages = new ArrayList<File>(); String dir = chimePath.getText(); dir = dir.replace('\\', '/'); while (dir.endsWith("/")) @@ -272,7 +273,7 @@ String name = f1.getName().toLowerCase(); if (name.endsWith(".htm") || name.endsWith(".html")) { if (justChecking) { - pages.addLast(f1); + pages.add(f1); log(f1.getAbsolutePath()); return true; } Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java =================================================================== --- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -72,10 +72,11 @@ import java.io.File; import java.io.FileInputStream; import java.io.IOException; -import org.jmol.util.JmolList; import java.util.Arrays; import java.util.Hashtable; +import java.util.ArrayList; +import java.util.List; import java.util.Map; import java.util.Properties; import java.util.StringTokenizer; @@ -285,9 +286,9 @@ say(GT._("Building Command Hooks...")); commands = new Hashtable<String, Action>(); if (display != null) { - Action[] actions = getActions(); - for (int i = 0; i < actions.length; i++) { - Action a = actions[i]; + List<Action> actions = getActions(); + for (int i = 0; i < actions.size(); i++) { + Action a = actions.get(i); commands.put(a.getValue(Action.NAME).toString(), a); } } @@ -555,13 +556,13 @@ * @return A list of Actions that is understood by the upper level * application */ - public Action[] getActions() { + public List<Action> getActions() { - JmolList<Action> actions = new JmolList<Action>(); + List<Action> actions = new ArrayList<Action>(); actions.addAll(Arrays.asList(defaultActions)); actions.addAll(Arrays.asList(display.getActions())); actions.addAll(Arrays.asList(preferencesDialog.getActions())); - return actions.toArray(new Action[0]); + return actions; } /** @@ -811,10 +812,10 @@ * @return Strings chopped on whitespace boundaries */ protected String[] tokenize(String input) { - JmolList<String> v = new JmolList<String>(); + List<String> v = new ArrayList<String>(); StringTokenizer t = new StringTokenizer(input); while (t.hasMoreTokens()) - v.addLast(t.nextToken()); + v.add(t.nextToken()); return v.toArray(new String[v.size()]); } Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java =================================================================== --- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -55,7 +55,6 @@ import org.jmol.console.JmolConsole; import org.jmol.i18n.GT; import org.jmol.util.CommandHistory; -import org.jmol.util.JmolList; import org.jmol.util.Logger; import org.jmol.util.Parser; import org.jmol.util.TextFormat; @@ -469,16 +468,16 @@ .scriptWaitStatus(strCommand.substring(5), "+fileLoaded,+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated"); if (o instanceof List) { - List<JmolList<JmolList<Object>>> info = (List<JmolList<JmolList<Object>>>) o; + List<List<List<Object>>> info = (List<List<List<Object>>>) o; /* * info = [ statusRecortSet0, statusRecortSet1, statusRecortSet2, ...] * statusRecordSet = [ statusRecord0, statusRecord1, statusRecord2, ...] * statusRecord = [int msgPtr, String statusName, int intInfo, String msg] */ for (int i = 0; i < info.size(); i++) { - JmolList<JmolList<Object>> statusRecordSet = info.get(i); + List<List<Object>> statusRecordSet = info.get(i); for (int j = 0; j < statusRecordSet.size(); j++) { - JmolList<Object> statusRecord = statusRecordSet.get(j); + List<Object> statusRecord = statusRecordSet.get(j); Logger.info("msg#=" + statusRecord.get(0) + " " + statusRecord.get(1) + " intInfo=" + statusRecord.get(2) + " stringInfo=" + statusRecord.get(3)); Modified: trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java =================================================================== --- trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -31,7 +31,8 @@ import java.io.InputStreamReader; import java.io.UnsupportedEncodingException; import java.net.InetSocketAddress; -import org.jmol.util.JmolList; +import java.util.List; +import java.util.ArrayList; import java.util.Hashtable; import java.util.Map; @@ -554,7 +555,7 @@ String script = null; if (contentJSON.has("scripts")) { //TODO -- this is not implemented, because JSONObject.getJSONArray is not implemented - JmolList<JSONObject> scripts = contentJSON.getJSONArray("scripts"); + List<JSONObject> scripts = contentJSON.getJSONArray("scripts"); for (int i = scripts.size(); --i >= 0;) { JSONObject scriptInfo = scripts.get(i); if (scriptInfo.getString("startup").equals("yes")) { @@ -734,13 +735,13 @@ } @SuppressWarnings("unchecked") - public JmolList<JSONObject> getJSONArray(String key) throws Exception { + public List<JSONObject> getJSONArray(String key) throws Exception { if (!has(key)) throw new Exception("JSON key not found:" + key); - JmolList<JSONObject> list = new JmolList<JSONObject>(); - JmolList<SV> svlist = ((SV) get(key)).getList(); + List<JSONObject> list = new ArrayList<JSONObject>(); + List<SV> svlist = ((SV) get(key)).getList(); for (int i = 0; i < svlist.size(); i++) - list.addLast(new JSONObject(Escape.escapeMap((Map<String, Object>)(svlist.get(i).value)))); + list.add(new JSONObject(Escape.escapeMap((Map<String, Object>)(svlist.get(i).value)))); return list; } Modified: trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java =================================================================== --- trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -25,7 +25,8 @@ package org.openscience.jmol.app.surfacetool; -import org.jmol.util.JmolList; +import java.util.ArrayList; +import java.util.List; import javax.swing.JOptionPane; @@ -58,7 +59,7 @@ private final P3 center = new P3(); private final V3 boxVec = new V3(); //surface specific parameters - private final JmolList<SurfaceStatus> surfaces = new JmolList<SurfaceStatus>(); + private final List<SurfaceStatus> surfaces = new ArrayList<SurfaceStatus>(); final static int DEGREES = 0; final static int RADIANS = 1; @@ -227,7 +228,7 @@ } for (int i = 0; i < meshIndexList.length; i++) { if (meshIndexList[i] == -1) - surfaces.addLast(new SurfaceStatus(mc.meshes[i], kind)); + surfaces.add(new SurfaceStatus(mc.meshes[i], kind)); } } } @@ -535,7 +536,7 @@ capOn = b; } - public JmolList<SurfaceStatus> getSurfaces() { + public List<SurfaceStatus> getSurfaces() { return surfaces; } } Modified: trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceToolGUI.java =================================================================== --- trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceToolGUI.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceToolGUI.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -65,7 +65,7 @@ import org.jmol.api.JmolViewer; import org.jmol.export.history.HistoryFile; import org.jmol.i18n.GT; -import org.jmol.util.JmolList; +import java.util.List; /** * GUI for the Jmol surfaceTool @@ -358,7 +358,7 @@ int[] selected = whichList.getSelectedIndices(); if (selected != null) { int lastIndex = selected[(selected.length - 1)]; - JmolList<SurfaceStatus> surfaces = slicer.getSurfaces(); + List<SurfaceStatus> surfaces = slicer.getSurfaces(); SurfaceStatus lastSurface = surfaces.get(lastIndex); if (lastSurface.beenSliced) { slicer.setSlice(lastSurface.slice.angleXY, @@ -383,7 +383,7 @@ if (whichSelected == null || whichSelected.length == 0) return; for (int i = 0; i < whichSelected.length; i++) { - JmolList<SurfaceStatus> surfaces = slicer.getSurfaces(); + List<SurfaceStatus> surfaces = slicer.getSurfaces(); int k = whichSelected[i]; slicer.sliceObject(surfaces.get(k).id, surfaces.get(k).kind); surfaces.get(k).beenSliced = true; Modified: trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java =================================================================== --- trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java 2013-03-11 16:18:28 UTC (rev 17968) +++ trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java 2013-03-12 02:59:05 UTC (rev 17969) @@ -41,10 +41,8 @@ import java.io.IOException; import java.io.InputStream; import java.net.URL; -import org.jmol.util.JmolList; - +import java.util.List; import java.util.ArrayList; -import java.util.List; import java.util.zip.GZIPOutputStream; import javax.swing.BorderFactory; @@ -656,18 +654,18 @@ } catch (IOException IOe) { throw IOe; } - JmolList<String> filesToCopy = new JmolList<String>(); + List<String> filesToCopy = new ArrayList<String>(); String localPath = localAppletPath.getText(); if (localPath.equals(".") || remoteAppletPath.getText().equals(".")) { - filesToCopy.addLast(localPath + "/Jmol.js"); - filesToCopy.addLast(localPath + "/JmolApplet.jar"); + filesToCopy.add(localPath + "/Jmol.js"); + filesToCopy.add(localPath + "/JmolApplet.jar"); } JmolBinary.getFileReferences(script, filesToCopy); - JmolList<String> copiedFileNames = new JmolList<String>(); + List<String> copiedFileNames = new ArrayList<String>(); int nFiles = filesToCopy.size(); for (int iFile = 0; iFile < nFiles; iFile++) { String newName = copyBinaryFile(filesToCopy.get(iFile), datadirPath); - copiedFileNames.addLast(newName.substring(newName.lastIndexOf('/') + 1)); + copiedFileNames.add(newName.substring(newName.lastIndexOf('/') + 1)); } script = TextFormat.replaceQuotedStrings(script, filesToCopy, copiedFileNames); LogPanel.log(" ..." + GT._("adding {0}", javaname + ".spt")); @@ -903,7 +901,7 @@ class ArrayListTransferHandler extends TransferHandler { DataFlavor localArrayListFlavor, serialArrayListFlavor; String localArrayListType = DataFlavor.javaJVMLocalObjectMimeType - + ";class=org.jmol.util.JmolList"; + + ";class=org.jmol.util.List"; JList<?> source = null; int[] sourceIndices = null; int addIndex = -1; // Location where items were added @@ -928,13 +926,13 @@ return false; } JList<?> target = null; - JmolList<?> alist = null; + List<?> alist = null; try { target = (JList<?>) c; if (hasLocalArrayListFlavor(t.getTransferDataFlavors())) { - alist = (JmolList<?>) t.getTransferData(localArrayListFlavor); + alist = (List<?>) t.getTransferData(localArrayListFlavor); } else if (hasSerialArrayListFlavor(t.getTransferDataFlavors())) { - alist = (JmolList<?>) t.getTransferData(serialArrayListFlavor); + alist = (List<?>) t.getTransferData(serialArrayListFlavor); } else { return false; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |