From: Jim Procter Date: Tue, 2 Jul 2019 20:19:46 +0000 (+0100) Subject: Merge branch 'tasks/JAL-3311_removeVamsasMenu' into develop X-Git-Tag: Release_2_11_0~2^2~12 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4f31ade7ad1723f8b1ea8b194de725260c81e5b6;hp=0563c3cb3209568f7fde6badd53d73a907372ecb Merge branch 'tasks/JAL-3311_removeVamsasMenu' into develop --- diff --git a/help/help/help.jhm b/help/help/help.jhm index 64f3d21..0802bf1 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -134,7 +134,6 @@ - diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index a0995c2..3827747 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -137,10 +137,6 @@ - - - - diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index fa273a5..ebdfcf3 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -139,29 +139,6 @@ -
-vdoc VAMSAS DOCUMENT FILE/URL
- -
- Import the given vamsas document into a new session.
- New in 2.5 -
- - - - -
-vsess VAMSAS SESSION URL
- -
- Join the given vamsas session
If a document was also - specified, this will be imported first and then committed as - new data from Jalview to the specified session (Experimental - - not yet enabled!).New in 2.5 -
- - - - -
-fasta FILE
diff --git a/help/help/html/menus/desktopMenu.html b/help/help/html/menus/desktopMenu.html index d716e33..49fbec3 100755 --- a/help/help/html/menus/desktopMenu.html +++ b/help/help/html/menus/desktopMenu.html @@ -89,31 +89,6 @@ -
  • Vamsas For more details, read the - Jalview VAMSAS documentation.
    - When no session is active, the menu provides options for - initiating a new VAMSAS session: -     -
      -
    • Connect to
       Connect to - one of the existing sessions available.
      • -
    • New VAMSAS session
       Initiates - a new local VAMSAS session.
      • -
    • Load VAMSAS session...
       Opens - a file browser allowing you to choose a VAMSAS document to - import into a new local session.
      • -
    When Jalview is joined to a VAMSAS session, the menu - contains the following: -
      -
    • Session Update
       Sends - alignment data in the Jalview desktop to the VAMSAS session.
      • -
    • Save VAMSAS Session...
       Saves - the current session to a VAMSAS document archive.
      • -
    • Stop VAMSAS Session
       Disconnects - from the current session. You may be asked if you want to - save the current session's data if no other VAMSAS clients - are connected.
      • -
  • Help
    • About
      diff --git a/help/help/html/vamsas/index.html b/help/help/html/vamsas/index.html deleted file mode 100644 index 72a336a..0000000 --- a/help/help/html/vamsas/index.html +++ /dev/null @@ -1,157 +0,0 @@ - - - -VAMSAS Interoperation - - -

      - VAMSAS Interoperation -

      -

      - Jalview can interact with other applications using "the VAMSAS - Interoperation framework" which is an experimental model for - interoperation between bioinformatics applications (Visualization - and Analysis of Molecular Sequences, - Alignements and Structures). - Currently, the only other VAMSAS enabled application is TOPALi - a user friendly - program for phylogenetics and evolutionary analysis. -

      - VAMSAS enabled applications access a shared bioinformatics dataset - containing sequences, alignments, annotation and trees, which can be - represented by an XML document analogous to a Jalview Project - Archive. -

      -
      - Connecting to a VAMSAS session -
      The VAMSAS functionality in Jalview is accessed through the - Desktop's - Vamsas menu. The options available in this menu - depend on whether the application is currently interacting with a - VAMSAS dataset in a - VAMSAS session. When the application is not connected - to a session is active, the menu options are as follows: -
      -
        -
      • Connect to an existing session
        If - visible, this submenu contains a list of existing sessions that - the VAMSAS framework has discovered on your computer.
        - Choose one to connect to it.
        • -
      • New VAMSAS Session
        This option will - create a new session on your computer.
        • -
      • Load VAMSAS Session...
        This option will - open a file browser window allowing you to select a VAMSAS session - archive from which a new session will be created.
        New - in 2.5:Sessions created from an imported document inherit the - file or URL for the document.
        • - -
      -
      - VAMSAS and Firewalls: VAMSAS uses sockets to - communicate between different programs. This means that after starting - a session, your firewall software may ask you whether to allow the - java executable access to the internet (port 53782). If you do not - allow this, messages will not be exchanged with other VAMSAS - applications. -
      -
      Once you have successfully connected to a VAMSAS session, - any data made available by other VAMSAS applications will be - automatically imported into Jalview. However, in order to share the - data in Jalview with other VAMSAS applications, you must manually - select the - Vamsas→"Session Update" entry that is - visible when a session is active. Selecting this option will update - the VAMSAS session document, with the data loaded into Jalview. Any - new alignments, trees and annotation will be written to the session, - in addition to any edits you have made to data originally stored in - the document. -
      - Saving the current session -
      You can save the current session as a VAMSAS Session archive - using the - Vamsas→"Session Update". The file - contains a snapshot of the current VAMSAS session, including data from - any other applications connected to the session. - Leaving a VAMSAS session -
      A session can be disconnected from at any time using the - Vamsas→"Stop Session" option. - Selecting this option will only disconnect Jalview from the session - - any other applications will remain connected to the session. If - Jalview is the only application connected to the session and you have - not yet saved the VAMSAS session then you will be prompted with an - optional 'Save VAMSAS session...' dialog box, allowing the session to - be saved and returned to at a later date. -
      - VAMSAS Session Persistence -
      VAMSAS sessions are persistent - this means that they exist - independently of any VAMSAS applications that are connected to them. - This means that if something goes wrong with a VAMSAS application and - it crashes or otherwise fails, the VAMSAS session it is connected to - will (hopefully) be unaffected. For instance, if Jalview is killed or - crashes whilst it is still connected to a session, that session can be - recovered in a new Jalview instance using the - Vamsas→"Existing session" sub menu. -

      -

      - A quick Demo
      Jalview can talk to itself - through VAMSAS. Simply start two copies of the application, create a - new vamsas session in one, and connect to the new session in the - other. Then load your data into one of the applications, and use the - Vamsas→"Session Update" menu entry - to try to propagate the data to the other application.
      - - - - - - - - - - - - - - - - - - - - - -
      Data Sharing CapabilityJalview Version
      Alignments, sequences and annotation, trees, database - references, cDNA/protein mappings.2.4
      Mouseover location across linked DNA, protein and - structure positions.2.4
      Jalview project settings (Multiple views, groups, tree - partitions, colouring, window positions)2.5
      Sequence region and column selections2.5
      -
      -

      - Version 0.2 of the VAMSAS client library is used in Jalview - 2.5. For further details about the VAMSAS framework, please check - the VAMSAS website. The VAMSAS - framework is implemented as a Java 1.4 Library and depends on a - number of other open source projects. Its source is released under - the LGPL license.   -

      - - diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 02e53ec..ca2a584 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -441,91 +441,6 @@ public class Jalview System.out.println("No files to open!"); System.exit(1); } - String vamsasImport = aparser.getValue("vdoc"); - String vamsasSession = aparser.getValue("vsess"); - if (vamsasImport != null || vamsasSession != null) - { - if (desktop == null || headless) - { - System.out.println( - "Headless vamsas sessions not yet supported. Sorry."); - System.exit(1); - } - // if we have a file, start a new session and import it. - boolean inSession = false; - if (vamsasImport != null) - { - try - { - DataSourceType viprotocol = AppletFormatAdapter - .checkProtocol(vamsasImport); - if (viprotocol == DataSourceType.FILE) - { - inSession = desktop.vamsasImport(new File(vamsasImport)); - } - else if (viprotocol == DataSourceType.URL) - { - inSession = desktop.vamsasImport(new URL(vamsasImport)); - } - - } catch (Exception e) - { - System.err.println("Exeption when importing " + vamsasImport - + " as a vamsas document."); - e.printStackTrace(); - } - if (!inSession) - { - System.err.println("Failed to import " + vamsasImport - + " as a vamsas document."); - } - else - { - System.out.println("Imported Successfully into new session " - + desktop.getVamsasApplication().getCurrentSession()); - } - } - if (vamsasSession != null) - { - if (vamsasImport != null) - { - // close the newly imported session and import the Jalview specific - // remnants into the new session later on. - desktop.vamsasStop_actionPerformed(null); - } - // now join the new session - try - { - if (desktop.joinVamsasSession(vamsasSession)) - { - System.out.println( - "Successfully joined vamsas session " + vamsasSession); - } - else - { - System.err.println("WARNING: Failed to join vamsas session " - + vamsasSession); - } - } catch (Exception e) - { - System.err.println( - "ERROR: Failed to join vamsas session " + vamsasSession); - e.printStackTrace(); - } - if (vamsasImport != null) - { - // the Jalview specific remnants can now be imported into the new - // session at the user's leisure. - Cache.log.info( - "Skipping Push for import of data into existing vamsas session."); // TODO: - // enable - // this - // when - // debugged - // desktop.getVamsasApplication().push_update(); - } - } - } long progress = -1; // Finally, deal with the remaining input data. if (file != null) @@ -761,7 +676,7 @@ public class Jalview // And the user // //////////////////// - if (!headless && file == null && vamsasImport == null + if (!headless && file == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault("STARTUP_FILE", @@ -867,10 +782,6 @@ public class Jalview // passed in correctly)" + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" - // + - // "-vdoc vamsas-document\tImport vamsas document into new - // session or join existing session with same URN\n" - // + "-vses vamsas-session\tJoin session with given URN\n" + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); } diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index cf91b9c..1ec6939 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -77,9 +77,7 @@ 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.net.URL; @@ -119,8 +117,6 @@ 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; @@ -346,7 +342,6 @@ public class Desktop extends jalview.jbgui.GDesktop * constructor. */ instance = this; - doVamsasClientCheck(); doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); @@ -675,46 +670,6 @@ 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(); @@ -1449,10 +1404,6 @@ 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 @@ -2042,364 +1993,6 @@ public class Desktop extends jalview.jbgui.GDesktop } - 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() - { - - @Override - public void actionPerformed(ActionEvent e) - { - 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); - } - // 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) - { - // 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); - } - } - } - } - - 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() { return desktop.getAllFrames(); @@ -2902,7 +2495,8 @@ 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; } diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index c094b1c..0848a4d 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -688,7 +688,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource public void disableGui(boolean b) { - Desktop.instance.setVamsasUpdate(b); + // JAL-3311 TODO: remove this class! + // Desktop.instance.setVamsasUpdate(b); } Hashtable _backup_vobj2jv; diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index f30fa9b..0ef3f46 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -51,10 +51,6 @@ public class GDesktop extends JFrame JMenu HelpMenu = new JMenu(); - protected JMenu VamsasMenu = new JMenu(); - - protected JMenu VamsasStMenu = new JMenu(); - JMenuItem inputLocalFileMenuItem = new JMenuItem(); JMenuItem inputURLMenuItem = new JMenuItem(); @@ -81,16 +77,8 @@ public class GDesktop extends JFrame JMenu inputMenu = new JMenu(); - protected JMenuItem vamsasStart = new JMenuItem(); - - protected JMenuItem vamsasImport = new JMenuItem(); - - protected JMenuItem vamsasSave = new JMenuItem(); - JMenuItem inputSequence = new JMenuItem(); - protected JMenuItem vamsasStop = new JMenuItem(); - JMenuItem closeAll = new JMenuItem(); JMenuItem raiseRelated = new JMenuItem(); @@ -129,7 +117,6 @@ public class GDesktop extends JFrame { FileMenu.setMnemonic('F'); inputLocalFileMenuItem.setMnemonic('L'); - VamsasMenu.setMnemonic('V'); inputURLMenuItem.setMnemonic('U'); inputTextboxMenuItem.setMnemonic('C'); quit.setMnemonic('Q'); @@ -150,12 +137,6 @@ public class GDesktop extends JFrame FileMenu.setText(MessageManager.getString("action.file")); HelpMenu.setText(MessageManager.getString("action.help")); - VamsasMenu.setText("Vamsas"); - VamsasMenu.setToolTipText(MessageManager - .getString("label.share_data_vamsas_applications")); - VamsasStMenu.setText(MessageManager.getString("label.connect_to")); - VamsasStMenu.setToolTipText( - MessageManager.getString("label.join_existing_vamsas_session")); inputLocalFileMenuItem .setText(MessageManager.getString("label.load_tree_from_file")); inputLocalFileMenuItem.setAccelerator( @@ -268,39 +249,6 @@ public class GDesktop extends JFrame } }); inputMenu.setText(MessageManager.getString("label.input_alignment")); - vamsasStart - .setText(MessageManager.getString("label.new_vamsas_session")); - vamsasStart.setVisible(false); - vamsasStart.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - vamsasStart_actionPerformed(e); - } - }); - vamsasImport.setText( - MessageManager.getString("action.load_vamsas_session")); - vamsasImport.setVisible(false); - vamsasImport.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - vamsasImport_actionPerformed(e); - } - }); - vamsasSave.setText( - MessageManager.getString("action.save_vamsas_session")); - vamsasSave.setVisible(false); - vamsasSave.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - vamsasSave_actionPerformed(e); - } - }); inputSequence .setText(MessageManager.getString("action.fetch_sequences")); inputSequence.addActionListener(new ActionListener() @@ -311,17 +259,6 @@ public class GDesktop extends JFrame inputSequence_actionPerformed(e); } }); - vamsasStop - .setText(MessageManager.getString("label.stop_vamsas_session")); - vamsasStop.setVisible(false); - vamsasStop.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - vamsasStop_actionPerformed(e); - } - }); closeAll.setText(MessageManager.getString("action.close_all")); closeAll.addActionListener(new ActionListener() { @@ -428,8 +365,6 @@ public class GDesktop extends JFrame desktopMenubar.add(FileMenu); desktopMenubar.add(toolsMenu); - VamsasMenu.setVisible(false); - desktopMenubar.add(VamsasMenu); desktopMenubar.add(HelpMenu); desktopMenubar.add(windowMenu); FileMenu.add(inputMenu); @@ -442,12 +377,6 @@ public class GDesktop extends JFrame FileMenu.add(quit); HelpMenu.add(aboutMenuItem); HelpMenu.add(documentationMenuItem); - VamsasMenu.add(VamsasStMenu); - VamsasStMenu.setVisible(false); - VamsasMenu.add(vamsasStart); - VamsasMenu.add(vamsasImport); - VamsasMenu.add(vamsasSave); - VamsasMenu.add(vamsasStop); if (!Platform.isAMac() || specversion < 11) { toolsMenu.add(preferences);