*/
package jalview.gui;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.UrlConstants;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.KeyEvent;
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.File;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.ListIterator;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Semaphore;
import javax.swing.AbstractAction;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
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.HyperlinkEvent.EventType;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
+ private static int DEFAULT_MIN_WIDTH = 300;
+
+ private static int DEFAULT_MIN_HEIGHT = 250;
+
+ private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
instance = this;
doVamsasClientCheck();
- 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);
showConsole(showjconsole);
showNews.setVisible(false);
+
+ experimentalFeatures.setSelected(showExperimental());
+
+ getIdentifiersOrgData();
+
+ checkURLLinks();
this.addWindowListener(new WindowAdapter()
{
@Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isPopupTrigger())
+ if (evt.isPopupTrigger()) // Mac
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
{
showPasteMenu(evt.getX(), evt.getY());
}
}
});
- // displayed.
// Thread off a new instance of the file chooser - this reduces the time it
// takes to open it later on.
new Thread(new Runnable()
Cache.log.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- // jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
- // jalview.io.AppletFormatAdapter.READABLE_FNAMES,
- fileFormat, true);
+ fileFormat);
Cache.log.debug("Filechooser init thread finished.");
}
}).start();
});
}
+ /**
+ * Answers true if user preferences to enable experimental features is True
+ * (on), else false
+ *
+ * @return
+ */
+ public boolean showExperimental()
+ {
+ String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+ Boolean.FALSE.toString());
+ return Boolean.valueOf(experimental).booleanValue();
+ }
+
public void doConfigureStructurePrefs()
{
// configure services
});
}
+ public void getIdentifiersOrgData()
+ {
+ // Thread off the identifiers fetcher
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Downloading data from identifiers.org");
+ UrlDownloadClient client = new UrlDownloadClient();
+ try
+ {
+ client.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ Cache.log.debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
+ }
+ });
+ }
+
@Override
protected void showNews_actionPerformed(ActionEvent e)
{
openFrameCount++;
+ frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
+ DEFAULT_MIN_HEIGHT));
frame.setVisible(makeVisible);
frame.setClosable(true);
frame.setResizable(resizable);
* ((openFrameCount - 1) % 10) + yOffset);
}
+ /*
+ * add an entry for the new frame in the Window menu
+ * (and remove it when the frame is closed)
+ */
final JMenuItem menuItem = new JMenuItem(title);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameActivated(
- javax.swing.event.InternalFrameEvent evt)
+ public void internalFrameActivated(InternalFrameEvent evt)
{
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
itf.requestFocus();
}
-
}
@Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ public void internalFrameClosed(InternalFrameEvent evt)
{
PaintRefresher.RemoveComponent(frame);
- openFrameCount--;
+
+ /*
+ * defensive check to prevent frames being
+ * added half off the window
+ */
+ if (openFrameCount > 0)
+ {
+ openFrameCount--;
+ }
+
+ /*
+ * ensure no reference to alignFrame retained by menu item listener
+ */
+ if (menuItem.getActionListeners().length > 0)
+ {
+ menuItem.removeActionListener(menuItem.getActionListeners()[0]);
+ }
windowMenu.remove(menuItem);
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
itf.requestFocus();
+ if (itf instanceof AlignFrame)
+ {
+ Jalview.setCurrentAlignFrame((AlignFrame) itf);
+ }
}
System.gc();
};
}
}
});
- 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)
- {
-
- }
- });
+ desktop.add(frame);
windowMenu.add(menuItem);
- desktop.add(frame);
frame.toFront();
try
{
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
List<String> files = new ArrayList<String>();
List<DataSourceType> protocols = new ArrayList<DataSourceType>();
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"),
- // AppletFormatAdapter.READABLE_EXTENSIONS,
- // AppletFormatAdapter.READABLE_FNAMES,
- fileFormat, true);
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
- FileFormatI format = null;
- if (chooser.getSelectedFormat() != null
- && chooser.getSelectedFormat() == FileFormat.Jalview)
- {
- format = FileFormat.Jalview;
- }
- else
+ FileFormatI format = chooser.getSelectedFormat();
+
+ /*
+ * Call IdentifyFile to verify the file contains what its extension implies.
+ * Skip this step for dynamically added file formats, because
+ * IdentifyFile does not know how to recognise them.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
{
try
{
format = new IdentifyFile().identify(choice, DataSourceType.FILE);
} catch (FileFormatException e)
{
- // format is null
+ // format = null; //??
}
}
*
* @param e
* DOCUMENT ME!
- * @throws FileFormatException
*/
@Override
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
- // throws FileFormatException
{
// This construct allows us to have a wider textfield
// for viewing
}
}
- int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+ int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
MessageManager.getString("label.input_alignment_from_url"),
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (reply != JOptionPane.OK_OPTION)
+ if (reply != JvOptionPane.OK_OPTION)
{
return;
}
if (format == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new Object[] { url }), MessageManager
.getString("label.url_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
// StringBuffer message = getAboutMessage(false);
- // JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
//
- // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
@Override
@Override
public void closeAll_actionPerformed(ActionEvent e)
{
+ // TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
{
}
}
+ Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
if (v_client != null)
{
{
ssm.resetAll();
}
+ System.gc();
}
@Override
@Override
public void saveState_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project",
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
"Jalview Project");
chooser.setFileView(new JalviewFileView());
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
+ JvOptionPane.showMessageDialog(me, MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
new Object[] { choice.getName() }), MessageManager
.getString("label.couldnt_save_project"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
{
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage(
"label.error_whilst_loading_project_from",
new Object[] { choice }), MessageManager
.getString("label.couldnt_load_project"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager.formatMessage(
new Object[] { fle }),
MessageManager
.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
{
if (v_client != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "vdj",
- "Vamsas Document", "Vamsas Document");
+ // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ JalviewFileChooser chooser = new JalviewFileChooser("vdj",
+ "Vamsas Document");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
removeProgressPanel(progpanel);
if (warnmsg != null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
*/
public void setVamsasUpdate(boolean b)
{
- jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+ Cache.log.debug("Setting gui for Vamsas update "
+ (b ? "in progress" : "finished"));
if (vamUpdate != null)
new Thread(jvq).start();
}
+ public void checkURLLinks()
+ {
+ // Thread off the URL link checker
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (Cache.getDefault("CHECKURLLINKS", true))
+ {
+ // check what the actual links are - if it's just the default don't
+ // bother with the warning
+ List<String> links = Preferences.sequenceUrlLinks
+ .getLinksForMenu();
+
+ // only need to check links if there is one with a
+ // SEQUENCE_ID which is not the default EMBL_EBI link
+ ListIterator<String> li = links.listIterator();
+ boolean check = false;
+ List<JLabel> urls = new ArrayList<JLabel>();
+ while (li.hasNext())
+ {
+ String link = li.next();
+ if (link.contains(SEQUENCE_ID)
+ && !link.equals(UrlConstants.DEFAULT_STRING))
+ {
+ check = true;
+ int barPos = link.indexOf("|");
+ String urlMsg = barPos == -1 ? link : link.substring(0,
+ barPos) + ": " + link.substring(barPos + 1);
+ urls.add(new JLabel(urlMsg));
+ }
+ }
+ if (!check)
+ {
+ return;
+ }
+
+ // ask user to check in case URL links use old style tokens
+ // ($SEQUENCE_ID$ for sequence id _or_ accession id)
+ JPanel msgPanel = new JPanel();
+ msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
+ msgPanel.add(Box.createVerticalGlue());
+ JLabel msg = new JLabel(
+ MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(
+ MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ msgPanel.add(msg);
+ for (JLabel url : urls)
+ {
+ msgPanel.add(url);
+ }
+ msgPanel.add(msg2);
+
+ final JCheckBox jcb = new JCheckBox(
+ MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // update Cache settings for "don't show this again"
+ boolean showWarningAgain = !jcb.isSelected();
+ Cache.setProperty("CHECKURLLINKS",
+ Boolean.valueOf(showWarningAgain).toString());
+ }
+ });
+ msgPanel.add(jcb);
+
+ JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ MessageManager
+ .getString("label.SEQUENCE_ID_no_longer_used"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ }
+
/**
* Proxy class for JDesktopPane which optionally displays the current memory
* usage and highlights the desktop area with a red bar if free memory runs
}
- protected JMenuItem groovyShell;
-
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
*
/**
* Add Groovy Support to Jalview
*/
+ @Override
public void groovyShell_actionPerformed()
{
try
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
{
getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()),
- "Quit");
+ .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
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;
{
*
* jd.waitForInput();
*/
- JOptionPane
+ JvOptionPane
.showConfirmDialog(
Desktop.desktop,
new JLabel(
+ "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ " Tools->Preferences dialog box to change them.</p></html>"),
"Web Service Configuration Problem",
- JOptionPane.DEFAULT_OPTION,
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
{
// Works on Windows and MacOSX
Cache.log.debug("Drop handled as javaFileListFlavor");
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
- files.add(((File)file).toString());
+ files.add(((File) file).toString());
protocols.add(DataSourceType.FILE);
}
}
{
Cache.log.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null)
{
Cache.log.debug("Supported transfer dataflavor: "
+ fl.toString());
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Object df = t.getTransferData(fl);
if (df != null)
{
}
}
}
+
+ /**
+ * Sets the Preferences property for experimental features to True or False
+ * depending on the state of the controlling menu item
+ */
+ @Override
+ protected void showExperimental_actionPerformed(boolean selected)
+ {
+ Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
+ }
}
git://source.jalview.org / jalview.git / blobdiff