X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=300fcc2a1091f0b7bf68625c3f5f7eca7359d5bc;hb=e9aa1cee679000405c5549829ee08e1c08b2ffd5;hp=580fcebd7a10fc6b432dfdf957c14b23ef989ef4;hpb=0c78f4668d4ea1332ddd3bf0eab6065daffb20fc;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java old mode 100755 new mode 100644 index 580fceb..300fcc2 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -18,27 +18,68 @@ package jalview.gui; import jalview.bin.Cache; -import jalview.io.*; +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.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; +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 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.MenuEvent; import javax.swing.event.MenuListener; @@ -47,15 +88,20 @@ import javax.swing.event.MenuListener; * * * @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 { 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) */ @@ -158,6 +204,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void dragFrame(JComponent f, int newX, int newY) { + if (newY<0) + { + newY=0; + } delegate.dragFrame(f, newX, newY); } @@ -194,6 +244,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); } @@ -231,13 +286,19 @@ 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 MyDesktopManager( new DefaultDesktopManager())); + Rectangle dims = getLastKnownDimensions(""); if (dims != null) { @@ -262,6 +323,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); + showNews.setVisible(false); + final Desktop me = this; + // Thread off the news reader, in case there are connection problems. + new Thread( 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."); + } + }).start(); + this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent evt) @@ -270,7 +346,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - this.addMouseListener(new MouseAdapter() + MouseAdapter ma; + this.addMouseListener(ma=new MouseAdapter() { public void mousePressed(MouseEvent evt) { @@ -280,7 +357,26 @@ 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() @@ -323,6 +419,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + 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(); + } + } + } + /** * recover the last known dimensions for a jalview window * @@ -577,6 +699,47 @@ 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); @@ -589,6 +752,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements } 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); + } } public void lostOwnership(Clipboard clipboard, Transferable contents) @@ -864,6 +1031,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); jconsole.stopConsole(); } + if (jvnews!=null) + { + storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + + } + System.exit(0); } @@ -887,30 +1060,77 @@ 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, - if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( - jalview.bin.Cache.getProperty("VERSION"))) + message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + } + + public StringBuffer getAboutMessage(boolean shortv) + { + StringBuffer message = new StringBuffer(); + message.append(""); + if (shortv) { - message.append("\n\n!! Jalview version " - + jalview.bin.Cache.getProperty("LATEST_VERSION") - + " is available for download from http://www.jalview.org !!\n"); + message.append("

Jalview " + + jalview.bin.Cache.getProperty("VERSION") + + "


"); + message.append("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: Jim Procter, Andrew Waterhouse, 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, + else + { - message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + message.append("Jalview version " + + jalview.bin.Cache.getProperty("VERSION") + + "; last updated: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + } + + 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("
!! Jalview 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; } /** @@ -1132,11 +1352,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { - java.io.File choice = chooser.getSelectedFile(); + 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); @@ -1149,12 +1376,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log .error("Problems whilst trying to save to " + choice.getName(), ex); - JOptionPane.showMessageDialog(this, + JOptionPane.showMessageDialog(me, "Error whilst saving current state to " + choice.getName(), "Couldn't save project", JOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); - + } + }).start(); } } @@ -1212,44 +1440,47 @@ 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); + thisprogress.add(new JLabel(string), BorderLayout.WEST); - progressPanel.add(progressBar, BorderLayout.CENTER); - - 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); @@ -1264,11 +1495,11 @@ 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(); @@ -1408,7 +1639,7 @@ 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++) { @@ -1715,7 +1946,7 @@ 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; @@ -1749,7 +1980,7 @@ 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. @@ -1882,7 +2113,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } } + } + /** + * fixes stacking order after a modal dialog to ensure windows that should be on top actually are + */ + public void relayerWindows() + { + } protected JMenuItem groovyShell; @@ -1944,6 +2182,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements avp.clear(); 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 @@ -1985,7 +2259,8 @@ 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) @@ -1996,13 +2271,13 @@ 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 + JPanel progressPanel = progressBars .remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { @@ -2123,7 +2398,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements // register PCS handler for desktop. discoverer.addPropertyChangeListener(changeSupport); } - if (Cache.getDefault("SHOW_JWS1_SERVICES", true)) + // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely + if (true) { (t0 = new Thread(discoverer)).start(); } @@ -2284,4 +2560,5 @@ public class Desktop extends jalview.jbgui.GDesktop implements return wsparamManager; } + }