X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=e65bffad20bb469c51c6178edb73b508125846f4;hb=04e9ac268a61d1cef5c65827942a2ec4b92f3814;hp=f77e64dff3712823b5e0f75592b66669aa05e31a;hpb=21c29b20790ac555b2e2a124a034f6c6b4486270;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index f77e64d..e65bffa 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,19 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -558,7 +561,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); - JMenuItem item = new JMenuItem("Paste To New Window"); + JMenuItem item = new JMenuItem( + MessageManager.getString("label.paste_new_window")); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -648,8 +652,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN // IF JALVIEW IS RUNNING HEADLESS // /////////////////////////////////////////////// - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + if (instance == null + || (System.getProperty("java.awt.headless") != null && System + .getProperty("java.awt.headless").equals("true"))) { return; } @@ -806,6 +811,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void drop(DropTargetDropEvent evt) { + boolean success = true; Transferable t = evt.getTransferable(); java.util.List files = null; java.util.List protocols = null; @@ -854,6 +860,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } catch (Exception e) { + success = false; } if (files != null) @@ -882,8 +889,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } catch (Exception ex) { + success = false; } } + evt.dropComplete(success); // need this to ensure input focus is properly + // transfered to any new windows created } /** @@ -901,8 +911,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Open local file"); - chooser.setToolTipText("Open"); + chooser.setDialogTitle(MessageManager + .getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); int value = chooser.showOpenDialog(this); @@ -913,7 +924,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getSelectedFile().getParent()); String format = null; - if (chooser.getSelectedFormat().equals("Jalview")) + if (chooser.getSelectedFormat() != null + && chooser.getSelectedFormat().equals("Jalview")) { format = "Jalview"; } @@ -944,7 +956,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // This construct allows us to have a wider textfield // for viewing - JLabel label = new JLabel(MessageManager.getString("label.input_file_url")); + JLabel label = new JLabel( + MessageManager.getString("label.input_file_url")); final JComboBox history = new JComboBox(); JPanel panel = new JPanel(new GridLayout(2, 1)); @@ -969,7 +982,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } int reply = JOptionPane.showInternalConfirmDialog(desktop, panel, - MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION); + MessageManager.getString("label.input_alignment_from_url"), + JOptionPane.OK_CANCEL_OPTION); if (reply != JOptionPane.OK_OPTION) { @@ -1146,11 +1160,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements message.append("
Authors: " + jalview.bin.Cache .getDefault( - "AUTHORNAMES", "Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton") + "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
" + "
For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list" + "
If you use Jalview, please cite:" + "AUTHORFNAMES", + "
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" + "
Bioinformatics doi: 10.1093/bioinformatics/btp033" @@ -1367,7 +1381,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jar" }, new String[] + { "jvp" }, new String[] { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1424,8 +1438,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jar" }, new String[] - { "Jalview Project" }, "Jalview Project"); + { "jvp", "jar" }, new String[] + { "Jalview Project", "Jalview Project (old)" }, + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Restore state"); @@ -1510,13 +1525,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressPanel != null) { - progressPanel.remove(progbar); - GridLayout gl = (GridLayout) progressPanel.getLayout(); - gl.setRows(gl.getRows() - 1); - if (--totalProgressCount < 1) + synchronized (progressPanel) { - this.getContentPane().remove(progressPanel); - progressPanel = null; + progressPanel.remove(progbar); + GridLayout gl = (GridLayout) progressPanel.getLayout(); + gl.setRows(gl.getRows() - 1); + if (--totalProgressCount < 1) + { + this.getContentPane().remove(progressPanel); + progressPanel = null; + } } } validate(); @@ -1527,9 +1545,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements fileLoadingCount--; if (fileLoadingCount < 1) { - for (JPanel flp : fileLoadingPanels) + while (fileLoadingPanels.size() > 0) { - removeProgressPanel(flp); + removeProgressPanel(fileLoadingPanels.remove(0)); } fileLoadingPanels.clear(); fileLoadingCount = 0; @@ -1712,7 +1730,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Open a saved VAMSAS session"); - chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session."); + chooser.setToolTipText(MessageManager + .getString("label.select_vamsas_session_opened_as_new_vamsas_session")); int value = chooser.showOpenDialog(this); @@ -1721,10 +1740,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}), - MessageManager.getString("label.vamsas_document_import_failed"), - JOptionPane.ERROR_MESSAGE); + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager.formatMessage( + "label.couldnt_import_as_vamsas_session", + new String[] + { fle }), + MessageManager + .getString("label.vamsas_document_import_failed"), + JOptionPane.ERROR_MESSAGE); } } } @@ -1878,7 +1903,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements vamsasSave.setVisible(false); vamsasStop.setVisible(false); vamsasImport.setVisible(true); - vamsasStart.setText(MessageManager.getString("label.new_vamsas_session")); + vamsasStart.setText(MessageManager + .getString("label.new_vamsas_session")); } public void vamsasStop_actionPerformed(ActionEvent e) @@ -1914,7 +1940,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); - sessit.setToolTipText("Connect to session " + sess[i]); + sessit.setToolTipText(MessageManager.formatMessage( + "label.connect_to_session", new String[] + { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() @@ -2136,8 +2164,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements FontMetrics fm = g.getFontMetrics(); if (fm != null) { - g.drawString( - MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10, + g.drawString(MessageManager.formatMessage( + "label.memory_stats", + new String[] + { df.format(totalFreeMemory), df.format(maxMemory), + df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); } } @@ -2340,7 +2371,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { - JButton cancel = new JButton(MessageManager.getString("action.cancel")); + JButton cancel = new JButton( + MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { @@ -2435,38 +2467,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements { boolean alive = true; Thread t0 = null, t1 = null, t2 = null; - - // todo: changesupport handlers need to be transferred - if (discoverer == null) - { - discoverer = new jalview.ws.jws1.Discoverer(); - // register PCS handler for desktop. - discoverer.addPropertyChangeListener(changeSupport); - } - // JAL-940 - disabled JWS1 service configuration - always start discoverer - // until we phase out completely + // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release if (true) { + // todo: changesupport handlers need to be transferred + if (discoverer == null) + { + discoverer = new jalview.ws.jws1.Discoverer(); + // register PCS handler for desktop. + discoverer.addPropertyChangeListener(changeSupport); + } + // JAL-940 - disabled JWS1 service configuration - always start discoverer + // until we phase out completely (t0 = new Thread(discoverer)).start(); } - try + // ENFIN services are EOLed as of Jalview 2.8.1 release + if (false) { - if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + try { - // EnfinEnvision web service menu entries are rebuild every time the - // menu is shown, so no changeSupport events are needed. - jalview.ws.EnfinEnvision2OneWay.getInstance(); - (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance())) - .start(); + if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + { + // EnfinEnvision web service menu entries are rebuild every time the + // menu is shown, so no changeSupport events are needed. + jalview.ws.EnfinEnvision2OneWay.getInstance(); + (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance())) + .start(); + } + } catch (Exception e) + { + Cache.log + .info("Exception when trying to launch Envision2 workflow discovery.", + e); + Cache.log.info(e.getStackTrace()); } - } catch (Exception e) - { - Cache.log - .info("Exception when trying to launch Envision2 workflow discovery.", - e); - Cache.log.info(e.getStackTrace()); } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())