import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.dnd.DropTargetListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.concurrent.Semaphore;
import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
+import javax.swing.InputMap;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import org.stackoverflowusers.file.WindowsShortcut;
+
/**
* Jalview Desktop
*
setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
900, 650);
}
- jconsole = new Console(this, showjconsole);
- // add essential build information
- jconsole.setHeader(
- "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
- + "\n" + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION",
- "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "\n" + "Java version: "
- + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
-
- showConsole(showjconsole);
-
- showNews.setVisible(false);
+ /**
+ * BH 2018
+ *
+ * @j2sNative
+ */
+ {
- experimentalFeatures.setSelected(showExperimental());
+ jconsole = new Console(this, showjconsole);
+ // add essential build information
+ jconsole.setHeader("Jalview Version: "
+ + jalview.bin.Cache.getProperty("VERSION") + "\n"
+ + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
+ + "\n" + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ + "Java version: " + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
- getIdentifiersOrgData();
+ showConsole(showjconsole);
- checkURLLinks();
+ showNews.setVisible(false);
- this.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent evt)
- {
- quit();
- }
- });
+ experimentalFeatures.setSelected(showExperimental());
- MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
+ getIdentifiersOrgData();
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
- });
- desktop.addMouseListener(ma);
+ checkURLLinks();
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
// Spawn a thread that shows the splashscreen
+
SwingUtilities.invokeLater(new Runnable()
{
@Override
}
});
+
+ } // end BH 2018 ignore
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
+
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ });
+ desktop.addMouseListener(ma);
+
}
/**
public void checkForNews()
{
+
+ /**
+ * BH 2018
+ *
+ * @j2sNative
+ */
+ {
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.");
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Starting news thread.");
- jvnews = new BlogReader(me);
- showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
- }
+ jvnews = new BlogReader(me);
+ showNews.setVisible(true);
+ Cache.log.debug("Completed news thread.");
+ }
});
+ }
}
public void getIdentifiersOrgData()
void showNews(boolean visible)
{
+ /**
+ * BH 2018
+ *
+ * @j2sNative
+ *
+ */
{
Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
private void doVamsasClientCheck()
{
- if (jalview.bin.Cache.vamsasJarsPresent())
+ if (/** @j2sNative false && */ // BH 2018
+ jalview.bin.Cache.vamsasJarsPresent())
{
setupVamsasDisconnectedGui();
VamsasMenu.setVisible(true);
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setOpaque(false);
+ frame.setOpaque(/** @j2sNative true || */
+ false);
if (frame.getX() < 1 && frame.getY() < 1)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
-
- System.gc();
};
});
}
});
+ setKeyBindings(frame);
+
desktop.add(frame);
windowMenu.add(menuItem);
}
}
+ /**
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+ * the window
+ *
+ * @param frame
+ */
+ private static void setKeyBindings(JInternalFrame frame)
+ {
+ @SuppressWarnings("serial")
+ final Action closeAction = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ frame.dispose();
+ }
+ };
+
+ /*
+ * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
+ */
+ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ InputEvent.CTRL_DOWN_MASK);
+ KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+
+ InputMap inputMap = frame
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+ String ctrlW = ctrlWKey.toString();
+ inputMap.put(ctrlWKey, ctrlW);
+ inputMap.put(cmdWKey, ctrlW);
+
+ ActionMap actionMap = frame.getActionMap();
+ actionMap.put(ctrlW, closeAction);
+ }
+
@Override
public void lostOwnership(Clipboard clipboard, Transferable contents)
{
// for viewing
JLabel label = new JLabel(
MessageManager.getString("label.input_file_url"));
- final JComboBox history = new JComboBox();
+ JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
panel.add(history);
}
}
- int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString("label.input_alignment_from_url"),
- JvOptionPane.OK_CANCEL_OPTION);
+ // BH 2018 -- providing a callback for SwingJS
+ // dialogOption is just a simple way to provide
+ // context for the modal-like response.
+ // The only requirement is that desktop implement
+ // PropertyChangeListener, which is used already in Java
+ // for changes in input value and such within the dialogs.
- if (reply != JvOptionPane.OK_OPTION)
- {
- return;
- }
-
- String url = history.getSelectedItem().toString();
-
- if (url.toLowerCase().endsWith(".jar"))
- {
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- }
- else
- {
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
- {
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
+ String dialogOption = "label.input_alignment_from_url";
+ desktop.dialogData = new Object[] { dialogOption, viewport, history };
+ desktop.onDialogReturn(
+ JvOptionPane.showInternalConfirmDialog(desktop, panel,
+ MessageManager.getString(dialogOption),
+ JvOptionPane.OK_CANCEL_OPTION));
- if (format == null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate",
- new Object[]
- { url }),
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ // no code may follow this, as SwingJS will not block
+ // callback in JavaScript comes via a property change event,
+ // thus going into desktop.onDialogReturn(int) just the same as
+ // in Java.
- return;
- }
-
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
- }
- }
}
+
/**
* Opens the CutAndPaste window for the user to paste an alignment in to
*
{
ssm.resetAll();
}
- System.gc();
}
@Override
*/
void showConsole(boolean selected)
{
- showConsole.setSelected(selected);
// TODO: decide if we should update properties file
- Cache.setProperty("SHOW_JAVA_CONSOLE",
- Boolean.valueOf(selected).toString());
- jconsole.setVisible(selected);
+ if (jconsole != null) // BH 2018
+ {
+ showConsole.setSelected(selected);
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
+ jconsole.setVisible(selected);
+ }
}
void reorderAssociatedWindows(boolean minimize, boolean close)
@Override
public void run()
{
- if (Cache.getDefault("CHECKURLLINKS", true))
+ if (/** @j2sNative false && */ // BH 2018
+ Cache.getDefault("CHECKURLLINKS", true))
{
// check what the actual links are - if it's just the default don't
// bother with the warning
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane implements Runnable
+ public class MyDesktopPane extends JDesktopPane
+ implements Runnable, PropertyChangeListener
{
+ public Object[] dialogData;
+
+ // @Override
+ @Override
+ public void propertyChange(PropertyChangeEvent event)
+ {
+ Object val = event.getNewValue();
+ String name = event.getPropertyName();
+ System.out.println(name);
+ switch (event.getSource().getClass().getName())
+ {
+ case "javax.swing.JOptionPane":
+ switch (name)
+ {
+ case "inputValue":
+ onDialogReturn(val);
+ return;
+ case "value":
+ if (val instanceof Integer)
+ {
+ onDialogReturn(((Integer) val).intValue());
+ }
+ else
+ {
+ onDialogReturn(val);
+ }
+ return;
+ }
+ break;
+ case "javax.swing.ColorChooserDialog":
+ switch (name)
+ {
+ case "SelectedColor":
+ onDialogReturn(val);
+ return;
+ }
+ break;
+ case "javax.swing.JFileChooser":
+ switch (name)
+ {
+ case "SelectedFile":
+ File file = (File) val;
+ byte[] array = (val == null ? null
+ : /** @j2sNative file._bytes || */
+ null);
+ onDialogReturn("fileName is '" + file.getName() + "'\n\n"
+ + new String(array));
+ return;
+ }
+ break;
+ }
+ System.out.println(event.getSource().getClass().getName() + " "
+ + event.getPropertyName() + ": " + event.getNewValue());
+ }
+
+ // JSCOmponent.DialogCaller interface
+ private void onDialogReturn(Object value)
+ {
+ System.out.println("not implemented");
+ }
+
+ // JSCOmponent.DialogCaller interface
+ void onDialogReturn(int value)
+ {
+ if (value != Math.floor(value))
+ {
+ // in JavaScript, this will be NaN, oddly enough
+ return;
+ }
+
+ switch ((String) dialogData[0])
+ {
+ case "label.input_alignment_from_url":
+ // reconstruct the parameter data
+ int reply = value;
+ AlignViewport viewport = (AlignViewport) dialogData[1];
+ JComboBox history = (JComboBox) dialogData[2];
+ // the rest of this is unchangaed
+ if (reply != JvOptionPane.OK_OPTION)
+ {
+ return;
+ }
+
+ String url = history.getSelectedItem().toString();
+
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
+
+ if (format == null)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.couldnt_locate",
+ new Object[]
+ { url }),
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL, format);
+ }
+ }
+
+ break;
+ }
+
+ }
+
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
return groovyConsole;
}
+ /**
+ * handles the payload of a drag and drop event.
+ *
+ * TODO refactor to desktop utilities class
+ *
+ * @param files
+ * - Data source strings extracted from the drop event
+ * @param protocols
+ * - protocol for each data source extracted from the drop event
+ * @param evt
+ * - the drop event
+ * @param t
+ * - the payload from the drop event
+ * @throws Exception
+ */
public static void transferFromDropTarget(List<String> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
+ "text/uri-list;class=java.lang.String"), urlFlavour = null;
+ try
+ {
+ urlFlavour = new DataFlavor(
+ "application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cfe)
+ {
+ Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ }
+
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+ {
+
+ try
+ {
+ java.net.URL url = (URL) t.getTransferData(urlFlavour);
+ // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
+ // means url may be null.
+ if (url != null)
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(url.toString());
+ Cache.log.debug("Drop handled as URL dataflavor "
+ + files.get(files.size() - 1));
+ return;
+ }
+ else
+ {
+ if (Platform.isAMac())
+ {
+ System.err.println(
+ "Please ignore plist error - occurs due to problem with java 8 on OSX");
+ }
+ ;
+ }
+ } catch (Throwable ex)
+ {
+ Cache.log.debug("URL drop handler failed.", ex);
+ }
+ }
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
// Works on Windows and MacOSX
// fallback to text: workaround - on OSX where there's a JVM bug
Cache.log.debug("standard URIListFlavor failed. Trying text");
// try text fallback
- data = (String) t.getTransferData(
- new DataFlavor("text/plain;class=java.lang.String"));
- if (Cache.log.isDebugEnabled())
+ DataFlavor textDf = new DataFlavor(
+ "text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf))
{
- Cache.log.debug("fallback returned " + data);
+ data = (String) t.getTransferData(textDf);
}
+
+ Cache.log.debug("Plain text drop content returned "
+ + (data == null ? "Null - failed" : data));
+
}
- while (protocols.size() < files.size())
- {
- Cache.log.debug("Adding missing FILE protocol for "
- + files.get(protocols.size()));
- protocols.add(DataSourceType.FILE);
- }
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
+ if (data != null)
{
- added = true;
- String s = st.nextToken();
- if (s.startsWith("#"))
+ while (protocols.size() < files.size())
{
- // the line is a comment (as per the RFC 2483)
- continue;
- }
- java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
- protocols.add(DataSourceType.URL);
- files.add(uri.toString());
+ Cache.log.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
+ protocols.add(DataSourceType.FILE);
}
- else
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
{
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- protocols.add(DataSourceType.FILE);
- files.add(file.toString());
+ added = true;
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+ java.net.URI uri = new java.net.URI(s);
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(DataSourceType.FILE);
+ files.add(file.toString());
+ }
}
}
+
if (Cache.log.isDebugEnabled())
{
if (data == null || !added)
{
- Cache.log.debug(
- "Couldn't resolve drop data. Here are the supported flavors:");
- for (DataFlavor fl : t.getTransferDataFlavors())
+
+ if (t.getTransferDataFlavors() != null
+ && t.getTransferDataFlavors().length > 0)
{
Cache.log.debug(
- "Supported transfer dataflavor: " + fl.toString());
- Object df = t.getTransferData(fl);
- if (df != null)
- {
- Cache.log.debug("Retrieves: " + df);
- }
- else
+ "Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug("Retrieved nothing");
+ Cache.log.debug(
+ "Supported transfer dataflavor: " + fl.toString());
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ Cache.log.debug("Retrieves: " + df);
+ }
+ else
+ {
+ Cache.log.debug("Retrieved nothing");
+ }
}
}
+ else
+ {
+ Cache.log.debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
+ }
+ }
+ }
+ }
+ if (Platform.isWindows())
+
+ {
+ Cache.log.debug("Scanning dropped content for Windows Link Files");
+
+ // resolve any .lnk files in the file drop
+ for (int f = 0; f < files.size(); f++)
+ {
+ String source = files.get(f).toLowerCase();
+ if (protocols.get(f).equals(DataSourceType.FILE)
+ && (source.endsWith(".lnk") || source.endsWith(".url")
+ || source.endsWith(".site")))
+ {
+ try {
+ File lf = new File(files.get(f));
+ // process link file to get a URL
+ Cache.log.debug("Found potential link file: " + lf);
+ WindowsShortcut wscfile = new WindowsShortcut(lf);
+ String fullname = wscfile.getRealFilename();
+ protocols.set(f, FormatAdapter.checkProtocol(fullname));
+ files.set(f, fullname);
+ Cache.log.debug("Parsed real filename " + fullname
+ + " to extract protocol: " + protocols.get(f));
+ }
+ catch (Exception ex)
+ {
+ Cache.log.error("Couldn't parse "+files.get(f)+" as a link file.",ex);
+ }
}
}
}
Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
}
+ /**
+ * Answers a (possibly empty) list of any structure viewer frames (currently
+ * for either Jmol or Chimera) which are currently open. This may optionally
+ * be restricted to viewers of a specified class, or viewers linked to a
+ * specified alignment panel.
+ *
+ * @param apanel
+ * if not null, only return viewers linked to this panel
+ * @param structureViewerClass
+ * if not null, only return viewers of this class
+ * @return
+ */
public List<StructureViewerBase> getStructureViewers(
AlignmentPanel apanel,
Class<? extends StructureViewerBase> structureViewerClass)
if (structureViewerClass == null
|| structureViewerClass.isInstance(frame))
{
- if (apanel == null
- || ((StructureViewerBase) frame).isLinkedWith(apanel))
- {
- result.add((StructureViewerBase) frame);
- }
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
}
}
}