X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=b2ff85c8054e1aeb79adbea1eed2a7ec5a08873d;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=471a40aa1e44d37c256ddfa7ab4b04e19cbe18ae;hpb=fe66b18b34201857669c2b5b44435a397af202d8;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java old mode 100755 new mode 100644 index 471a40a..b2ff85c --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,69 +1,160 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * 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. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import jalview.bin.Cache; -import jalview.io.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.ws.params.ParamManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.ClipboardOwner; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +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.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; -import java.io.InputStream; import java.lang.reflect.Constructor; import java.net.URL; -import java.net.URLConnection; -import java.nio.channels.ReadableByteChannel; -import java.util.*; - -import javax.swing.*; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.Semaphore; + +import javax.swing.DefaultDesktopManager; +import javax.swing.DesktopManager; +import javax.swing.JButton; +import javax.swing.JComboBox; +import javax.swing.JComponent; +import javax.swing.JDesktopPane; +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; +import javax.swing.SwingUtilities; +import javax.swing.event.HyperlinkEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +import javax.swing.event.HyperlinkEvent.EventType; /** - * DOCUMENT ME! + * Jalview Desktop + * * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.155 $ */ public class Desktop extends jalview.jbgui.GDesktop implements - DropTargetListener, ClipboardOwner, IProgressIndicator + DropTargetListener, ClipboardOwner, IProgressIndicator, + jalview.api.StructureSelectionManagerProvider { - /** DOCUMENT ME!! */ + + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); + + /** + * news reader - null if it was never started. + */ + private BlogReader jvnews = null; + + /** + * @param listener + * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void addJalviewPropertyChangeListener( + PropertyChangeListener listener) + { + changeSupport.addJalviewPropertyChangeListener(listener); + } + + /** + * @param propertyName + * @param listener + * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, + * java.beans.PropertyChangeListener) + */ + public void addJalviewPropertyChangeListener(String propertyName, + PropertyChangeListener listener) + { + changeSupport.addJalviewPropertyChangeListener(propertyName, listener); + } + + /** + * @param propertyName + * @param listener + * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, + * java.beans.PropertyChangeListener) + */ + public void removeJalviewPropertyChangeListener(String propertyName, + PropertyChangeListener listener) + { + changeSupport.removeJalviewPropertyChangeListener(propertyName, + listener); + } + + /** Singleton Desktop instance */ public static Desktop instance; - // Need to decide if the Memory Usage is to be included in - // Next release or not. public static MyDesktopPane desktop; - // public static JDesktopPane desktop; - static int openFrameCount = 0; static final int xOffset = 30; static final int yOffset = 30; - public static jalview.ws.Discoverer discoverer; + public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; @@ -71,6 +162,113 @@ public class Desktop extends jalview.jbgui.GDesktop implements static int fileLoadingCount = 0; + class MyDesktopManager implements DesktopManager + { + + private DesktopManager delegate; + + public MyDesktopManager(DesktopManager delegate) + { + this.delegate = delegate; + } + + public void activateFrame(JInternalFrame f) + { + try + { + delegate.activateFrame(f); + } catch (NullPointerException npe) + { + Point p = getMousePosition(); + instance.showPasteMenu(p.x, p.y); + } + } + + public void beginDraggingFrame(JComponent f) + { + delegate.beginDraggingFrame(f); + } + + public void beginResizingFrame(JComponent f, int direction) + { + delegate.beginResizingFrame(f, direction); + } + + public void closeFrame(JInternalFrame f) + { + delegate.closeFrame(f); + } + + public void deactivateFrame(JInternalFrame f) + { + delegate.deactivateFrame(f); + } + + public void deiconifyFrame(JInternalFrame f) + { + delegate.deiconifyFrame(f); + } + + public void dragFrame(JComponent f, int newX, int newY) + { + if (newY < 0) + { + newY = 0; + } + delegate.dragFrame(f, newX, newY); + } + + public void endDraggingFrame(JComponent f) + { + delegate.endDraggingFrame(f); + } + + public void endResizingFrame(JComponent f) + { + delegate.endResizingFrame(f); + } + + public void iconifyFrame(JInternalFrame f) + { + delegate.iconifyFrame(f); + } + + public void maximizeFrame(JInternalFrame f) + { + delegate.maximizeFrame(f); + } + + public void minimizeFrame(JInternalFrame f) + { + delegate.minimizeFrame(f); + } + + public void openFrame(JInternalFrame f) + { + delegate.openFrame(f); + } + + public void resizeFrame(JComponent f, int newX, int newY, int newWidth, + int newHeight) + { + Rectangle b = desktop.getBounds(); + if (newY < 0) + { + newY = 0; + } + delegate.resizeFrame(f, newX, newY, newWidth, newHeight); + } + + public void setBoundsForFrame(JComponent f, int newX, int newY, + int newWidth, int newHeight) + { + delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight); + } + + // All other methods, simply delegate + + } + /** * Creates a new Desktop object. */ @@ -95,12 +293,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); + // alternate config - have scrollbars - see notes in JAL-153 + // JScrollPane sp = new JScrollPane(); + // sp.getViewport().setView(desktop); + // getContentPane().add(sp, BorderLayout.CENTER); getContentPane().add(desktop, BorderLayout.CENTER); desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised - desktop.setDesktopManager(new DefaultDesktopManager()); + desktop.setDesktopManager(new MyDesktopManager( + new DefaultDesktopManager())); Rectangle dims = getLastKnownDimensions(""); if (dims != null) @@ -113,9 +316,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements setBounds((int) (screenSize.width - 900) / 2, (int) (screenSize.height - 650) / 2, 900, 650); } - jconsole = new Console(this); - // immediately output essential build information - System.out.println("Jalview Desktop " + jconsole = new Console(this, showjconsole); + // add essential build information + jconsole.setHeader("Jalview Desktop " + jalview.bin.Cache.getProperty("VERSION") + "\n" + "Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" @@ -126,6 +329,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); + showNews.setVisible(false); + this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent evt) @@ -134,7 +339,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - this.addMouseListener(new MouseAdapter() + MouseAdapter ma; + this.addMouseListener(ma = new MouseAdapter() { public void mousePressed(MouseEvent evt) { @@ -144,7 +350,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } }); + desktop.addMouseListener(ma); + + this.addFocusListener(new FocusListener() + { + + @Override + public void focusLost(FocusEvent e) + { + // TODO Auto-generated method stub + } + + @Override + public void focusGained(FocusEvent e) + { + Cache.log.debug("Relaying windows after focus gain"); + // make sure that we sort windows properly after we gain focus + instance.relayerWindows(); + } + }); this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); // Spawn a thread that shows the splashscreen SwingUtilities.invokeLater(new Runnable() @@ -155,7 +380,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is // displayed. // Thread off a new instance of the file chooser - this reduces the time it // takes to open it later on. @@ -172,6 +396,66 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.debug("Filechooser init thread finished."); } }).start(); + // Add the service change listener + changeSupport.addJalviewPropertyChangeListener("services", + new PropertyChangeListener() + { + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + Cache.log.debug("Firing service changed event for " + + evt.getNewValue()); + JalviewServicesChanged(evt); + } + + }); + } + + public void checkForNews() + { + final Desktop me = this; + // Thread off the news reader, in case there are connection problems. + addDialogThread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Starting news thread."); + + jvnews = new BlogReader(me); + showNews.setVisible(true); + Cache.log.debug("Completed news thread."); + } + }); + } + + protected void showNews_actionPerformed(ActionEvent e) + { + showNews(showNews.isSelected()); + } + + void showNews(boolean visible) + { + { + Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); + showNews.setSelected(visible); + if (visible && !jvnews.isVisible()) + { + new Thread(new Runnable() + { + @Override + public void run() + { + long instance = System.currentTimeMillis(); + Desktop.instance.setProgressBar("Refreshing news", instance); + jvnews.refreshNews(); + Desktop.instance.setProgressBar(null, instance); + jvnews.showNews(); + } + }).start(); + } + } } /** @@ -212,6 +496,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements iw = (int) (iw * sw); iy = (int) (iy * sh); ih = (int) (ih * sh); + while (ix >= screenSize.width) + { + jalview.bin.Cache.log + .debug("Window geometry location recall error: shifting horizontal to within screenbounds."); + ix -= screenSize.width; + } + while (iy >= screenSize.height) + { + jalview.bin.Cache.log + .debug("Window geometry location recall error: shifting vertical to within screenbounds."); + iy -= screenSize.height; + } jalview.bin.Cache.log.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw + " height:" + ih); @@ -374,34 +670,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements } final JMenuItem menuItem = new JMenuItem(title); - frame - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameActivated( - javax.swing.event.InternalFrameEvent evt) - { - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - { - itf.requestFocus(); - } + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameActivated( + javax.swing.event.InternalFrameEvent evt) + { + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + { + itf.requestFocus(); + } - } + } - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - PaintRefresher.RemoveComponent(frame); - openFrameCount--; - windowMenu.remove(menuItem); - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - { - itf.requestFocus(); - } - System.gc(); - }; - }); + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + PaintRefresher.RemoveComponent(frame); + openFrameCount--; + windowMenu.remove(menuItem); + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + { + itf.requestFocus(); + } + System.gc(); + }; + }); menuItem.addActionListener(new ActionListener() { @@ -417,6 +712,47 @@ 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); @@ -428,6 +764,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements frame.requestFocus(); } catch (java.beans.PropertyVetoException ve) { + } 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", + cex); } } @@ -553,8 +894,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), + JalviewFileChooser chooser = 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")); @@ -704,6 +1045,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); jconsole.stopConsole(); } + if (jvnews != null) + { + storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + + } + if (dialogExecutor != null) + { + dialogExecutor.shutdownNow(); + } + System.exit(0); } @@ -727,32 +1078,84 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void aboutMenuItem_actionPerformed(ActionEvent e) { - StringBuffer message = new StringBuffer("Jalview version " - + jalview.bin.Cache.getProperty("VERSION") + "; last updated: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + // StringBuffer message = getAboutMessage(false); + // JOptionPane.showInternalMessageDialog(Desktop.desktop, + // + // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + new Thread(new Runnable() + { + public void run() + { + new SplashScreen(true); + } + }).start(); + } + + public StringBuffer getAboutMessage(boolean shortv) + { + StringBuffer message = new StringBuffer(); + message.append(""); + if (shortv) + { + message.append("

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


"); + message.append("Last Updated: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + + ""); - if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( - jalview.bin.Cache.getProperty("VERSION"))) + } + else { - message - .append("\n\n!! Jalview version " - + jalview.bin.Cache.getProperty("LATEST_VERSION") - + " is available for download from http://www.jalview.org !!\n"); + message.append("Version " + + jalview.bin.Cache.getProperty("VERSION") + + "; last updated: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); } - // TODO: update this text for each release or centrally store it for lite - // and application - message - .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton." - + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n" - + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n" - + "\nIf you use Jalview, please cite:" - + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" - + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench" - + "\nBioinformatics doi: 10.1093/bioinformatics/btp033"); - JOptionPane.showInternalMessageDialog(Desktop.desktop, - message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals( + "Checking")) + { + message.append("
...Checking latest version...
"); + } + else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") + .equals(jalview.bin.Cache.getProperty("VERSION"))) + { + boolean red = false; + if (jalview.bin.Cache.getProperty("VERSION").toLowerCase() + .indexOf("automated build") == -1) + { + red = true; + // Displayed when code version and jnlp version do not match and code + // version is not a development build + message.append("
"); + } + + message.append("
!! Version " + + jalview.bin.Cache.getDefault("LATEST_VERSION", + "..Checking..") + + " is available for download from " + + jalview.bin.Cache.getDefault("www.jalview.org", + "http://www.jalview.org") + " !!"); + if (red) + { + message.append("
"); + } + } + 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:" + + "
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" + + ""); + return message; } /** @@ -962,10 +1365,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void saveState_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "jar" }, new String[] - { "Jalview Project" }, "Jalview Project"); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "jar" }, new String[] + { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save State"); @@ -974,14 +1377,40 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { - java.io.File choice = chooser.getSelectedFile(); - JProgressBar progpanel = addProgressPanel("Saving jalview project " - + choice.getName()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - // TODO catch and handle errors for savestate - new Jalview2XML().SaveState(choice); - removeProgressPanel(progpanel); + final Desktop me = this; + final java.io.File choice = chooser.getSelectedFile(); + new Thread(new Runnable() + { + public void run() + { + setProgressBar("Saving jalview project " + choice.getName(), + choice.hashCode()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + choice.getParent()); + // TODO catch and handle errors for savestate + // TODO prevent user from messing with the Desktop whilst we're saving + try + { + new Jalview2XML().SaveState(choice); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst saving current state to " + + choice.getName(), oom); + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst trying to save to " + choice.getName(), + ex); + JOptionPane.showMessageDialog( + me, + "Error whilst saving current state to " + + choice.getName(), "Couldn't save project", + JOptionPane.WARNING_MESSAGE); + } + setProgressBar(null, choice.hashCode()); + } + }).start(); } } @@ -993,10 +1422,10 @@ 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[] - { "jar" }, new String[] - { "Jalview Project" }, "Jalview Project"); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "jar" }, new String[] + { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Restore state"); @@ -1004,13 +1433,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getAbsolutePath(); - setProgressBar("loading jalview project " - + chooser.getSelectedFile().getName(), choice.hashCode()); + final String choice = chooser.getSelectedFile().getAbsolutePath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); - new Jalview2XML().LoadJalviewAlign(choice); - setProgressBar(null, choice.hashCode()); + new Thread(new Runnable() + { + public void run() + { + setProgressBar("loading jalview project " + choice, + choice.hashCode()); + try + { + new Jalview2XML().LoadJalviewAlign(choice); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst loading project from " + choice, oom); + } catch (Exception ex) + { + Cache.log.error("Problems whilst loading project from " + + choice, ex); + JOptionPane.showMessageDialog(Desktop.desktop, + "Error whilst loading project from " + choice, + "Couldn't load project", JOptionPane.WARNING_MESSAGE); + } + setProgressBar(null, choice.hashCode()); + } + }).start(); } } @@ -1021,43 +1469,50 @@ public class Desktop extends jalview.jbgui.GDesktop implements JPanel progressPanel; + ArrayList fileLoadingPanels = new ArrayList(); + public void startLoading(final String fileName) { if (fileLoadingCount == 0) { - addProgressPanel("Loading File: " + fileName + " "); - + fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + + " ")); } fileLoadingCount++; } - private JProgressBar addProgressPanel(String string) + private JPanel addProgressPanel(String string) { if (progressPanel == null) { - progressPanel = new JPanel(new BorderLayout()); + progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; + instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); } + JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); - progressPanel.add(new JLabel(string), BorderLayout.WEST); - - progressPanel.add(progressBar, BorderLayout.CENTER); + thisprogress.add(new JLabel(string), BorderLayout.WEST); - instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); - totalProgressCount++; - validate(); - return progressBar; + thisprogress.add(progressBar, BorderLayout.CENTER); + progressPanel.add(thisprogress); + ((GridLayout) progressPanel.getLayout()) + .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1); + ++totalProgressCount; + instance.validate(); + return thisprogress; } int totalProgressCount = 0; - private void removeProgressPanel(JProgressBar progbar) + private void removeProgressPanel(JPanel progbar) { if (progressPanel != null) { progressPanel.remove(progbar); + GridLayout gl = (GridLayout) progressPanel.getLayout(); + gl.setRows(gl.getRows() - 1); if (--totalProgressCount < 1) { this.getContentPane().remove(progressPanel); @@ -1072,28 +1527,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements fileLoadingCount--; if (fileLoadingCount < 1) { - if (progressPanel != null) + for (JPanel flp : fileLoadingPanels) { - this.getContentPane().remove(progressPanel); - progressPanel = null; + removeProgressPanel(flp); } + fileLoadingPanels.clear(); fileLoadingCount = 0; } validate(); } - public static int getViewCount(String viewId) + public static int getViewCount(String alignmentId) { - AlignViewport[] aps = getViewports(viewId); + AlignViewport[] aps = getViewports(alignmentId); return (aps == null) ? 0 : aps.length; } /** * - * @param viewId - * @return all AlignmentPanels concerning the viewId sequence set + * @param alignmentId + * @return all AlignmentPanels concerning the alignmentId sequence set */ - public static AlignmentPanel[] getAlignmentPanels(String viewId) + public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { int count = 0; if (Desktop.desktop == null) @@ -1111,9 +1566,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements AlignFrame af = (AlignFrame) frames[t]; for (int a = 0; a < af.alignPanels.size(); a++) { - if (viewId - .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av - .getSequenceSetId())) + if (alignmentId.equals(((AlignmentPanel) af.alignPanels + .elementAt(a)).av.getSequenceSetId())) { aps.add(af.alignPanels.elementAt(a)); } @@ -1216,7 +1670,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements source.viewport.gatherViewsHere = true; source.viewport.explodedPosition = source.getBounds(); JInternalFrame[] frames = desktop.getAllFrames(); - String viewId = source.viewport.sequenceSetID; + String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) { @@ -1253,13 +1707,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client == null) { // Load and try to start a session. - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); 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("select a vamsas session to be opened as a new vamsas session."); int value = chooser.showOpenDialog(this); @@ -1314,8 +1767,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } bis.close(); fos.close(); - v_client = new jalview.gui.VamsasApplication(this, file, url - .toExternalForm()); + v_client = new jalview.gui.VamsasApplication(this, file, + url.toExternalForm()); } catch (Exception ex) { jalview.bin.Cache.log.error( @@ -1344,8 +1797,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements return false; } - setProgressBar("Importing VAMSAS session from " + file.getName(), file - .hashCode()); + setProgressBar("Importing VAMSAS session from " + file.getName(), + file.hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); @@ -1359,8 +1812,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? - setProgressBar("Importing VAMSAS session from " + file.getName(), file - .hashCode()); + setProgressBar("Importing VAMSAS session from " + file.getName(), + file.hashCode()); return v_client.inSession(); } @@ -1510,9 +1963,9 @@ 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 + 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"); @@ -1524,7 +1977,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); - JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to " + JPanel progpanel = addProgressPanel("Saving VAMSAS Document to " + choice.getName()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; @@ -1558,7 +2011,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - JProgressBar vamUpdate = null; + JPanel vamUpdate = null; /** * hide vamsas user gui bits when a vamsas document event is being handled. @@ -1676,20 +2129,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void paintComponent(Graphics g) { - if (showMemoryUsage && g != null) + if (showMemoryUsage && g != null && df != null) { if (percentUsage < 20) g.setColor(Color.red); FontMetrics fm = g.getFontMetrics(); if (fm != null) { - g.drawString("Total Free Memory: " + df.format(totalFreeMemory) - + "MB; Max Memory: " + df.format(maxMemory) + "MB; " - + df.format(percentUsage) + "%", 10, getHeight() - - fm.getHeight()); + g.drawString( + "Total Free Memory: " + df.format(totalFreeMemory) + + "MB; Max Memory: " + df.format(maxMemory) + + "MB; " + df.format(percentUsage) + "%", 10, + getHeight() - fm.getHeight()); } } } + } + + /** + * fixes stacking order after a modal dialog to ensure windows that should be + * on top actually are + */ + public void relayerWindows() + { } @@ -1753,6 +2215,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements return afs; } + public AppJmol[] getJmols() + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + + if (frames == null) + { + return null; + } + Vector avp = new Vector(); + try + { + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AppJmol) + { + AppJmol af = (AppJmol) frames[i]; + avp.addElement(af); + } + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + if (avp.size() == 0) + { + return null; + } + AppJmol afs[] = new AppJmol[avp.size()]; + for (int i = 0, j = avp.size(); i < j; i++) + { + afs[i] = (AppJmol) avp.elementAt(i); + } + avp.clear(); + return afs; + } + /** * Add Groovy Support to Jalview */ @@ -1793,7 +2292,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Progress bars managed by the IProgressIndicator method. */ - private Hashtable progressBars, progressBarHandlers; + private Hashtable progressBars; + + private Hashtable progressBarHandlers; /* * (non-Javadoc) @@ -1804,14 +2305,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressBars == null) { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); + progressBars = new Hashtable(); + progressBarHandlers = new Hashtable(); } if (progressBars.get(new Long(id)) != null) { - JProgressBar progressPanel = (JProgressBar) progressBars - .remove(new Long(id)); + JPanel progressPanel = progressBars.remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); @@ -1850,8 +2350,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar("Cancelled " - + ((JLabel) progressPanel.getComponent(0)).getText(), id); + us.setProgressBar( + "Cancelled " + + ((JLabel) progressPanel.getComponent(0)) + .getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -1859,6 +2361,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** + * + * @return true if any progress bars are still active + */ + @Override + public boolean operationInProgress() + { + if (progressBars != null && progressBars.size() > 0) + { + return true; + } + return false; + } + + /** * This will return the first AlignFrame viewing AlignViewport av. It will * break if there are more than one AlignFrames viewing a particular av. This * @@ -1887,9 +2403,337 @@ public class Desktop extends jalview.jbgui.GDesktop implements } + /** + * flag set if jalview GUI is being operated programmatically + */ + private boolean inBatchMode = false; + + /** + * check if jalview GUI is being operated programmatically + * + * @return inBatchMode + */ + public boolean isInBatchMode() + { + return inBatchMode; + } + + /** + * set flag if jalview GUI is being operated programmatically + * + * @param inBatchMode + */ + public void setInBatchMode(boolean inBatchMode) + { + this.inBatchMode = inBatchMode; + } + public void startServiceDiscovery() { - discoverer.start(); - new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()).start(); + startServiceDiscovery(false); + } + + public void startServiceDiscovery(boolean blocking) + { + 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 + if (true) + { + (t0 = new Thread(discoverer)).start(); + } + + try + { + 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()); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning()) + { + jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true); + } + t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer( + changeSupport); + + } + Thread t3 = null; + { + // TODO: do rest service discovery + } + if (blocking) + { + while (alive) + { + try + { + Thread.sleep(15); + } catch (Exception e) + { + } + alive = (t1 != null && t1.isAlive()) + || (t2 != null && t2.isAlive()) + || (t3 != null && t3.isAlive()) + || (t0 != null && t0.isAlive()); + } + } + } + + /** + * called to check if the service discovery process completed successfully. + * + * @param evt + */ + protected void JalviewServicesChanged(PropertyChangeEvent evt) + { + if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) + { + final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + .getErrorMessages(); + if (ermsg != null) + { + if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) + { + if (serviceChangedDialog == null) + { + // only run if we aren't already displaying one of these. + addDialogThread(serviceChangedDialog = new Runnable() + { + public void run() + { + + /* + * JalviewDialog jd =new JalviewDialog() { + * + * @Override protected void cancelPressed() { // TODO + * Auto-generated method stub + * + * }@Override protected void okPressed() { // TODO + * Auto-generated method stub + * + * }@Override protected void raiseClosed() { // TODO + * Auto-generated method stub + * + * } }; jd.initDialogFrame(new + * JLabel("
" + ermsg + + * "
It may be that you have invalid JABA URLs in your web service preferences," + * + " or mis-configured HTTP proxy settings.
" + + * "Check the Connections and Web services tab of the" + * + + * " Tools->Preferences dialog box to change them.
" + * ), true, true, "Web Service Configuration Problem", 450, + * 400); + * + * jd.waitForInput(); + */ + JOptionPane + .showConfirmDialog( + Desktop.desktop, + new JLabel( + "
" + + ermsg + + "
" + + "

It may be that you have invalid JABA URLs
in your web service preferences," + + " or mis-configured HTTP proxy settings.

" + + "

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); + serviceChangedDialog = null; + + } + }); + } + } + else + { + Cache.log + .error("Errors reported by JABA discovery service. Check web services preferences.\n" + + ermsg); + } + } + } + } + + private Runnable serviceChangedDialog = null; + + /** + * start a thread to open a URL in the configured browser. Pops up a warning + * dialog to the user if there is an exception when calling out to the browser + * to open the URL. + * + * @param url + */ + public static void showUrl(final String url) + { + showUrl(url, Desktop.instance); + } + + /** + * Like showUrl but allows progress handler to be specified + * + * @param url + * @param progress + * (null) or object implementing IProgressIndicator + */ + public static void showUrl(final String url, + final IProgressIndicator progress) + { + new Thread(new Runnable() + { + public void run() + { + try + { + if (progress != null) + { + progress.setProgressBar("Opening " + url, this.hashCode()); + } + jalview.util.BrowserLauncher.openURL(url); + } catch (Exception ex) + { + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + "Unixers: Couldn't find default web browser." + + "\nAdd the full path to your browser in Preferences.", + "Web browser not found", + JOptionPane.WARNING_MESSAGE); + + ex.printStackTrace(); + } + if (progress != null) + { + progress.setProgressBar(null, this.hashCode()); + } + } + }).start(); + } + + public static WsParamSetManager wsparamManager = null; + + public static ParamManager getUserParameterStore() + { + if (wsparamManager == null) + { + wsparamManager = new WsParamSetManager(); + } + return wsparamManager; + } + + /** + * static hyperlink handler proxy method for use by Jalview's internal windows + * + * @param e + */ + public static void hyperlinkUpdate(HyperlinkEvent e) + { + if (e.getEventType() == EventType.ACTIVATED) + { + String url = null; + try + { + url = e.getURL().toString(); + Desktop.showUrl(url); + } catch (Exception x) + { + if (url != null) + { + if (Cache.log != null) + { + Cache.log.error("Couldn't handle string " + url + " as a URL."); + } + else + { + System.err.println("Couldn't handle string " + url + + " as a URL."); + } + } + // ignore any exceptions due to dud links. + } + + } + } + + /** + * single thread that handles display of dialogs to user. + */ + ExecutorService dialogExecutor = Executors.newSingleThreadExecutor(); + + /** + * flag indicating if dialogExecutor should try to acquire a permit + */ + private volatile boolean dialogPause = true; + + /** + * pause the queue + */ + private java.util.concurrent.Semaphore block = new Semaphore(0); + + /** + * add another dialog thread to the queue + * + * @param prompter + */ + public void addDialogThread(final Runnable prompter) + { + dialogExecutor.submit(new Runnable() + { + public void run() + { + if (dialogPause) + { + try + { + block.acquire(); + } catch (InterruptedException x) + { + } + ; + } + if (instance == null) + { + return; + } + try + { + SwingUtilities.invokeAndWait(prompter); + } catch (Exception q) + { + Cache.log.warn("Unexpected Exception in dialog thread.", q); + } + } + }); + } + + public void startDialogQueue() + { + // set the flag so we don't pause waiting for another permit and semaphore + // the current task to begin + dialogPause = false; + block.release(); } }