X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9dd46d648572dfa7ea924c4333fd3af16f7aa9cd;hb=4f77328104498504339216829abf5ea87e2791ec;hp=774dd4c3af2b25765b334143da02e44daebe2533;hpb=7b21db5b8c3f010f481ac13cc13c67d34f3d1d9c;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 774dd4c..9dd46d6 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,12 +20,12 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.SEQUENCE_ID; - import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.bin.Jalview; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; @@ -38,13 +38,14 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; +import jalview.project.Jalview2XML; import jalview.structure.StructureSelectionManager; import jalview.urls.IdOrgSettings; -import jalview.util.ImageMaker; +import jalview.util.BrowserLauncher; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; -import jalview.util.dialogrunner.RunResponse; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; @@ -81,13 +82,14 @@ import java.beans.PropertyChangeListener; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; +import java.io.FileWriter; import java.io.IOException; import java.net.URL; import java.util.ArrayList; +import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.ListIterator; -import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; @@ -106,13 +108,13 @@ import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; -import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; +import javax.swing.JTextField; import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; @@ -145,6 +147,10 @@ public class Desktop extends jalview.jbgui.GDesktop private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; + protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; + + public static HashMap savingFiles = new HashMap<>(); + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** @@ -343,36 +349,91 @@ public class Desktop extends jalview.jbgui.GDesktop */ public Desktop() { + super(); /** - * A note to implementors. It is ESSENTIAL that any activities that might block - * are spawned off as threads rather than waited for during this constructor. + * A note to implementors. It is ESSENTIAL that any activities that might + * block are spawned off as threads rather than waited for during this + * constructor. */ instance = this; - doVamsasClientCheck(); + if (!Platform.isJS()) + { + doVamsasClientCheck(); + } doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + /* + if (!Platform.isAMac()) + { + // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE); + } + else + { + this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); + } + */ + + try + { + if (!Platform.isJS()) + /* + * @j2sIgnore + */ + { + APQHandlers.setAPQHandlers(this); + } + } catch (Exception e) + { + System.out.println("Cannot set APQHandlers"); + // e.printStackTrace(); + } catch (Throwable t) + { + System.out.println("Cannot set APQHandlers"); + // t.printStackTrace(); + } + + + addWindowListener(new WindowAdapter() + { + + @Override + public void windowClosing(WindowEvent ev) + { + quit(); + } + }); + boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", false); + boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", false); desktop = new MyDesktopPane(selmemusage); + showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); + getContentPane().setLayout(new BorderLayout()); // alternate config - have scrollbars - see notes in JAL-153 // JScrollPane sp = new JScrollPane(); // sp.getViewport().setView(desktop); // getContentPane().add(sp, BorderLayout.CENTER); + + // BH 2018 - just an experiment to try unclipped JInternalFrames. + if (Platform.isJS()) + { + getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); + } + getContentPane().add(desktop, BorderLayout.CENTER); desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised desktop.setDesktopManager(new MyDesktopManager( - (Platform.isWindows() ? new DefaultDesktopManager() - : Platform.isAMac() + (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() + : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager( desktop.getDesktopManager()) : desktop.getDesktopManager()))); @@ -389,10 +450,12 @@ public class Desktop extends jalview.jbgui.GDesktop int yPos = Math.max(5, (screenSize.height - 650) / 2); setBounds(xPos, yPos, 900, 650); } + + if (!Platform.isJS()) /** - * BH 2018 + * Java only * - * @j2sNative + * @j2sIgnore */ { @@ -407,7 +470,14 @@ public class Desktop extends jalview.jbgui.GDesktop + "Java version: " + System.getProperty("java.version") + "\n" + System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " - + System.getProperty("os.version")); + + System.getProperty("os.version") + + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT") + ? "\nJava path:" + + System.getProperty( + "java.home") + + File.separator + "bin" + + File.separator + "java" + : "")); showConsole(showjconsole); @@ -430,8 +500,8 @@ public class Desktop extends jalview.jbgui.GDesktop } }); - // Thread off a new instance of the file chooser - this reduces the time it - // takes to open it later on. + // Thread off a new instance of the file chooser - this reduces the time + // it takes to open it later on. new Thread(new Runnable() { @Override @@ -459,7 +529,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); - } // end BH 2018 ignore + } this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); @@ -534,34 +604,25 @@ public class Desktop extends jalview.jbgui.GDesktop public void checkForNews() { - - /** - * BH 2018 - * - * @j2sNative - */ + final Desktop me = this; + // Thread off the news reader, in case there are connection problems. + new Thread(new Runnable() { - final Desktop me = this; - // Thread off the news reader, in case there are connection problems. - addDialogThread(new Runnable() + @Override + public void run() { - @Override - public void run() - { - Cache.log.debug("Starting news thread."); - - jvnews = new BlogReader(me); - showNews.setVisible(true); - Cache.log.debug("Completed news thread."); - } - }); - } + Cache.log.debug("Starting news thread."); + jvnews = new BlogReader(me); + showNews.setVisible(true); + Cache.log.debug("Completed news thread."); + } + }).start(); } public void getIdentifiersOrgData() { // Thread off the identifiers fetcher - addDialogThread(new Runnable() + new Thread(new Runnable() { @Override public void run() @@ -578,7 +639,8 @@ public class Desktop extends jalview.jbgui.GDesktop + e.getMessage()); } } - }); + }).start(); + } @Override @@ -589,32 +651,23 @@ public class Desktop extends jalview.jbgui.GDesktop void showNews(boolean visible) { - /** - * BH 2018 - * - * @j2sNative - * - */ + Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); + showNews.setSelected(visible); + if (visible && !jvnews.isVisible()) { - Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); - showNews.setSelected(visible); - if (visible && !jvnews.isVisible()) + new Thread(new Runnable() { - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() - { - long now = System.currentTimeMillis(); - Desktop.instance.setProgressBar( - MessageManager.getString("status.refreshing_news"), - now); - jvnews.refreshNews(); - Desktop.instance.setProgressBar(null, now); - jvnews.showNews(); - } - }).start(); - } + long now = System.currentTimeMillis(); + Desktop.instance.setProgressBar( + MessageManager.getString("status.refreshing_news"), now); + jvnews.refreshNews(); + Desktop.instance.setProgressBar(null, now); + jvnews.showNews(); + } + }).start(); } } @@ -678,8 +731,7 @@ public class Desktop extends jalview.jbgui.GDesktop private void doVamsasClientCheck() { - if (/** @j2sNative false && */ // BH 2018 - jalview.bin.Cache.vamsasJarsPresent()) + if (Cache.vamsasJarsPresent()) { setupVamsasDisconnectedGui(); VamsasMenu.setVisible(true); @@ -888,8 +940,7 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); - frame.setOpaque(/** @j2sNative true || */ - false); + frame.setOpaque(Platform.isJS()); if (frame.getX() < 1 && frame.getY() < 1) { @@ -940,7 +991,7 @@ public class Desktop extends jalview.jbgui.GDesktop menuItem.removeActionListener(menuItem.getActionListeners()[0]); } windowMenu.remove(menuItem); - }; + } }); menuItem.addActionListener(new ActionListener() @@ -954,7 +1005,7 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { - + // System.err.println(ex.toString()); } } }); @@ -1004,7 +1055,7 @@ public class Desktop extends jalview.jbgui.GDesktop KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK); KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); InputMap inputMap = frame .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); @@ -1096,7 +1147,10 @@ public class Desktop extends jalview.jbgui.GDesktop { format = new IdentifyFile().identify(file, protocol); } - + if (file instanceof File) + { + Platform.cacheFileData((File) file); + } new FileLoader().LoadFile(null, file, protocol, format); } @@ -1119,17 +1173,16 @@ public class Desktop extends jalview.jbgui.GDesktop public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - final JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); + JalviewFileChooser chooser = JalviewFileChooser + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); - chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { - @Override public void run() { @@ -1158,14 +1211,14 @@ public class Desktop extends jalview.jbgui.GDesktop new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format); } - }).openDialog(this); + }); + chooser.showOpenDialog(this); } /** - * DOCUMENT ME! + * Shows a dialog for input of a URL at which to retrieve alignment data * - * @param e - * DOCUMENT ME! + * @param viewport */ @Override public void inputURLMenuItem_actionPerformed(AlignViewport viewport) @@ -1175,46 +1228,111 @@ public class Desktop extends jalview.jbgui.GDesktop JLabel label = new JLabel( MessageManager.getString("label.input_file_url")); - JComboBox history = new JComboBox(); JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(label); - panel.add(history); - history.setPreferredSize(new Dimension(400, 20)); - history.setEditable(true); - history.addItem("http://www."); - - String historyItems = jalview.bin.Cache.getProperty("RECENT_URL"); - StringTokenizer st; - - if (historyItems != null) + /* + * the URL to fetch is + * Java: an editable combobox with history + * JS: (pending JAL-3038) a plain text field + */ + JComponent history; + String urlBase = "http://www."; + if (Platform.isJS()) { - st = new StringTokenizer(historyItems, "\t"); - - while (st.hasMoreTokens()) + history = new JTextField(urlBase, 35); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + JComboBox asCombo = new JComboBox<>(); + asCombo.setPreferredSize(new Dimension(400, 20)); + asCombo.setEditable(true); + asCombo.addItem(urlBase); + String historyItems = Cache.getProperty("RECENT_URL"); + if (historyItems != null) { - history.addItem(st.nextElement()); + for (String token : historyItems.split("\\t")) + { + asCombo.addItem(token); + } } + history = asCombo; } + panel.add(history); - // BH 2018 -- providing a callback for SwingJS - // dialogOption is just a simple way to provide - // context for the modal-like response. - // The only requirement is that desktop implement - // PropertyChangeListener, which is used already in Java - // for changes in input value and such within the dialogs. + Object[] options = new Object[] { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + Runnable action = new Runnable() + { + @Override + public void run() + { + @SuppressWarnings("unchecked") + String url = (history instanceof JTextField + ? ((JTextField) history).getText() + : ((JComboBox) history).getSelectedItem() + .toString()); + + if (url.toLowerCase().endsWith(".jar")) + { + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + FileFormat.Jalview); + } + else + { + new FileLoader().LoadFile(url, DataSourceType.URL, + FileFormat.Jalview); + } + } + else + { + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - String dialogOption = "label.input_alignment_from_url"; - desktop.dialogData = new Object[] { dialogOption, viewport, history }; - desktop.onDialogReturn(JvOptionPane.showInternalConfirmDialog(desktop, - panel, MessageManager.getString(dialogOption), - JvOptionPane.OK_CANCEL_OPTION)); + if (format == null) + { + String msg = MessageManager + .formatMessage("label.couldnt_locate", url); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + MessageManager.getString("label.url_not_found"), + JvOptionPane.WARNING_MESSAGE); - // no code may follow this, as SwingJS will not block - // callback in JavaScript comes via a property change event, - // thus going into desktop.onDialogReturn(int) just the same as - // in Java. + return; + } + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + format); + } + else + { + new FileLoader().LoadFile(url, DataSourceType.URL, format); + } + } + } + }; + String dialogOption = MessageManager + .getString("label.input_alignment_from_url"); + JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action) + .showInternalDialog(panel, dialogOption, + JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, + MessageManager.getString("action.ok")); } /** @@ -1376,19 +1494,29 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on requesting Help documentation */ @Override - public void documentationMenuItem_actionPerformed(ActionEvent e) + public void documentationMenuItem_actionPerformed() { try { - Help.showHelpWindow(); + if (Platform.isJS()) + { + BrowserLauncher.openURL("http://www.jalview.org/help.html"); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + Help.showHelpWindow(); + } } catch (Exception ex) { + System.err.println("Error opening help: " + ex.getMessage()); } } @@ -1592,30 +1720,49 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Prompts the user to choose a file and then saves the Jalview state as a + * Jalview project file */ @Override - public void saveState_actionPerformed(ActionEvent e) + public void saveState_actionPerformed() { - // TODO: JAL-3048 not needed for Jalview-JS + saveState_actionPerformed(false); + } - JalviewFileChooser chooser = new JalviewFileChooser("jvp", - "Jalview Project"); + public void saveState_actionPerformed(boolean saveAs) + { + java.io.File projectFile = getProjectFile(); + // autoSave indicates we already have a file and don't need to ask + boolean autoSave = projectFile != null && !saveAs + && BackupFiles.getEnabled(); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_state")); + // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"', + // saveAs="+saveAs+", Backups + // "+(BackupFiles.getEnabled()?"enabled":"disabled")); - int value = chooser.showSaveDialog(this); + boolean approveSave = false; + if (!autoSave) + { + JalviewFileChooser chooser = new JalviewFileChooser("jvp", + "Jalview Project"); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.save_state")); - if (value == JalviewFileChooser.APPROVE_OPTION) + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + projectFile = chooser.getSelectedFile(); + setProjectFile(projectFile); + approveSave = true; + } + } + + if (approveSave || autoSave) { final Desktop me = this; - final java.io.File choice = chooser.getSelectedFile(); - setProjectFile(choice); - + final java.io.File chosenFile = projectFile; new Thread(new Runnable() { @Override @@ -1624,36 +1771,49 @@ public class Desktop extends jalview.jbgui.GDesktop // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( "label.saving_jalview_project", new Object[] - { choice.getName() }), choice.hashCode()); + { chosenFile.getName() }), chosenFile.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", - choice.getParent()); + chosenFile.getParent()); // TODO catch and handle errors for savestate // TODO prevent user from messing with the Desktop whilst we're saving try { - new Jalview2XML().saveState(choice); + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null; + + new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile); + + if (doBackup) + { + backupfiles.setWriteSuccess(true); + backupfiles.rollBackupsAndRenameTempFile(); + } } catch (OutOfMemoryError oom) { - new OOMWarning( - "Whilst saving current state to " + choice.getName(), - oom); + new OOMWarning("Whilst saving current state to " + + chosenFile.getName(), oom); } catch (Exception ex) { - Cache.log.error( - "Problems whilst trying to save to " + choice.getName(), - ex); + Cache.log.error("Problems whilst trying to save to " + + chosenFile.getName(), ex); JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", new Object[] - { choice.getName() }), + { chosenFile.getName() }), MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); } - setProgressBar(null, choice.hashCode()); + setProgressBar(null, chosenFile.hashCode()); } }).start(); - } + } + } + + @Override + public void saveAsState_actionPerformed(ActionEvent e) + { + saveState_actionPerformed(true); } private void setProjectFile(File choice) @@ -1667,63 +1827,59 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a file chooser dialog and tries to read in the selected file as a + * Jalview project */ @Override - public void loadState_actionPerformed(ActionEvent e) + public void loadState_actionPerformed() { - // TODO: JAL-3048 not needed for Jalview-JS - + final String[] suffix = new String[] { "jvp", "jar" }; + final String[] desc = new String[] { "Jalview Project", + "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp", "jar" }, - new String[] - { "Jalview Project", "Jalview Project (old)" }, - "Jalview Project"); + Cache.getProperty("LAST_DIRECTORY"), suffix, desc, + "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles, + // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { - final File selectedFile = chooser.getSelectedFile(); - setProjectFile(selectedFile); - final String choice = selectedFile.getAbsolutePath(); - Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() + File selectedFile = chooser.getSelectedFile(); + setProjectFile(selectedFile); + String choice = selectedFile.getAbsolutePath(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + new Thread(new Runnable() { - setProgressBar(MessageManager.formatMessage( - "label.loading_jalview_project", new Object[] - { choice }), choice.hashCode()); - try - { - new Jalview2XML().loadJalviewAlign(choice); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) + @Override + public void run() { - Cache.log.error( - "Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.error_whilst_loading_project_from", - new Object[] - { choice }), - MessageManager.getString("label.couldnt_load_project"), - JvOptionPane.WARNING_MESSAGE); + try + { + new Jalview2XML().loadJalviewAlign(choice); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst loading project from " + choice, oom); + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst loading project from " + choice, ex); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), + MessageManager.getString("label.couldnt_load_project"), + JvOptionPane.WARNING_MESSAGE); + } } - setProgressBar(null, choice.hashCode()); - } - }).start(); - } + }).start(); + } + }); + + chooser.showOpenDialog(this); } @Override @@ -2237,7 +2393,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); rthr.start(); } - }; + } }); VamsasStMenu.add(sessit); } @@ -2367,8 +2523,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void run() { - if (/** @j2sNative false && */ // BH 2018 - Cache.getDefault("CHECKURLLINKS", true)) + if (Cache.getDefault("CHECKURLLINKS", true)) { // check what the actual links are - if it's just the default don't // bother with the warning @@ -2383,7 +2538,7 @@ public class Desktop extends jalview.jbgui.GDesktop while (li.hasNext()) { String link = li.next(); - if (link.contains(SEQUENCE_ID) + if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) { check = true; @@ -2446,158 +2601,8 @@ public class Desktop extends jalview.jbgui.GDesktop * @author AMW */ public class MyDesktopPane extends JDesktopPane - implements Runnable, PropertyChangeListener + implements Runnable { - - public Object[] dialogData; - - // @Override - @Override - public void propertyChange(PropertyChangeEvent event) - { - Object val = event.getNewValue(); - String name = event.getPropertyName(); - System.out.println(name); - switch (event.getSource().getClass().getName()) - { - case "javax.swing.JOptionPane": - switch (name) - { - case "inputValue": - onDialogReturn(val); - return; - case "value": - if (val instanceof Integer) - { - onDialogReturn(((Integer) val).intValue()); - } - else - { - onDialogReturn(val); - } - return; - } - break; - case "javax.swing.ColorChooserDialog": - switch (name) - { - case "SelectedColor": - onDialogReturn(val); - return; - } - break; - case "javax.swing.JFileChooser": - switch (name) - { - case "SelectedFile": - // in JavaScript, this File object will have a _bytes property, - // because the file data has already been loaded - onDialogReturn(new Object[] { (File) val }); - return; - } - break; - } - System.out.println(event.getSource().getClass().getName() + " " - + event.getPropertyName() + ": " + event.getNewValue()); - } - - // JSCOmponent.DialogCaller interface - void onDialogReturn(Object value) - { - switch ((String) dialogData[0]) - { - case "SelectedFile": - case "runnable": - dialogData[0] = value; - ((Runnable) dialogData[1]).run(); - break; - case "label.select_feature_colour": - ((FeatureRenderer) dialogData[1]).processColorDialog((Color) value); - break; - } - } - - // JSCOmponent.DialogCaller interface - void onDialogReturn(int value) - { - if (value != Math.floor(value)) - { - // in JavaScript, this will be NaN, oddly enough - return; - } - - switch ((String) dialogData[0]) - { - case "runnable": - dialogData[0] = Integer.valueOf(value); - ((Runnable) dialogData[1]).run(); - break; - case "label.input_alignment_from_url": - // reconstruct the parameter data - int reply = value; - AlignViewport viewport = (AlignViewport) dialogData[1]; - JComboBox history = (JComboBox) dialogData[2]; - // the rest of this is unchangaed - if (reply != JvOptionPane.OK_OPTION) - { - return; - } - - String url = history.getSelectedItem().toString(); - - if (url.toLowerCase().endsWith(".jar")) - { - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - FileFormat.Jalview); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, - FileFormat.Jalview); - } - } - else - { - FileFormatI format = null; - try - { - format = new IdentifyFile().identify(url, DataSourceType.URL); - } catch (FileFormatException e) - { - // TODO revise error handling, distinguish between - // URL not found and response not valid - } - - if (format == null) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_locate", - new Object[] - { url }), - MessageManager.getString("label.url_not_found"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - format); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, format); - } - } - - break; - } - - } - private static final float ONE_MB = 1048576f; boolean showMemoryUsage = false; @@ -2840,7 +2845,7 @@ public class Desktop extends jalview.jbgui.GDesktop { getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()), + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @@ -2891,24 +2896,26 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void setProgressBar(String message, long id) { + Platform.timeCheck("Desktop " + message, Platform.TIME_MARK); + if (progressBars == null) { progressBars = new Hashtable<>(); progressBarHandlers = new Hashtable<>(); } - if (progressBars.get(new Long(id)) != null) + if (progressBars.get(Long.valueOf(id)) != null) { - JPanel panel = progressBars.remove(new Long(id)); - if (progressBarHandlers.contains(new Long(id))) + JPanel panel = progressBars.remove(Long.valueOf(id)); + if (progressBarHandlers.contains(Long.valueOf(id))) { - progressBarHandlers.remove(new Long(id)); + progressBarHandlers.remove(Long.valueOf(id)); } removeProgressPanel(panel); } else { - progressBars.put(new Long(id), addProgressPanel(message)); + progressBars.put(Long.valueOf(id), addProgressPanel(message)); } } @@ -2923,13 +2930,13 @@ public class Desktop extends jalview.jbgui.GDesktop final IProgressIndicatorHandler handler) { if (progressBarHandlers == null - || !progressBars.containsKey(new Long(id))) + || !progressBars.containsKey(Long.valueOf(id))) { throw new Error(MessageManager.getString( "error.call_setprogressbar_before_registering_handler")); } - progressBarHandlers.put(new Long(id), handler); - final JPanel progressPanel = progressBars.get(new Long(id)); + progressBarHandlers.put(Long.valueOf(id), handler); + final JPanel progressPanel = progressBars.get(Long.valueOf(id)); if (handler.canCancel()) { JButton cancel = new JButton( @@ -3283,7 +3290,6 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (InterruptedException x) { } - ; } if (instance == null) { @@ -3308,28 +3314,39 @@ public class Desktop extends jalview.jbgui.GDesktop block.release(); } + /** + * Outputs an image of the desktop to file in EPS format, after prompting the + * user for choice of Text or Lineart character rendering (unless a preference + * has been set). The file name is generated as + * + * 
+   * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+   *
+ */ @Override protected void snapShotWindow_actionPerformed(ActionEvent e) { + // currently the menu option to do this is not shown invalidate(); - File of; - ImageMaker im = new jalview.util.ImageMaker( - this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(), - getHeight(), of = new File("Jalview_snapshot" - + System.currentTimeMillis() + ".eps"), - "View of desktop", null, 0, false); - try - { - paintAll(im.getGraphics()); - im.writeImage(); - } catch (Exception q) + + int width = getWidth(); + int height = getHeight(); + File of = new File( + "Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); + ImageWriterI writer = new ImageWriterI() { - Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(), - q); - return; - } - Cache.log.info("Successfully written snapshot to file " - + of.getAbsolutePath()); + @Override + public void exportImage(Graphics g) throws Exception + { + paintAll(g); + Cache.log.info("Successfully written snapshot to file " + + of.getAbsolutePath()); + } + }; + String title = "View of desktop"; + ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, + title); + exporter.doExport(of, this, width, height, title); } /** @@ -3555,12 +3572,11 @@ public class Desktop extends jalview.jbgui.GDesktop } else { - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { System.err.println( "Please ignore plist error - occurs due to problem with java 8 on OSX"); } - ; } } catch (Throwable ex) { @@ -3672,8 +3688,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } } - if (Platform.isWindows()) - + if (Platform.isWindowsAndNotJS()) { Cache.log.debug("Scanning dropped content for Windows Link Files");