X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=e9cc8e919442a449b14ab1119c9d07efc470ffce;hb=c679cc5e0b230c59517b89d50eb5b94dfe4a382a;hp=98584bce54a1023daee5a57256acd7340a31c57a;hpb=1f6504bd0b7187c99cd4a2551c15e854d14583b5;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 98584bc..e9cc8e9 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,34 +20,6 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.bin.Jalview; -import jalview.io.BackupFiles; -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.FormatAdapter; -import jalview.io.IdentifyFile; -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.MessageManager; -import jalview.util.Platform; -import jalview.util.UrlConstants; -import jalview.viewmodel.AlignmentViewport; -import jalview.ws.params.ParamManager; -import jalview.ws.utils.UrlDownloadClient; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -77,11 +49,10 @@ import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; 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.lang.reflect.Field; import java.net.URL; import java.util.ArrayList; import java.util.HashMap; @@ -119,11 +90,37 @@ 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; import org.stackoverflowusers.file.WindowsShortcut; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.io.BackupFiles; +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.FormatAdapter; +import jalview.io.IdentifyFile; +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.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.params.ParamManager; +import jalview.ws.utils.UrlDownloadClient; + /** * Jalview Desktop * @@ -147,7 +144,7 @@ public class Desktop extends jalview.jbgui.GDesktop protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; - public static HashMap savingFiles = new HashMap<>(); + public static HashMap savingFiles = new HashMap(); private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); @@ -346,10 +343,10 @@ public class Desktop extends jalview.jbgui.GDesktop * constructor. */ instance = this; - doVamsasClientCheck(); doConfigureStructurePrefs(); - setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); + String title = "Jalview " + Cache.getProperty("VERSION"); + setTitle(title); /* if (!Platform.isAMac()) { @@ -374,6 +371,20 @@ public class Desktop extends jalview.jbgui.GDesktop // t.printStackTrace(); } + if (Platform.isLinux()) + { + try + { + Toolkit xToolkit = Toolkit.getDefaultToolkit(); + Field awtAppClassNameField = xToolkit.getClass() + .getDeclaredField("awtAppClassName"); + awtAppClassNameField.setAccessible(true); + awtAppClassNameField.set(xToolkit, "Jalview"); + } catch (Exception e) + { + Cache.log.debug("Could not set awtAppClassName"); + } + } addWindowListener(new WindowAdapter() { @@ -424,26 +435,7 @@ public class Desktop extends jalview.jbgui.GDesktop } jconsole = new Console(this, showjconsole); // add essential build information - jconsole.setHeader( - "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION") - + "\n" + "Jalview Installation: " - + jalview.bin.Cache.getDefault("INSTALLATION", - "unknown") - + "\n" + "Build Date: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") - + "\n" + "Java version: " - + System.getProperty("java.version") + "\n" - + System.getProperty("os.arch") + " " - + System.getProperty("os.name") + " " - + System.getProperty("os.version") - + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT") - ? "\nJava path:" - + System.getProperty( - "java.home") - + File.separator + "bin" - + File.separator + "java" - : "") - ); + jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole()); showConsole(showjconsole); @@ -583,26 +575,27 @@ public class Desktop extends jalview.jbgui.GDesktop public void getIdentifiersOrgData() { - // Thread off the identifiers fetcher - new Thread(new Runnable() - { - @Override - public void run() + if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) + {// Thread off the identifiers fetcher + new Thread(new Runnable() { - Cache.log.debug("Downloading data from identifiers.org"); - UrlDownloadClient client = new UrlDownloadClient(); - try - { - client.download(IdOrgSettings.getUrl(), - IdOrgSettings.getDownloadLocation()); - } catch (IOException e) + @Override + public void run() { - Cache.log.debug("Exception downloading identifiers.org data" - + e.getMessage()); + Cache.log.debug("Downloading data from identifiers.org"); + try + { + UrlDownloadClient.download(IdOrgSettings.getUrl(), + IdOrgSettings.getDownloadLocation()); + } catch (IOException e) + { + Cache.log.debug("Exception downloading identifiers.org data" + + e.getMessage()); + } } - } - }).start(); - ; + }).start(); + ; + } } @Override @@ -694,46 +687,6 @@ public class Desktop extends jalview.jbgui.GDesktop return null; } - private void doVamsasClientCheck() - { - if (jalview.bin.Cache.vamsasJarsPresent()) - { - setupVamsasDisconnectedGui(); - VamsasMenu.setVisible(true); - final Desktop us = this; - VamsasMenu.addMenuListener(new MenuListener() - { - // this listener remembers when the menu was first selected, and - // doesn't rebuild the session list until it has been cleared and - // reselected again. - boolean refresh = true; - - @Override - public void menuCanceled(MenuEvent e) - { - refresh = true; - } - - @Override - public void menuDeselected(MenuEvent e) - { - refresh = true; - } - - @Override - public void menuSelected(MenuEvent e) - { - if (refresh) - { - us.buildVamsasStMenu(); - refresh = false; - } - } - }); - vamsasStart.setVisible(true); - } - } - void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); @@ -991,7 +944,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (java.lang.ClassCastException cex) { Cache.log.warn( - "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", + "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869", cex); } } @@ -1020,7 +973,8 @@ 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx()); InputMap inputMap = frame .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); @@ -1133,8 +1087,9 @@ public class Desktop extends jalview.jbgui.GDesktop public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat, + BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( @@ -1199,7 +1154,7 @@ public class Desktop extends jalview.jbgui.GDesktop panel.add(history); history.setPreferredSize(new Dimension(400, 20)); history.setEditable(true); - history.addItem("http://www."); + history.addItem("https://www."); String historyItems = jalview.bin.Cache.getProperty("RECENT_URL"); @@ -1299,8 +1254,6 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void quit() { - //System.out.println("********** Desktop.quit()"); - //System.out.println(savingFiles.toString()); Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); @@ -1378,9 +1331,10 @@ public class Desktop extends jalview.jbgui.GDesktop message.append("

Version: " + jalview.bin.Cache.getProperty("VERSION") + "

"); - message.append("Last Updated: " + message.append("Built: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") - + ""); + + " from " + jalview.bin.Cache.getBuildDetailsForSplash() + + ""); } else @@ -1395,7 +1349,8 @@ public class Desktop extends jalview.jbgui.GDesktop if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") .equals("Checking")) { - message.append("
...Checking latest version...
"); + // JBP removed this message for 2.11: May be reinstated in future version + // message.append("
...Checking latest version...
"); } else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") .equals(jalview.bin.Cache.getProperty("VERSION"))) @@ -1415,7 +1370,7 @@ public class Desktop extends jalview.jbgui.GDesktop "..Checking..") + " is available for download from " + jalview.bin.Cache.getDefault("www.jalview.org", - "http://www.jalview.org") + "https://www.jalview.org") + " !!"); if (red) { @@ -1426,7 +1381,7 @@ public class Desktop extends jalview.jbgui.GDesktop "AUTHORFNAMES", "The Jalview Authors (See AUTHORS file for current list)") + "

Development managed by The Barton Group, University of Dundee, Scotland, UK.
" - + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list" + + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list" + "

If you use Jalview, please cite:" + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" @@ -1468,10 +1423,6 @@ public class Desktop extends jalview.jbgui.GDesktop } Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); - if (v_client != null) - { - // TODO clear binding to vamsas document objects on close_all - } /* * reset state of singleton objects as appropriate (clear down session state @@ -1763,8 +1714,10 @@ public class Desktop extends jalview.jbgui.GDesktop "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), suffix, desc, - "Jalview Project", true, true); // last two booleans: allFiles, - // allowBackupFiles + "Jalview Project", true, BackupFiles.getEnabled()); // last two + // booleans: + // allFiles, + // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); @@ -1991,11 +1944,26 @@ public class Desktop extends jalview.jbgui.GDesktop return; } + // FIXME: ideally should use UI interface API + FeatureSettings viewFeatureSettings = (af.featureSettings != null + && af.featureSettings.isOpen()) ? af.featureSettings : null; + Rectangle fsBounds = af.getFeatureSettingsGeometry(); for (int i = 0; i < size; i++) { AlignmentPanel ap = af.alignPanels.get(i); + AlignFrame newaf = new AlignFrame(ap); + // transfer reference for existing feature settings to new alignFrame + if (ap == af.alignPanel) + { + if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) + { + newaf.featureSettings = viewFeatureSettings; + } + newaf.setFeatureSettingsGeometry(fsBounds); + } + /* * Restore the view's last exploded frame geometry if known. Multiple * views from one exploded frame share and restore the same (frame) @@ -2011,8 +1979,18 @@ public class Desktop extends jalview.jbgui.GDesktop addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + // and materialise a new feature settings dialog instance for the new + // alignframe + // (closes the old as if 'OK' was pressed) + if (ap == af.alignPanel && newaf.featureSettings != null + && newaf.featureSettings.isOpen() + && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) + { + newaf.showFeatureSettingsUI(); + } } + af.featureSettings = null; af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); @@ -2032,7 +2010,6 @@ public class Desktop extends jalview.jbgui.GDesktop source.viewport.setExplodedGeometry(source.getBounds()); JInternalFrame[] frames = desktop.getAllFrames(); String viewId = source.viewport.getSequenceSetId(); - for (int t = 0; t < frames.length; t++) { if (frames[t] instanceof AlignFrame && frames[t] != source) @@ -2053,370 +2030,32 @@ public class Desktop extends jalview.jbgui.GDesktop if (gatherThis) { - af.alignPanels.clear(); - af.closeMenuItem_actionPerformed(true); - } - } - } - - } - - jalview.gui.VamsasApplication v_client = null; - - @Override - public void vamsasImport_actionPerformed(ActionEvent e) - { - if (v_client == null) - { - // Load and try to start a session. - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.open_saved_vamsas_session")); - chooser.setToolTipText(MessageManager.getString( - "label.select_vamsas_session_opened_as_new_vamsas_session")); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String fle = chooser.getSelectedFile().toString(); - if (!vamsasImport(chooser.getSelectedFile())) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.couldnt_import_as_vamsas_session", - new Object[] - { fle }), - MessageManager - .getString("label.vamsas_document_import_failed"), - JvOptionPane.ERROR_MESSAGE); - } - } - } - else - { - jalview.bin.Cache.log.error( - "Implementation error - load session from a running session is not supported."); - } - } - - /** - * import file into a new vamsas session (uses jalview.gui.VamsasApplication) - * - * @param file - * @return true if import was a success and a session was started. - */ - public boolean vamsasImport(URL url) - { - // TODO: create progress bar - if (v_client != null) - { - - jalview.bin.Cache.log.error( - "Implementation error - load session from a running session is not supported."); - return false; - } - - try - { - // copy the URL content to a temporary local file - // TODO: be a bit cleverer here with nio (?!) - File file = File.createTempFile("vdocfromurl", ".vdj"); - FileOutputStream fos = new FileOutputStream(file); - BufferedInputStream bis = new BufferedInputStream(url.openStream()); - byte[] buffer = new byte[2048]; - int ln; - while ((ln = bis.read(buffer)) > -1) - { - fos.write(buffer, 0, ln); - } - bis.close(); - fos.close(); - v_client = new jalview.gui.VamsasApplication(this, file, - url.toExternalForm()); - } catch (Exception ex) - { - jalview.bin.Cache.log.error( - "Failed to create new vamsas session from contents of URL " - + url, - ex); - return false; - } - setupVamsasConnectedGui(); - v_client.initial_update(); // TODO: thread ? - return v_client.inSession(); - } - - /** - * import file into a new vamsas session (uses jalview.gui.VamsasApplication) - * - * @param file - * @return true if import was a success and a session was started. - */ - public boolean vamsasImport(File file) - { - if (v_client != null) - { - - jalview.bin.Cache.log.error( - "Implementation error - load session from a running session is not supported."); - return false; - } - - setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); - try - { - v_client = new jalview.gui.VamsasApplication(this, file, null); - } catch (Exception ex) - { - setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); - jalview.bin.Cache.log.error( - "New vamsas session from existing session file failed:", ex); - return false; - } - setupVamsasConnectedGui(); - v_client.initial_update(); // TODO: thread ? - setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); - return v_client.inSession(); - } - - public boolean joinVamsasSession(String mysesid) - { - if (v_client != null) - { - throw new Error(MessageManager - .getString("error.try_join_vamsas_session_another")); - } - if (mysesid == null) - { - throw new Error( - MessageManager.getString("error.invalid_vamsas_session_id")); - } - v_client = new VamsasApplication(this, mysesid); - setupVamsasConnectedGui(); - v_client.initial_update(); - return (v_client.inSession()); - } - - @Override - public void vamsasStart_actionPerformed(ActionEvent e) - { - if (v_client == null) - { - // Start a session. - // we just start a default session for moment. - /* - * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - * getProperty("LAST_DIRECTORY")); - * - * chooser.setFileView(new JalviewFileView()); - * chooser.setDialogTitle("Load Vamsas file"); - * chooser.setToolTipText("Import"); - * - * int value = chooser.showOpenDialog(this); - * - * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new - * jalview.gui.VamsasApplication(this, chooser.getSelectedFile()); - */ - v_client = new VamsasApplication(this); - setupVamsasConnectedGui(); - v_client.initial_update(); // TODO: thread ? - } - else - { - // store current data in session. - v_client.push_update(); // TODO: thread - } - } - - protected void setupVamsasConnectedGui() - { - vamsasStart.setText(MessageManager.getString("label.session_update")); - vamsasSave.setVisible(true); - vamsasStop.setVisible(true); - vamsasImport.setVisible(false); // Document import to existing session is - // not possible for vamsas-client-1.0. - } - - protected void setupVamsasDisconnectedGui() - { - vamsasSave.setVisible(false); - vamsasStop.setVisible(false); - vamsasImport.setVisible(true); - vamsasStart - .setText(MessageManager.getString("label.new_vamsas_session")); - } - - @Override - public void vamsasStop_actionPerformed(ActionEvent e) - { - if (v_client != null) - { - v_client.end_session(); - v_client = null; - setupVamsasDisconnectedGui(); - } - } - - protected void buildVamsasStMenu() - { - if (v_client == null) - { - String[] sess = null; - try - { - sess = VamsasApplication.getSessionList(); - } catch (Exception e) - { - jalview.bin.Cache.log.warn("Problem getting current sessions list.", - e); - sess = null; - } - if (sess != null) - { - jalview.bin.Cache.log.debug( - "Got current sessions list: " + sess.length + " entries."); - VamsasStMenu.removeAll(); - for (int i = 0; i < sess.length; i++) - { - JMenuItem sessit = new JMenuItem(); - sessit.setText(sess[i]); - sessit.setToolTipText(MessageManager - .formatMessage("label.connect_to_session", new Object[] - { sess[i] })); - final Desktop dsktp = this; - final String mysesid = sess[i]; - sessit.addActionListener(new ActionListener() + if (af.featureSettings != null && af.featureSettings.isOpen()) { - - @Override - public void actionPerformed(ActionEvent e) + if (source.featureSettings == null) { - if (dsktp.v_client == null) - { - Thread rthr = new Thread(new Runnable() - { - - @Override - public void run() - { - dsktp.v_client = new VamsasApplication(dsktp, mysesid); - dsktp.setupVamsasConnectedGui(); - dsktp.v_client.initial_update(); - } - - }); - rthr.start(); - } - }; - }); - VamsasStMenu.add(sessit); + // preserve the feature settings geometry for this frame + source.featureSettings = af.featureSettings; + source.setFeatureSettingsGeometry( + af.getFeatureSettingsGeometry()); + } + else + { + // close it and forget + af.featureSettings.close(); + } + } + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); } - // don't show an empty menu. - VamsasStMenu.setVisible(sess.length > 0); - } - else - { - jalview.bin.Cache.log.debug("No current vamsas sessions."); - VamsasStMenu.removeAll(); - VamsasStMenu.setVisible(false); - } - } - else - { - // Not interested in the content. Just hide ourselves. - VamsasStMenu.setVisible(false); } - } - - @Override - public void vamsasSave_actionPerformed(ActionEvent e) - { - if (v_client != null) + // refresh the feature setting UI for the source frame if it exists + if (source.featureSettings != null && source.featureSettings.isOpen()) { - // TODO: VAMSAS DOCUMENT EXTENSION is VDJ - JalviewFileChooser chooser = new JalviewFileChooser("vdj", - "Vamsas Document"); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_vamsas_document_archive")); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - java.io.File choice = chooser.getSelectedFile(); - JPanel progpanel = addProgressPanel(MessageManager - .formatMessage("label.saving_vamsas_doc", new Object[] - { choice.getName() })); - Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - String warnmsg = null; - String warnttl = null; - try - { - v_client.vclient.storeDocument(choice); - } catch (Error ex) - { - warnttl = "Serious Problem saving Vamsas Document"; - warnmsg = ex.toString(); - jalview.bin.Cache.log - .error("Error Whilst saving document to " + choice, ex); - - } catch (Exception ex) - { - warnttl = "Problem saving Vamsas Document."; - warnmsg = ex.toString(); - jalview.bin.Cache.log.warn( - "Exception Whilst saving document to " + choice, ex); - - } - removeProgressPanel(progpanel); - if (warnmsg != null) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - - warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); - } - } + source.showFeatureSettingsUI(); } - } - - JPanel vamUpdate = null; - /** - * hide vamsas user gui bits when a vamsas document event is being handled. - * - * @param b - * true to hide gui, false to reveal gui - */ - public void setVamsasUpdate(boolean b) - { - Cache.log.debug("Setting gui for Vamsas update " - + (b ? "in progress" : "finished")); - - if (vamUpdate != null) - { - this.removeProgressPanel(vamUpdate); - } - if (b) - { - vamUpdate = this.addProgressPanel( - MessageManager.getString("label.updating_vamsas_session")); - } - vamsasStart.setVisible(!b); - vamsasStop.setVisible(!b); - vamsasSave.setVisible(!b); } public JInternalFrame[] getAllFrames() @@ -2766,9 +2405,12 @@ public class Desktop extends jalview.jbgui.GDesktop */ protected void addQuitHandler() { - getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) - .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()), + getRootPane() + .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( + KeyStroke + .getKeyStroke(KeyEvent.VK_Q, + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @@ -2921,7 +2563,8 @@ public class Desktop extends jalview.jbgui.GDesktop public VamsasApplication getVamsasApplication() { - return v_client; + // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS + return null; } @@ -2950,13 +2593,36 @@ public class Desktop extends jalview.jbgui.GDesktop this.inBatchMode = inBatchMode; } + /** + * start service discovery and wait till it is done + */ public void startServiceDiscovery() { startServiceDiscovery(false); } + /** + * start service discovery threads - blocking or non-blocking + * + * @param blocking + */ public void startServiceDiscovery(boolean blocking) { + startServiceDiscovery(blocking, false); + } + + /** + * start service discovery threads + * + * @param blocking + * - false means call returns immediately + * @param ignore_SHOW_JWS2_SERVICES_preference + * - when true JABA services are discovered regardless of user's JWS2 + * discovery preference setting + */ + public void startServiceDiscovery(boolean blocking, + boolean ignore_SHOW_JWS2_SERVICES_preference) + { boolean alive = true; Thread t0 = null, t1 = null, t2 = null; // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release @@ -2974,7 +2640,8 @@ public class Desktop extends jalview.jbgui.GDesktop (t0 = new Thread(discoverer)).start(); } - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + if (ignore_SHOW_JWS2_SERVICES_preference + || Cache.getDefault("SHOW_JWS2_SERVICES", true)) { t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() .startDiscoverer(changeSupport);