X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=d7e830582f4385b28c8be6970737154369554ae8;hb=c3b8fbc19c04c2daec702a2bffdfab5d10555143;hp=28d2c6438bdd1159668f5b707133534c024a1a35;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 28d2c64..d7e8305 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -67,7 +66,6 @@ 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;
@@ -79,6 +77,9 @@ 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 +129,7 @@ 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 +299,7 @@ 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 +310,10 @@ 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
@@ -381,10 +380,7 @@ 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 +392,12 @@ 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 +505,7 @@ 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 +522,13 @@ 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;
       }
     }
@@ -1071,7 +1028,7 @@ 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)