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.FocusEvent;
-import java.awt.event.FocusListener;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import org.stackoverflowusers.file.WindowsShortcut;
+
/**
* Jalview Desktop
*
new MyDesktopManager(
(Platform.isWindows() ? new DefaultDesktopManager()
: Platform.isAMac()
- ? new AquaInternalFrameManager()
+ ? new AquaInternalFrameManager(
+ desktop.getDesktopManager())
: desktop.getDesktopManager())));
Rectangle dims = getLastKnownDimensions("");
});
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()
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
+ frame.setOpaque(false);
if (frame.getX() < 1 && frame.getY() < 1)
{
JInternalFrame itf = desktop.getSelectedFrame();
if (itf != null)
{
+ if (itf instanceof AlignFrame)
+ {
+ Jalview.setCurrentAlignFrame((AlignFrame) itf);
+ }
itf.requestFocus();
}
}
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();
};
});
{
String link = li.next();
if (link.contains(SEQUENCE_ID)
- && !link.equals(UrlConstants.DEFAULT_STRING))
+ && !UrlConstants.isDefaultString(link))
{
check = true;
int barPos = link.indexOf("|");
}
}
- /**
- * fixes stacking order after a modal dialog to ensure windows that should be
- * on top actually are
- */
- public void relayerWindows()
- {
-
- }
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
{
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
new DataFlavor("text/plain;class=java.lang.String"));
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("fallback returned " + data);
+ Cache.log.debug("Plain text drop content returned " + data);
}
}
while (protocols.size() < files.size())
files.add(file.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++)
+ {
+ if (protocols.get(f).equals(DataSourceType.FILE)) {
+ File lf = new File(files.get(f));
+ if (WindowsShortcut.isPotentialValidLink(lf)) {
+ // 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));
+ }
+ }
+ }
+ }
+
if (Cache.log.isDebugEnabled())
{
if (data == null || !added)
{
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)
+ {
+ List<StructureViewerBase> result = new ArrayList<>();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ if (structureViewerClass == null
+ || structureViewerClass.isInstance(frame))
+ {
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
+ }
+ }
+ }
+ return result;
+ }
}