X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FDesktop.java;h=7f36f7ffd13c34c8a506fe1c7e6376adc9de119b;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=b8f629abd777405ca4f25b48237a1d6293183f99;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index b8f629a..7f36f7f 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -20,15 +20,22 @@
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
import java.awt.BorderLayout;
@@ -40,6 +47,7 @@ import java.awt.GridLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Toolkit;
+import java.awt.Window;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.ClipboardOwner;
import java.awt.datatransfer.DataFlavor;
@@ -64,10 +72,10 @@ import java.beans.PropertyVetoException;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileOutputStream;
-import java.lang.reflect.Constructor;
import java.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
@@ -113,6 +121,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
private BlogReader jvnews = null;
+ private File projectFile;
+
/**
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
@@ -159,6 +169,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
static final int yOffset = 30;
+ private static AlignFrame currentAlignFrame;
+
public static jalview.ws.jws1.Discoverer discoverer;
public static Object[] jalviewClipboard;
@@ -177,6 +189,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
this.delegate = delegate;
}
+ @Override
public void activateFrame(JInternalFrame f)
{
try
@@ -189,31 +202,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void beginDraggingFrame(JComponent f)
{
delegate.beginDraggingFrame(f);
}
+ @Override
public void beginResizingFrame(JComponent f, int direction)
{
delegate.beginResizingFrame(f, direction);
}
+ @Override
public void closeFrame(JInternalFrame f)
{
delegate.closeFrame(f);
}
+ @Override
public void deactivateFrame(JInternalFrame f)
{
delegate.deactivateFrame(f);
}
+ @Override
public void deiconifyFrame(JInternalFrame f)
{
delegate.deiconifyFrame(f);
}
+ @Override
public void dragFrame(JComponent f, int newX, int newY)
{
if (newY < 0)
@@ -223,40 +242,46 @@ public class Desktop extends jalview.jbgui.GDesktop implements
delegate.dragFrame(f, newX, newY);
}
+ @Override
public void endDraggingFrame(JComponent f)
{
delegate.endDraggingFrame(f);
}
+ @Override
public void endResizingFrame(JComponent f)
{
delegate.endResizingFrame(f);
}
+ @Override
public void iconifyFrame(JInternalFrame f)
{
delegate.iconifyFrame(f);
}
+ @Override
public void maximizeFrame(JInternalFrame f)
{
delegate.maximizeFrame(f);
}
+ @Override
public void minimizeFrame(JInternalFrame f)
{
delegate.minimizeFrame(f);
}
+ @Override
public void openFrame(JInternalFrame f)
{
delegate.openFrame(f);
}
+ @Override
public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
int newHeight)
{
- Rectangle b = desktop.getBounds();
if (newY < 0)
{
newY = 0;
@@ -264,6 +289,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
}
+ @Override
public void setBoundsForFrame(JComponent f, int newX, int newY,
int newWidth, int newHeight)
{
@@ -286,7 +312,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
instance = this;
doVamsasClientCheck();
- doGroovyCheck();
+
+ groovyShell = new JMenuItem();
+ groovyShell.setText(MessageManager.getString("label.groovy_console"));
+ groovyShell.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ groovyShell_actionPerformed();
+ }
+ });
+ toolsMenu.add(groovyShell);
+ groovyShell.setVisible(true);
+
doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
@@ -295,6 +334,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
boolean showjconsole = jalview.bin.Cache.getDefault(
"SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
+ if (Platform.isAMac())
+ {
+ desktop.setDoubleBuffered(false);
+ }
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
@@ -327,8 +370,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
+ jalview.bin.Cache.getProperty("VERSION") + "\n"
+ "Jalview Installation: "
+ jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
- + "\n"
- + "Build Date: "
+ + "\n" + "Build Date: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ "Java version: " + System.getProperty("java.version") + "\n"
+ System.getProperty("os.arch") + " "
@@ -341,6 +383,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
quit();
@@ -350,9 +393,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
MouseAdapter ma;
this.addMouseListener(ma = new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
{
showPasteMenu(evt.getX(), evt.getY());
}
@@ -382,6 +426,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// Spawn a thread that shows the splashscreen
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
new SplashScreen();
@@ -393,10 +438,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// takes to open it later on.
new Thread(new Runnable()
{
+ @Override
public void run()
{
Cache.log.debug("Filechooser init thread started.");
- JalviewFileChooser chooser = new JalviewFileChooser(
+ new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
jalview.io.AppletFormatAdapter.READABLE_FNAMES,
@@ -429,9 +475,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW,
- true));
+ ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
+ Preferences.STRUCT_FROM_PDB, true));
+ ssm.setSecStructServices(jalview.bin.Cache.getDefault(
+ Preferences.USE_RNAVIEW, true));
}
else
{
@@ -459,6 +506,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
});
}
+ @Override
protected void showNews_actionPerformed(ActionEvent e)
{
showNews(showNews.isSelected());
@@ -476,10 +524,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
@Override
public void run()
{
- long instance = System.currentTimeMillis();
- Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance);
+ long now = System.currentTimeMillis();
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, instance);
+ Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
}
}).start();
@@ -561,16 +610,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// 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)
@@ -591,6 +643,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
paste();
@@ -613,7 +666,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
String file = (String) contents
.getTransferData(DataFlavor.stringFlavor);
- String format = new IdentifyFile().Identify(file,
+ String format = new IdentifyFile().identify(file,
FormatAdapter.PASTE);
new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
@@ -645,7 +698,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
addInternalFrame(frame, title, true, w, h, true);
}
-
/**
* Add an internal frame to the Jalview desktop
*
@@ -739,8 +791,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setFrameIcon(null);
-
+ if (Platform.isAMac())
+ {
+ frame.setIconifiable(false);
+ frame.setFrameIcon(null);
+ // frame.setDesktopIcon(null);
+ frame.setDoubleBuffered(false);
+ }
if (frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount, yOffset
@@ -750,6 +807,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
final JMenuItem menuItem = new JMenuItem(title);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameActivated(
javax.swing.event.InternalFrameEvent evt)
{
@@ -761,6 +819,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -778,6 +837,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
try
@@ -850,6 +910,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void lostOwnership(Clipboard clipboard, Transferable contents)
{
if (!internalCopy)
@@ -860,18 +921,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements
internalCopy = false;
}
+ @Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+ @Override
public void dragExit(DropTargetEvent evt)
{
}
+ @Override
public void dragOver(DropTargetDragEvent evt)
{
}
+ @Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
@@ -882,6 +947,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
@@ -954,7 +1020,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
else
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
new FileLoader().LoadFile(file, protocol, format);
@@ -975,6 +1041,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
JalviewFileChooser chooser = new JalviewFileChooser(
@@ -1004,7 +1071,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
else
{
- format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+ format = new IdentifyFile().identify(choice, FormatAdapter.FILE);
}
if (viewport != null)
@@ -1025,6 +1092,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
// This construct allows us to have a wider textfield
@@ -1079,12 +1147,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
else
{
- String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+ String format = new IdentifyFile().identify(url, FormatAdapter.URL);
if (format.equals("URL NOT FOUND"))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.url_not_found"),
+ MessageManager.formatMessage("label.couldnt_locate",
+ new Object[] { url }), MessageManager
+ .getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -1102,15 +1172,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
/**
- * DOCUMENT ME!
+ * Opens the CutAndPaste window for the user to paste an alignment in to
*
- * @param e
- * DOCUMENT ME!
+ * @param viewPanel
+ * - if not null, the pasted alignment is added to the current
+ * alignment; if null, to a new alignment window
*/
- public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+ @Override
+ public void inputTextboxMenuItem_actionPerformed(
+ AlignmentViewPanel viewPanel)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(viewport);
+ cap.setForInput(viewPanel);
Desktop.addInternalFrame(cap,
MessageManager.getString("label.cut_paste_alignmen_file"),
true, 600, 500);
@@ -1119,6 +1192,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/*
* Exit the program
*/
+ @Override
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
@@ -1143,7 +1217,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
dialogExecutor.shutdownNow();
}
-
+ closeAll_actionPerformed(null);
System.exit(0);
}
@@ -1165,6 +1239,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
// StringBuffer message = getAboutMessage(false);
@@ -1173,6 +1248,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
+ @Override
public void run()
{
new SplashScreen(true);
@@ -1187,8 +1263,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (shortv)
{
message.append("
Version: "
- + jalview.bin.Cache.getProperty("VERSION")
- + "
");
+ + jalview.bin.Cache.getProperty("VERSION") + "");
message.append("Last Updated: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "");
@@ -1234,8 +1309,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
message.append("
Authors: "
+ jalview.bin.Cache
- .getDefault(
- "AUTHORFNAMES",
+ .getDefault("AUTHORFNAMES",
"The Jalview Authors (See AUTHORS file for current list)")
+ "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
+ "
For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
@@ -1253,6 +1327,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
public void documentationMenuItem_actionPerformed(ActionEvent e)
{
try
@@ -1263,6 +1338,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void closeAll_actionPerformed(ActionEvent e)
{
JInternalFrame[] frames = desktop.getAllFrames();
@@ -1279,15 +1355,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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
+ * when all windows are closed)
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (ssm != null)
+ {
+ ssm.resetAll();
}
}
+ @Override
public void raiseRelated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(false, false);
}
+ @Override
public void minimizeAssociated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(true, false);
@@ -1304,6 +1392,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
@@ -1319,6 +1408,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
desktop.showMemoryUsage(showMemusage.isSelected());
@@ -1331,6 +1421,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showConsole_actionPerformed(ActionEvent e)
{
showConsole(showConsole.isSelected());
@@ -1360,7 +1451,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return;
}
- AlignViewport source = null, target = null;
+ AlignmentViewport source = null, target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
@@ -1435,6 +1526,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void preferences_actionPerformed(ActionEvent e)
{
new Preferences();
@@ -1446,12 +1538,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "jvp" }, new String[] { "Jalview Project" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
@@ -1462,20 +1555,24 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
final Desktop me = this;
final java.io.File choice = chooser.getSelectedFile();
+ setProjectFile(choice);
+
new Thread(new Runnable()
{
+ @Override
public void run()
{
-
- setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{choice.getName()}),
- choice.hashCode());
+ // TODO: refactor to Jalview desktop session controller action.
+ setProgressBar(MessageManager.formatMessage(
+ "label.saving_jalview_project",
+ new Object[] { 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);
+ new Jalview2XML().saveState(choice);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst saving current state to "
@@ -1485,10 +1582,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JOptionPane.showMessageDialog(
- me,
- MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new String[]{ choice.getName()}),
- MessageManager.getString("label.couldnt_save_project"),
+ JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[] { choice.getName() }), MessageManager
+ .getString("label.couldnt_save_project"),
JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
@@ -1497,19 +1594,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ private void setProjectFile(File choice)
+ {
+ this.projectFile = choice;
+ }
+
+ public File getProjectFile()
+ {
+ return this.projectFile;
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
public void loadState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp", "jar" }, new String[]
- { "Jalview Project", "Jalview Project (old)" },
- "Jalview Project");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+ "jvp", "jar" }, new String[] { "Jalview Project",
+ "Jalview Project (old)" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
@@ -1517,18 +1624,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- final String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ final File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ selectedFile.getParent());
new Thread(new Runnable()
{
+ @Override
public void run()
{
- setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{choice}),
- choice.hashCode());
+ setProgressBar(
+ MessageManager.formatMessage(
+ "label.loading_jalview_project",
+ new Object[] { choice }), choice.hashCode());
try
{
- new Jalview2XML().LoadJalviewAlign(choice);
+ new Jalview2XML().loadJalviewAlign(choice);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst loading project from " + choice, oom);
@@ -1536,9 +1648,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}),
- MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[] { choice }), MessageManager
+ .getString("label.couldnt_load_project"),
+ JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
@@ -1546,6 +1661,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void inputSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
@@ -1559,7 +1675,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (fileLoadingCount == 0)
{
- fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName})));
+ fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
+ "label.loading_file", new Object[] { fileName })));
}
fileLoadingCount++;
}
@@ -1625,38 +1742,38 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public static int getViewCount(String alignmentId)
{
- AlignViewport[] aps = getViewports(alignmentId);
+ AlignmentViewport[] aps = getViewports(alignmentId);
return (aps == null) ? 0 : aps.length;
}
/**
*
* @param alignmentId
+ * - if null, all sets are returned
* @return all AlignmentPanels concerning the alignmentId sequence set
*/
public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
- int count = 0;
if (Desktop.desktop == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
return null;
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- ArrayList aps = new ArrayList();
- for (int t = 0; t < frames.length; t++)
+ List aps = new ArrayList();
+ AlignFrame[] frames = getAlignFrames();
+ if (frames == null)
+ {
+ return null;
+ }
+ for (AlignFrame af : frames)
{
- if (frames[t] instanceof AlignFrame)
+ for (AlignmentPanel ap : af.alignPanels)
{
- AlignFrame af = (AlignFrame) frames[t];
- for (int a = 0; a < af.alignPanels.size(); a++)
+ if (alignmentId == null
+ || alignmentId.equals(ap.av.getSequenceSetId()))
{
- if (alignmentId.equals(((AlignmentPanel) af.alignPanels
- .elementAt(a)).av.getSequenceSetId()))
- {
- aps.add(af.alignPanels.elementAt(a));
- }
+ aps.add(ap);
}
}
}
@@ -1664,11 +1781,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
return null;
}
- AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
- for (int t = 0; t < vap.length; t++)
- {
- vap[t] = (AlignmentPanel) aps.get(t);
- }
+ AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
return vap;
}
@@ -1676,52 +1789,53 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* get all the viewports on an alignment.
*
* @param sequenceSetId
- * unique alignment id
+ * unique alignment id (may be null - all viewports returned in that
+ * case)
* @return all viewports on the alignment bound to sequenceSetId
*/
- public static AlignViewport[] getViewports(String sequenceSetId)
+ public static AlignmentViewport[] getViewports(String sequenceSetId)
{
- Vector viewp = new Vector();
+ List viewp = new ArrayList();
if (desktop != null)
{
- javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+ AlignFrame[] frames = Desktop.getAlignFrames();
- for (int t = 0; t < frames.length; t++)
+ for (AlignFrame afr : frames)
{
- if (frames[t] instanceof AlignFrame)
+ if (sequenceSetId == null
+ || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
{
- AlignFrame afr = ((AlignFrame) frames[t]);
- if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
+ if (afr.alignPanels != null)
{
- if (afr.alignPanels != null)
+ for (AlignmentPanel ap : afr.alignPanels)
{
- for (int a = 0; a < afr.alignPanels.size(); a++)
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
{
- if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels
- .elementAt(a)).av.getSequenceSetId()))
- {
- viewp.addElement(((AlignmentPanel) afr.alignPanels
- .elementAt(a)).av);
- }
+ viewp.add(ap.av);
}
}
- else
- {
- viewp.addElement(((AlignFrame) frames[t]).getViewport());
- }
+ }
+ else
+ {
+ viewp.add(afr.getViewport());
}
}
}
if (viewp.size() > 0)
{
- AlignViewport[] vp = new AlignViewport[viewp.size()];
- viewp.copyInto(vp);
- return vp;
+ return viewp.toArray(new AlignmentViewport[viewp.size()]);
}
}
return null;
}
+ /**
+ * Explode the views in the given frame into separate AlignFrame
+ *
+ * @param af
+ */
public void explodeViews(AlignFrame af)
{
int size = af.alignPanels.size();
@@ -1732,15 +1846,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
for (int i = 0; i < size; i++)
{
- AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
+ AlignmentPanel ap = af.alignPanels.get(i);
AlignFrame newaf = new AlignFrame(ap);
- if (ap.av.explodedPosition != null
- && !ap.av.explodedPosition.equals(af.getBounds()))
+
+ /*
+ * Restore the view's last exploded frame geometry if known. Multiple
+ * views from one exploded frame share and restore the same (frame)
+ * position and size.
+ */
+ Rectangle geometry = ap.av.getExplodedGeometry();
+ if (geometry != null)
{
- newaf.setBounds(ap.av.explodedPosition);
+ newaf.setBounds(geometry);
}
- ap.av.gatherViewsHere = false;
+ ap.av.setGatherViewsHere(false);
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
@@ -1751,10 +1871,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
+ /**
+ * Gather expanded views (separate AlignFrame's) with the same sequence set
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
+ *
+ * @param source
+ */
public void gatherViews(AlignFrame source)
{
- source.viewport.gatherViewsHere = true;
- source.viewport.explodedPosition = source.getBounds();
+ source.viewport.setGatherViewsHere(true);
+ source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
@@ -1766,12 +1894,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
boolean gatherThis = false;
for (int a = 0; a < af.alignPanels.size(); a++)
{
- AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+ AlignmentPanel ap = af.alignPanels.get(a);
if (viewId.equals(ap.av.getSequenceSetId()))
{
gatherThis = true;
- ap.av.gatherViewsHere = false;
- ap.av.explodedPosition = af.getBounds();
+ ap.av.setGatherViewsHere(false);
+ ap.av.setExplodedGeometry(af.getBounds());
source.addAlignmentPanel(ap, false);
}
}
@@ -1788,6 +1916,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
jalview.gui.VamsasApplication v_client = null;
+ @Override
public void vamsasImport_actionPerformed(ActionEvent e)
{
if (v_client == null)
@@ -1797,7 +1926,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.open_saved_vamsas_session"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_saved_vamsas_session"));
chooser.setToolTipText(MessageManager
.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
@@ -1813,8 +1943,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
Desktop.desktop,
MessageManager.formatMessage(
"label.couldnt_import_as_vamsas_session",
- new String[]
- { fle }),
+ new Object[] { fle }),
MessageManager
.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
@@ -1890,23 +2019,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return false;
}
- setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
- file.hashCode());
+ 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 String[]{file.getName()}),
- file.hashCode());
+ 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 String[]{file.getName()}),
- file.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from",
+ new Object[] { file.getName() }), file.hashCode());
return v_client.inSession();
}
@@ -1914,11 +2046,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (v_client != null)
{
- throw new Error(MessageManager.getString("error.try_join_vamsas_session_another"));
+ throw new Error(
+ MessageManager
+ .getString("error.try_join_vamsas_session_another"));
}
if (mysesid == null)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_session_id"));
+ throw new Error(
+ MessageManager.getString("error.invalid_vamsas_session_id"));
}
v_client = new VamsasApplication(this, mysesid);
setupVamsasConnectedGui();
@@ -1926,6 +2061,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return (v_client.inSession());
}
+ @Override
public void vamsasStart_actionPerformed(ActionEvent e)
{
if (v_client == null)
@@ -1974,6 +2110,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
.getString("label.new_vamsas_session"));
}
+ @Override
public void vamsasStop_actionPerformed(ActionEvent e)
{
if (v_client != null)
@@ -2008,13 +2145,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
sessit.setToolTipText(MessageManager.formatMessage(
- "label.connect_to_session", new String[]
- { sess[i] }));
+ "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)
@@ -2022,6 +2159,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
Thread rthr = new Thread(new Runnable()
{
+ @Override
public void run()
{
dsktp.v_client = new VamsasApplication(dsktp, mysesid);
@@ -2054,6 +2192,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void vamsasSave_actionPerformed(ActionEvent e)
{
if (v_client != null)
@@ -2061,18 +2200,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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");
+ new String[] { "Vamsas Document" }, "Vamsas Document");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_vamsas_document_archive"));
+ 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 String[]{choice.getName()}));
+ JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
+ "label.saving_vamsas_doc",
+ new Object[] { choice.getName() }));
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
@@ -2124,7 +2265,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
if (b)
{
- vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session"));
+ vamUpdate = this.addProgressPanel(MessageManager
+ .getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
@@ -2159,6 +2301,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public class MyDesktopPane extends JDesktopPane implements Runnable
{
+ private static final float ONE_MB = 1048576f;
+
boolean showMemoryUsage = false;
Runtime runtime;
@@ -2173,10 +2317,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
showMemoryUsage(showMemoryUsage);
}
- public void showMemoryUsage(boolean showMemoryUsage)
+ public void showMemoryUsage(boolean showMemory)
{
- this.showMemoryUsage = showMemoryUsage;
- if (showMemoryUsage)
+ this.showMemoryUsage = showMemory;
+ if (showMemory)
{
Thread worker = new Thread(this);
worker.start();
@@ -2188,6 +2332,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return showMemoryUsage;
}
+ @Override
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
@@ -2198,9 +2343,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
try
{
- maxMemory = runtime.maxMemory() / 1048576f;
- allocatedMemory = runtime.totalMemory() / 1048576f;
- freeMemory = runtime.freeMemory() / 1048576f;
+ maxMemory = runtime.maxMemory() / ONE_MB;
+ allocatedMemory = runtime.totalMemory() / ONE_MB;
+ freeMemory = runtime.freeMemory() / ONE_MB;
totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
percentUsage = (totalFreeMemory / maxMemory) * 100;
@@ -2221,6 +2366,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ @Override
public void paintComponent(Graphics g)
{
if (showMemoryUsage && g != null && df != null)
@@ -2234,9 +2380,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
g.drawString(MessageManager.formatMessage(
"label.memory_stats",
- new String[]
- { df.format(totalFreeMemory), df.format(maxMemory),
- df.format(percentUsage) }), 10,
+ new Object[] { df.format(totalFreeMemory),
+ df.format(maxMemory), df.format(percentUsage) }), 10,
getHeight() - fm.getHeight());
}
}
@@ -2254,65 +2399,63 @@ public class Desktop extends jalview.jbgui.GDesktop implements
protected JMenuItem groovyShell;
- public void doGroovyCheck()
- {
- if (jalview.bin.Cache.groovyJarsPresent())
- {
- groovyShell = new JMenuItem();
- groovyShell.setText(MessageManager.getString("label.groovy_console"));
- groovyShell.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groovyShell_actionPerformed(e);
- }
- });
- toolsMenu.add(groovyShell);
- groovyShell.setVisible(true);
- }
- }
-
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
+ *
+ * @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignframes()
+ public static AlignFrame[] getAlignFrames()
{
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { currentAlignFrame };
+ }
+
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
{
return null;
}
- Vector avp = new Vector();
- try
+ List avp = new ArrayList();
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
{
- // REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ if (frames[i] instanceof AlignFrame)
{
- if (frames[i] instanceof AlignFrame)
+ avp.add((AlignFrame) frames[i]);
+ }
+ else if (frames[i] instanceof SplitFrame)
+ {
+ /*
+ * Also check for a split frame containing an AlignFrame
+ */
+ GSplitFrame sf = (GSplitFrame) frames[i];
+ if (sf.getTopFrame() instanceof AlignFrame)
{
- AlignFrame af = (AlignFrame) frames[i];
- avp.addElement(af);
+ avp.add((AlignFrame) sf.getTopFrame());
+ }
+ if (sf.getBottomFrame() instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) sf.getBottomFrame());
}
}
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
if (avp.size() == 0)
{
return null;
}
- AlignFrame afs[] = new AlignFrame[avp.size()];
- for (int i = 0, j = avp.size(); i < j; i++)
- {
- afs[i] = (AlignFrame) avp.elementAt(i);
- }
- avp.clear();
+ AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
return afs;
}
- public AppJmol[] getJmols()
+ /**
+ * Returns an array of any AppJmol frames in the Desktop (or null if none).
+ *
+ * @return
+ */
+ public GStructureViewer[] getJmols()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2320,68 +2463,99 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
return null;
}
- Vector avp = new Vector();
- try
+ List avp = new ArrayList();
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
{
- // REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ if (frames[i] instanceof AppJmol)
{
- if (frames[i] instanceof AppJmol)
- {
- AppJmol af = (AppJmol) frames[i];
- avp.addElement(af);
- }
+ GStructureViewer af = (GStructureViewer) frames[i];
+ avp.add(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();
+ GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
return afs;
}
/**
* Add Groovy Support to Jalview
*/
- public void groovyShell_actionPerformed(ActionEvent e)
+ public void groovyShell_actionPerformed()
{
- // use reflection to avoid creating compilation dependency.
- if (!jalview.bin.Cache.groovyJarsPresent())
- {
- throw new Error(MessageManager.getString("error.implementation_error_cannot_create_groovyshell"));
- }
try
{
- Class gcClass = Desktop.class.getClassLoader().loadClass(
- "groovy.ui.Console");
- Constructor gccons = gcClass.getConstructor(null);
- java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
- new Class[]
- { String.class, Object.class });
- java.lang.reflect.Method run = gcClass.getMethod("run", null);
- Object gc = gccons.newInstance(null);
- setvar.invoke(gc, new Object[]
- { "Jalview", this });
- run.invoke(gc, null);
+ openGroovyConsole();
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * Open the Groovy console
+ */
+ void openGroovyConsole()
+ {
+ groovyConsole = new groovy.ui.Console();
+
+ /*
+ * bind groovy variable 'Jalview' to the Desktop object
+ */
+ groovyConsole.setVariable("Jalview", this);
+
+ /*
+ * start the console
+ */
+ groovyConsole.run();
+
+ /*
+ * Allow only one console at a time, so that the AlignFrame menu option
+ * 'Calculate | Run Groovy script' is unambiguous.
+ * Disable 'new console', and enable 'Run script', when the console is
+ * opened, and the reverse when it is closed
+ */
+ Window window = (Window) groovyConsole.getFrame();
+ window.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ groovyShell.setEnabled(true);
+ enableExecuteGroovy(false);
+ }
+ });
- MessageManager.getString("label.couldnt_create_groovy_shell"),
- MessageManager.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ /*
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus
+ * and disable opening a second console
+ */
+ groovyShell.setEnabled(false);
+ enableExecuteGroovy(true);
+ }
+
+ /**
+ * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
+ *
+ * @param enabled
+ */
+ public void enableExecuteGroovy(boolean enabled)
+ {
+ AlignFrame[] alignFrames = getAlignFrames();
+ if (alignFrames != null)
+ {
+ for (AlignFrame af : alignFrames)
+ {
+ af.setGroovyEnabled(enabled);
+ }
}
}
@@ -2397,6 +2571,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
if (progressBars == null)
@@ -2407,12 +2582,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (progressBars.get(new Long(id)) != null)
{
- JPanel progressPanel = progressBars.remove(new Long(id));
+ JPanel panel = progressBars.remove(new Long(id));
if (progressBarHandlers.contains(new Long(id)))
{
progressBarHandlers.remove(new Long(id));
}
- removeProgressPanel(progressPanel);
+ removeProgressPanel(panel);
}
else
{
@@ -2426,12 +2601,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* @see jalview.gui.IProgressIndicator#registerHandler(long,
* jalview.gui.IProgressIndicatorHandler)
*/
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
- if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ if (progressBarHandlers == null
+ || !progressBars.containsKey(new Long(id)))
{
- throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ throw new Error(
+ MessageManager
+ .getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = progressBars.get(new Long(id));
@@ -2443,10 +2622,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ us.setProgressBar(MessageManager.formatMessage(
+ "label.cancelled_params",
+ new Object[] { ((JLabel) progressPanel.getComponent(0))
+ .getText() }), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
@@ -2468,20 +2651,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
/**
- * This will return the first AlignFrame viewing AlignViewport av. It will
- * break if there are more than one AlignFrames viewing a particular av. This
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
*
- * @param av
- * @return alignFrame for av
+ * @param viewport
+ * @return alignFrame for viewport
*/
- public static AlignFrame getAlignFrameFor(AlignViewport av)
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+ AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
for (int panel = 0; aps != null && panel < aps.length; panel++)
{
- if (aps[panel] != null && aps[panel].av == av)
+ if (aps[panel] != null && aps[panel].av == viewport)
{
return aps[panel].alignFrame;
}
@@ -2545,28 +2729,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
(t0 = new Thread(discoverer)).start();
}
- // ENFIN services are EOLed as of Jalview 2.8.1 release
- if (false)
- {
- 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())
@@ -2619,6 +2781,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// only run if we aren't already displaying one of these.
addDialogThread(serviceChangedDialog = new Runnable()
{
+ @Override
public void run()
{
@@ -2702,23 +2865,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
{
if (progress != null)
{
- progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new String[]{url}), this.hashCode());
+ progress.setProgressBar(MessageManager.formatMessage(
+ "status.opening_params", new Object[] { url }), this
+ .hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
@@ -2790,6 +2955,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
private java.util.concurrent.Semaphore block = new Semaphore(0);
+ private static groovy.ui.Console groovyConsole;
+
/**
* add another dialog thread to the queue
*
@@ -2799,6 +2966,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
dialogExecutor.submit(new Runnable()
{
+ @Override
public void run()
{
if (dialogPause)
@@ -2833,6 +3001,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
dialogPause = false;
block.release();
}
+
@Override
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
@@ -2841,15 +3010,184 @@ public class Desktop extends jalview.jbgui.GDesktop implements
ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
"View of Desktop", getWidth(), getHeight(), of = new File(
"Jalview_snapshot" + System.currentTimeMillis()
- + ".eps"), "View of desktop");
- try {
+ + ".eps"), "View of desktop", null, 0, false);
+ try
+ {
paintAll(im.getGraphics());
im.writeImage();
} catch (Exception q)
{
- Cache.log.error("Couldn't write snapshot to "+of.getAbsolutePath(),q);
+ Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
+ q);
+ return;
+ }
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+
+ /**
+ * Explode the views in the given SplitFrame into separate SplitFrame windows.
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
+ * remember the split pane divider location - this is set to match the
+ * 'exploding' frame.
+ *
+ * @param sf
+ */
+ public void explodeViews(SplitFrame sf)
+ {
+ AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
+ List extends AlignmentViewPanel> topPanels = oldTopFrame
+ .getAlignPanels();
+ List extends AlignmentViewPanel> bottomPanels = oldBottomFrame
+ .getAlignPanels();
+ int viewCount = topPanels.size();
+ if (viewCount < 2)
+ {
return;
}
- Cache.log.info("Successfully written snapshot to file "+of.getAbsolutePath());
+
+ /*
+ * Processing in reverse order works, forwards order leaves the first panels
+ * not visible. I don't know why!
+ */
+ for (int i = viewCount - 1; i >= 0; i--)
+ {
+ /*
+ * Make new top and bottom frames. These take over the respective
+ * AlignmentPanel objects, including their AlignmentViewports, so the
+ * cdna/protein relationships between the viewports is carried over to the
+ * new split frames.
+ *
+ * explodedGeometry holds the (x, y) position of the previously exploded
+ * SplitFrame, and the (width, height) of the AlignFrame component
+ */
+ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
+ AlignFrame newTopFrame = new AlignFrame(topPanel);
+ newTopFrame.setSize(oldTopFrame.getSize());
+ newTopFrame.setVisible(true);
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newTopFrame.setSize(geometry.getSize());
+ }
+
+ AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
+ AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
+ newBottomFrame.setSize(oldBottomFrame.getSize());
+ newBottomFrame.setVisible(true);
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newBottomFrame.setSize(geometry.getSize());
+ }
+
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+ newBottomFrame);
+ if (geometry != null)
+ {
+ splitFrame.setLocation(geometry.getLocation());
+ }
+ Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ }
+
+ /*
+ * Clear references to the panels (now relocated in the new SplitFrames)
+ * before closing the old SplitFrame.
+ */
+ topPanels.clear();
+ bottomPanels.clear();
+ sf.close();
}
+
+ /**
+ * Gather expanded split frames, sharing the same pairs of sequence set ids,
+ * back into the given SplitFrame as additional views. Note that the gathered
+ * frames may themselves have multiple views.
+ *
+ * @param source
+ */
+ public void gatherViews(GSplitFrame source)
+ {
+ /*
+ * special handling of explodedGeometry for a view within a SplitFrame: - it
+ * holds the (x, y) position of the enclosing SplitFrame, and the (width,
+ * height) of the AlignFrame component
+ */
+ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
+ AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
+ myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myBottomFrame.getWidth(), myBottomFrame
+ .getHeight()));
+ myTopFrame.viewport.setGatherViewsHere(true);
+ myBottomFrame.viewport.setGatherViewsHere(true);
+ String topViewId = myTopFrame.viewport.getSequenceSetId();
+ String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
+
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof SplitFrame && frame != source)
+ {
+ SplitFrame sf = (SplitFrame) frame;
+ AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
+ boolean gatherThis = false;
+ for (int a = 0; a < topFrame.alignPanels.size(); a++)
+ {
+ AlignmentPanel topPanel = topFrame.alignPanels.get(a);
+ AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
+ if (topViewId.equals(topPanel.av.getSequenceSetId())
+ && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
+ topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(new Rectangle(sf
+ .getLocation(), bottomFrame.getSize()));
+ myTopFrame.addAlignmentPanel(topPanel, false);
+ myBottomFrame.addAlignmentPanel(bottomPanel, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ topFrame.getAlignPanels().clear();
+ bottomFrame.getAlignPanels().clear();
+ sf.close();
+ }
+ }
+ }
+
+ /*
+ * The dust settles...give focus to the tab we did this from.
+ */
+ myTopFrame.setDisplayedView(myTopFrame.alignPanel);
+
+ }
+
+ public static AlignFrame getCurrentAlignFrame()
+ {
+ return currentAlignFrame;
+ }
+
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+ {
+ Desktop.currentAlignFrame = currentAlignFrame;
+ }
+
+ public static groovy.ui.Console getGroovyConsole()
+ {
+ return groovyConsole;
+ }
+
}