JAL-2358 ensure mappings removed on close Chimera; pull up method;

[jalview.git] / src / jalview / gui / AppJmol.java

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 24604ed..a30f6d3 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -50,7 +50,6 @@ import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.io.BufferedReader;
@@ -65,10 +64,7 @@ import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
-import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -79,6 +75,9 @@ import javax.swing.event.MenuListener;
 
 public class AppJmol extends StructureViewerBase
 {
+  // ms to wait for Jmol to load files
+  private static final int JMOL_LOAD_TIMEOUT = 20000;
+
   private static final String SPACE = " ";
 
   private static final String BACKSLASH = "\"";
@@ -128,7 +127,7 @@ public class AppJmol extends StructureViewerBase
     // / TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
-            pdbentrys, seqs, null, null);
+            pdbentrys, seqs, null);
 
     jmb.setLoadingFromArchive(true);
     addAlignmentPanel(ap);
@@ -298,7 +297,7 @@ public class AppJmol extends StructureViewerBase
   {
     progressBar = ap.alignFrame;
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
-            pdbentrys, seqs, null, null);
+            pdbentrys, seqs, null);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
     if (pdbentrys.length > 1)
@@ -309,12 +308,10 @@ public class AppJmol extends StructureViewerBase
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
-    worker = null;
-    {
-      addingStructures = false;
-      worker = new Thread(this);
-      worker.start();
-    }
+    addingStructures = false;
+    worker = new Thread(this);
+    worker.start();
+
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -339,30 +336,6 @@ public class AppJmol extends StructureViewerBase
     openNewJmol(ap, pe, seqs);
   }
 
-  /**
-   * Returns a list of any Jmol viewers. The list is restricted to those linked
-   * to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
-  {
-    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof AppJmol)
-      {
-        if (apanel == null
-                || ((StructureViewerBase) frame).isLinkedWith(apanel))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
-
   void initJmol(String command)
   {
     jmb.setFinishedInit(false);
@@ -381,10 +354,7 @@ public class AppJmol extends StructureViewerBase
       scriptWindow.setVisible(false);
     }
 
-    /*
-     * -i for no info logging (less verbose)
-     */
-    jmb.allocateViewer(renderPanel, true, "", null, null, "-i",
+    jmb.allocateViewer(renderPanel, true, "", null, null, "",
             scriptWindow, null);
     // jmb.newJmolPopup("Jmol");
     if (command == null)
@@ -396,57 +366,12 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  void setChainMenuItems(Vector<String> chains)
-  {
-    chainMenu.removeAll();
-    if (chains == null)
-    {
-      return;
-    }
-    JMenuItem menuItem = new JMenuItem(
-            MessageManager.getString("label.all"));
-    menuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent evt)
-      {
-        allChainsSelected = true;
-        for (int i = 0; i < chainMenu.getItemCount(); i++)
-        {
-          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-          {
-            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
-          }
-        }
-        centerViewer();
-        allChainsSelected = false;
-      }
-    });
-
-    chainMenu.add(menuItem);
 
-    for (String chain : chains)
-    {
-      menuItem = new JCheckBoxMenuItem(chain, true);
-      menuItem.addItemListener(new ItemListener()
-      {
-        @Override
-        public void itemStateChanged(ItemEvent evt)
-        {
-          if (!allChainsSelected)
-          {
-            centerViewer();
-          }
-        }
-      });
-
-      chainMenu.add(menuItem);
-    }
-  }
 
   boolean allChainsSelected = false;
 
-  void centerViewer()
+  @Override
+  void showSelectedChains()
   {
     Vector<String> toshow = new Vector<String>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
@@ -554,7 +479,7 @@ public class AppJmol extends StructureViewerBase
     }
 
     // need to wait around until script has finished
-    int waitMax = 5000; // give up after 5 seconds
+    int waitMax = JMOL_LOAD_TIMEOUT;
     int waitFor = 35;
     int waitTotal = 0;
     while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
@@ -571,7 +496,13 @@ public class AppJmol extends StructureViewerBase
       }
       if (waitTotal > waitMax)
       {
-        System.err.println("Timed out waiting for Jmol to load files");
+        System.err
+                .println("Timed out waiting for Jmol to load files after "
+                        + waitTotal + "ms");
+//        System.err.println("finished: " + jmb.isFinishedInit()
+//                + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+//                + "; files: " + files.toString());
+        jmb.getPdbFile();
         break;
       }
     }
@@ -718,11 +649,11 @@ public class AppJmol extends StructureViewerBase
     }
     if (errormsgs.length() > 0)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
                       new String[] { errormsgs.toString() }),
               MessageManager.getString("label.couldnt_load_file"),
-              JOptionPane.ERROR_MESSAGE);
+              JvOptionPane.ERROR_MESSAGE);
     }
     return files;
   }
@@ -1071,7 +1002,7 @@ public class AppJmol extends StructureViewerBase
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
 
     this.setTitle(jmb.getViewerTitle());
     if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)