X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=03216624900fba740606837d8ca38241f04817ee;hb=8b844f70b97629d597be49cb6ac0d83c8da007c9;hp=78100998651ad95b8ff78d2414f63049aba024f0;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 7810099..0321662 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,15 +20,18 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.EMBLEBI_STRING; +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.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; @@ -68,12 +71,10 @@ import java.awt.event.FocusListener; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -import java.beans.PropertyVetoException; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; @@ -81,6 +82,7 @@ import java.net.URL; import java.util.ArrayList; 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; @@ -88,9 +90,12 @@ import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; +import javax.swing.Box; +import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; @@ -98,7 +103,6 @@ import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; @@ -106,6 +110,8 @@ import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; @@ -386,6 +392,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + checkURLLinks(); + this.addWindowListener(new WindowAdapter() { @Override @@ -401,7 +409,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void mousePressed(MouseEvent evt) { - if (evt.isPopupTrigger()) + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows { showPasteMenu(evt.getX(), evt.getY()); } @@ -438,7 +455,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - // displayed. // Thread off a new instance of the file chooser - this reduces the time it // takes to open it later on. new Thread(new Runnable() @@ -447,11 +463,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void run() { Cache.log.debug("Filechooser init thread started."); - new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.READABLE_FNAMES, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), + fileFormat); Cache.log.debug("Filechooser init thread finished."); } }).start(); @@ -809,32 +823,53 @@ public class Desktop extends jalview.jbgui.GDesktop implements * ((openFrameCount - 1) % 10) + yOffset); } + /* + * add an entry for the new frame in the Window menu + * (and remove it when the frame is closed) + */ final JMenuItem menuItem = new JMenuItem(title); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + frame.addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameActivated( - javax.swing.event.InternalFrameEvent evt) + public void internalFrameActivated(InternalFrameEvent evt) { JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); } - } @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + public void internalFrameClosed(InternalFrameEvent evt) { PaintRefresher.RemoveComponent(frame); - openFrameCount--; + + /* + * defensive check to prevent frames being + * added half off the window + */ + if (openFrameCount > 0) + { + openFrameCount--; + } + + /* + * ensure no reference to alignFrame retained by menu item listener + */ + if (menuItem.getActionListeners().length > 0) + { + menuItem.removeActionListener(menuItem.getActionListeners()[0]); + } windowMenu.remove(menuItem); JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); + if (itf instanceof AlignFrame) + { + Jalview.setCurrentAlignFrame((AlignFrame) itf); + } } System.gc(); }; @@ -855,51 +890,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } }); - menuItem.addMouseListener(new MouseListener() - { - - @Override - public void mouseReleased(MouseEvent e) - { - } - - @Override - public void mousePressed(MouseEvent e) - { - } - - @Override - public void mouseExited(MouseEvent e) - { - try - { - frame.setSelected(false); - } catch (PropertyVetoException e1) - { - } - } - - @Override - public void mouseEntered(MouseEvent e) - { - try - { - frame.setSelected(true); - } catch (PropertyVetoException e1) - { - } - } - - @Override - public void mouseClicked(MouseEvent e) - { - } - }); + desktop.add(frame); windowMenu.add(menuItem); - desktop.add(frame); frame.toFront(); try { @@ -956,6 +951,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void drop(DropTargetDropEvent evt) { boolean success = true; + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); List files = new ArrayList(); List protocols = new ArrayList(); @@ -1011,11 +1009,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), - AppletFormatAdapter.READABLE_EXTENSIONS, - AppletFormatAdapter.READABLE_FNAMES, - Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1030,20 +1026,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); - FileFormatI format = null; - if (chooser.getSelectedFormat() != null - && chooser.getSelectedFormat() == FileFormat.Jalview) - { - format = FileFormat.Jalview; - } - else + FileFormatI format = chooser.getSelectedFormat(); + + /* + * Call IdentifyFile to verify the file contains what its extension implies. + * Skip this step for dynamically added file formats, because + * IdentifyFile does not know how to recognise them. + */ + if (FileFormats.getInstance().isIdentifiable(format)) { try { format = new IdentifyFile().identify(choice, DataSourceType.FILE); } catch (FileFormatException e) { - // format is null + // format = null; //?? } } @@ -1064,11 +1061,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * @param e * DOCUMENT ME! - * @throws FileFormatException */ @Override public void inputURLMenuItem_actionPerformed(AlignViewport viewport) - throws FileFormatException { // This construct allows us to have a wider textfield // for viewing @@ -1097,11 +1092,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - int reply = JOptionPane.showInternalConfirmDialog(desktop, panel, + int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel, MessageManager.getString("label.input_alignment_from_url"), - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (reply != JOptionPane.OK_OPTION) + if (reply != JvOptionPane.OK_OPTION) { return; } @@ -1123,16 +1118,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements } else { - FileFormatI format = new IdentifyFile().identify(url, - DataSourceType.URL); + 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.equals("URL NOT FOUND")) + if (format == null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", new Object[] { url }), MessageManager .getString("label.url_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -1228,9 +1230,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); - // JOptionPane.showInternalMessageDialog(Desktop.desktop, + // JvOptionPane.showInternalMessageDialog(Desktop.desktop, // - // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { @Override @@ -1326,6 +1328,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void closeAll_actionPerformed(ActionEvent e) { + // TODO show a progress bar while closing? JInternalFrame[] frames = desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { @@ -1336,6 +1339,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } + Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); if (v_client != null) { @@ -1352,6 +1356,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { ssm.resetAll(); } + System.gc(); } @Override @@ -1526,9 +1531,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void saveState_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "jvp" }, new String[] { "Jalview Project" }, + JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1567,11 +1570,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.error( "Problems whilst trying to save to " + choice.getName(), ex); - JOptionPane.showMessageDialog(me, MessageManager.formatMessage( + JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", new Object[] { choice.getName() }), MessageManager .getString("label.couldnt_save_project"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1599,7 +1602,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void loadState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { + Cache.getProperty("LAST_DIRECTORY"), new String[] { "jvp", "jar" }, new String[] { "Jalview Project", "Jalview Project (old)" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1612,7 +1615,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements final File selectedFile = chooser.getSelectedFile(); setProjectFile(selectedFile); final String choice = selectedFile.getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); new Thread(new Runnable() { @@ -1633,12 +1636,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.error("Problems whilst loading project from " + choice, ex); - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage( "label.error_whilst_loading_project_from", new Object[] { choice }), MessageManager .getString("label.couldnt_load_project"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1821,7 +1824,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * @param af */ - public void explodeViews(AlignFrame af) + public static void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); if (size < 2) @@ -1923,7 +1926,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( @@ -1931,7 +1934,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } @@ -2182,10 +2185,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (v_client != null) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ - new String[] { "Vamsas Document" }, "Vamsas Document"); + // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + JalviewFileChooser chooser = new JalviewFileChooser("vdj", + "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2199,7 +2201,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JPanel progpanel = addProgressPanel(MessageManager.formatMessage( "label.saving_vamsas_doc", new Object[] { choice.getName() })); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; try @@ -2223,9 +2225,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements removeProgressPanel(progpanel); if (warnmsg != null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - warnmsg, warnttl, JOptionPane.ERROR_MESSAGE); + warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } } } @@ -2241,7 +2243,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void setVamsasUpdate(boolean b) { - jalview.bin.Cache.log.debug("Setting gui for Vamsas update " + Cache.log.debug("Setting gui for Vamsas update " + (b ? "in progress" : "finished")); if (vamUpdate != null) @@ -2276,6 +2278,84 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Thread(jvq).start(); } + public void checkURLLinks() + { + // Thread off the URL link checker + addDialogThread(new Runnable() + { + @Override + public void run() + { + if (Cache.getDefault("CHECKURLLINKS", true)) + { + // check what the actual links are - if it's just the default don't + // bother with the warning + Vector links = Preferences.sequenceURLLinks; + + // only need to check links if there is one with a + // SEQUENCE_ID which is not the default EMBL_EBI link + ListIterator li = links.listIterator(); + boolean check = false; + List urls = new ArrayList(); + while (li.hasNext()) + { + String link = li.next(); + if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING)) + { + check = true; + int barPos = link.indexOf("|"); + String urlMsg = barPos == -1 ? link : link.substring(0, + barPos) + ": " + link.substring(barPos + 1); + urls.add(new JLabel(urlMsg)); + } + } + if (!check) + { + return; + } + + // ask user to check in case URL links use old style tokens + // ($SEQUENCE_ID$ for sequence id _or_ accession id) + JPanel msgPanel = new JPanel(); + msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); + msgPanel.add(Box.createVerticalGlue()); + JLabel msg = new JLabel( + MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); + JLabel msg2 = new JLabel( + MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); + msgPanel.add(msg); + for (JLabel url : urls) + { + msgPanel.add(url); + } + msgPanel.add(msg2); + + final JCheckBox jcb = new JCheckBox( + MessageManager.getString("label.do_not_display_again")); + jcb.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // update Cache settings for "don't show this again" + boolean showWarningAgain = !jcb.isSelected(); + Cache.setProperty("CHECKURLLINKS", + Boolean.valueOf(showWarningAgain).toString()); + } + }); + msgPanel.add(jcb); + + JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + MessageManager + .getString("label.SEQUENCE_ID_no_longer_used"), + JvOptionPane.WARNING_MESSAGE); + } + } + }); + } + /** * Proxy class for JDesktopPane which optionally displays the current memory * usage and highlights the desktop area with a red bar if free memory runs @@ -2477,11 +2557,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -2537,8 +2617,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask()), - "Quit"); + .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @Override @@ -2823,7 +2902,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * jd.waitForInput(); */ - JOptionPane + JvOptionPane .showConfirmDialog( Desktop.desktop, new JLabel( @@ -2835,8 +2914,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements + "

Check the Connections and Web services tab
of the" + " Tools->Preferences dialog box to change them.

"), "Web Service Configuration Problem", - JOptionPane.DEFAULT_OPTION, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.ERROR_MESSAGE); serviceChangedDialog = null; } @@ -2893,11 +2972,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -3205,11 +3284,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // Works on Windows and MacOSX Cache.log.debug("Drop handled as javaFileListFlavor"); - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { - files.add(((File)file).toString()); + files.add(((File) file).toString()); protocols.add(DataSourceType.FILE); } } @@ -3222,7 +3300,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.debug("Drop handled as uriListFlavor"); // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); data = (String) t.getTransferData(uriListFlavor); } if (data == null) @@ -3277,7 +3354,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.debug("Supported transfer dataflavor: " + fl.toString()); - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Object df = t.getTransferData(fl); if (df != null) {