X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=0e1811dd527ab824b9d849060d083d8d0c260c6f;hb=06faf90ba52bfcdc4547a68cb3df86c14a5c6e05;hp=5f45dc1fbff0e07f175b3bf516a2d4992d2f7393;hpb=f27f81a74bbe1be141d23df8aba578515e3179a2;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 5f45dc1..0e1811d 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,6 +20,22 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+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.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -84,22 +100,6 @@ import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-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.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-
 /**
  * Jalview Desktop
  * 
@@ -169,6 +169,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private static final int THREE = 3;
 
+  private static AlignFrame currentAlignFrame;
+
   public static jalview.ws.jws1.Discoverer discoverer;
 
   public static Object[] jalviewClipboard;
@@ -263,10 +265,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       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;
@@ -1022,6 +1024,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
                 format);
+        // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled());
+        // AlignFrame af = viewport.getAlignPanel().alignFrame;
+        // if (af != null)
+        // {
+        // af.changeColour(JSONFile.getColourScheme());
+        // af.setMenusForViewport();
+        // }
       }
       else
       {
@@ -1124,7 +1133,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    cap.setForInput(viewport);
+//    cap.setForInput(viewport.getAlignPanel());
+    cap.setForInput(null);
     Desktop.addInternalFrame(cap,
             MessageManager.getString("label.cut_paste_alignmen_file"),
             true, 600, 500);
@@ -1157,7 +1167,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       dialogExecutor.shutdownNow();
     }
-
+    closeAll_actionPerformed(null);
     System.exit(0);
   }
 
@@ -1291,7 +1301,17 @@ 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();
     }
   }
 
@@ -1476,9 +1496,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       final java.io.File choice = chooser.getSelectedFile();
       setProjectFile(choice);
 
-      // TODO or move inside the new Thread?
-      saveChimeraSessions(choice.getAbsolutePath());
-
       new Thread(new Runnable()
       {
         public void run()
@@ -1516,32 +1533,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
   }
 
-  /**
-   * Request any open, linked Chimera sessions to save their state.
-   * 
-   * @param jalviewProjectFilename
-   *          the filename of the Jalview project; Chimera session files should
-   *          be given distinct, but obviously related, names.
-   */
-  public void saveChimeraSessions(String jalviewProjectFilename)
-  {
-    int i = 0;
-    for (JInternalFrame frame : getAllFrames())
-    {
-      if (frame instanceof ChimeraViewFrame)
-      {
-        /*
-         * Construct a filename for the Chimera session by append _chimera<n>.py
-         * to the Jalview project file name.
-         */
-        String chimeraPath = jalviewProjectFilename + "_chimera_" + i
-                + ".py";
-        ((ChimeraViewFrame) frame).saveSession(chimeraPath);
-        i++;
-      }
-    }
-  }
-
   private void setProjectFile(File choice)
   {
     this.projectFile = choice;
@@ -2306,6 +2297,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
 
+    @Override
     public void paintComponent(Graphics g)
     {
       if (showMemoryUsage && g != null && df != null)
@@ -2513,7 +2505,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   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
@@ -2635,28 +2628,6 @@ 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())
@@ -3073,4 +3044,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     myTopFrame.setDisplayedView(myTopFrame.alignPanel);
 
   }
+
+  // public static AlignFrame getCurrentAlignFrame()
+  // {
+  // return currentAlignFrame;
+  // }
+  //
+  // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  // {
+  // Desktop.currentAlignFrame = currentAlignFrame;
+  // }
+
+
 }