X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=bdd8c4b7b5141351b1612cb0f378d49577c2100e;hb=500bc57b2d6901ff09f6b1511289f85ba9dec823;hp=1c0dfe6c2e534bddc3d733588bfdc9542c17e5a0;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 1c0dfe6..bdd8c4b 100644
--- 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;
@@ -67,8 +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;
 import javax.swing.SwingUtilities;
@@ -131,7 +128,7 @@ 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);
@@ -166,7 +163,7 @@ public class AppJmol extends StructureViewerBase
         closeViewer(false);
       }
     });
-    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!ˇ
 
   }
 
@@ -249,6 +246,11 @@ public class AppJmol extends StructureViewerBase
 
   IProgressIndicator progressBar = null;
 
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return progressBar;
+  }
   /**
    * add a single PDB structure to a new or existing Jmol view
    * 
@@ -301,7 +303,7 @@ 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)
@@ -394,57 +396,12 @@ 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++)
@@ -722,11 +679,11 @@ 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;
   }
@@ -1075,7 +1032,7 @@ 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)