X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=41ce9a7fc8d3448c29c7226e1709f38bf754c841;hb=e63a4d52c27252dfb83efeeee1bda6c89b6dddec;hp=3cc2c1439369bead240cfe297864b14909f56513;hpb=c708b0d5bed26752c34e62960f0acdeada8742df;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 3cc2c14..41ce9a7 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.SEQUENCE_ID; + import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; @@ -32,10 +34,13 @@ import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; import jalview.structure.StructureSelectionManager; +import jalview.urls.IdOrgSettings; import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; +import jalview.ws.UrlDownloadClient; import jalview.ws.params.ParamManager; import java.awt.BorderLayout; @@ -64,19 +69,19 @@ 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; +import java.io.IOException; 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; @@ -84,9 +89,12 @@ 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; @@ -102,6 +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; @@ -382,6 +392,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + getIdentifiersOrgData(); + + checkURLLinks(); + this.addWindowListener(new WindowAdapter() { @Override @@ -397,7 +411,16 @@ 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()); } @@ -507,6 +530,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + public void getIdentifiersOrgData() + { + // Thread off the identifiers fetcher + addDialogThread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Downloading data from identifiers.org"); + UrlDownloadClient client = new UrlDownloadClient(); + try + { + client.download(IdOrgSettings.getUrl(), + IdOrgSettings.getDownloadLocation()); + } catch (IOException e) + { + Cache.log.debug("Exception downloading identifiers.org data" + + e.getMessage()); + } + } + }); + } + @Override protected void showNews_actionPerformed(ActionEvent e) { @@ -805,24 +851,25 @@ 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); @@ -834,11 +881,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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(); }; @@ -859,47 +918,6 @@ 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) - { - - } - }); windowMenu.add(menuItem); @@ -960,6 +978,9 @@ 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(); java.util.List files = new ArrayList(); java.util.List protocols = new ArrayList(); @@ -1319,6 +1340,7 @@ 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++) { @@ -1329,6 +1351,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } + Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); if (v_client != null) { @@ -1345,6 +1368,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { ssm.resetAll(); } + System.gc(); } @Override @@ -2269,6 +2293,86 @@ 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 + .getLinksForMenu(); + + // 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(UrlConstants.DEFAULT_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); + + JOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + MessageManager + .getString("label.SEQUENCE_ID_no_longer_used"), + JOptionPane.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 @@ -2530,8 +2634,7 @@ 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 @@ -3197,11 +3300,10 @@ 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(FormatAdapter.FILE); } } @@ -3214,7 +3316,6 @@ 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) @@ -3269,7 +3370,6 @@ 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) {