JAL-1528 bug fixes and adjustments to Chimera interface

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5d4b910..fcb31eb 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -176,14 +176,14 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
       jmb.setColourBySequence(false);
       seqColour.setSelected(false);
-      jmolColour.setSelected(true);
+      viewerColour.setSelected(true);
     }
     if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
       seqColour.setSelected(true);
-      jmolColour.setSelected(false);
+      viewerColour.setSelected(false);
     }
     this.setBounds(bounds);
     initMenus();
@@ -205,7 +205,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
   private void initMenus()
   {
     seqColour.setSelected(jmb.isColourBySequence());
-    jmolColour.setSelected(!jmb.isColourBySequence());
+    viewerColour.setSelected(!jmb.isColourBySequence());
     if (_colourwith == null)
     {
       _colourwith = new Vector<AlignmentPanel>();
@@ -251,8 +251,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
               }
             });
     handler.itemStateChanged(null);
-    jmolActionMenu.add(alpanels);
-    jmolActionMenu.addMenuListener(new MenuListener()
+    viewerActionMenu.add(alpanels);
+    viewerActionMenu.addMenuListener(new MenuListener()
     {
 
       @Override
@@ -303,8 +303,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
                       "label.pdb_entry_is_already_displayed", new String[]
                       { pdbentry.getId() }), MessageManager.formatMessage(
                       "label.map_sequences_to_visible_window", new String[]
-                      { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
+                      { pdbentry.getId() }),
+              JOptionPane.YES_NO_CANCEL_OPTION);
 
+      if (option == JOptionPane.CANCEL_OPTION)
+      {
+        return;
+      }
       if (option == JOptionPane.YES_OPTION)
       {
         // TODO : Fix multiple seq to one chain issue here.
@@ -366,7 +371,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
                                 { pdbentry.getId(), topJmol.getTitle() }),
                         MessageManager
                                 .getString("label.align_to_existing_structure_view"),
-                        JOptionPane.YES_NO_OPTION);
+                        JOptionPane.YES_NO_CANCEL_OPTION);
+        if (option == JOptionPane.CANCEL_OPTION)
+        {
+          return;
+        }
         if (option == JOptionPane.YES_OPTION)
         {
           topJmol.useAlignmentPanelForSuperposition(ap);
@@ -533,7 +542,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     useAlignmentPanelForColourbyseq(nap);
     jmb.setColourBySequence(enableColourBySeq);
     seqColour.setSelected(enableColourBySeq);
-    jmolColour.setSelected(!enableColourBySeq);
+    viewerColour.setSelected(!enableColourBySeq);
   }
 
   public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
@@ -614,25 +623,22 @@ public class AppJmol extends GStructureViewer implements Runnable,
     return;
   }
 
-  private Vector getJmolsFor(AlignmentPanel ap2)
+  private Vector getJmolsFor(AlignmentPanel apanel)
   {
-    Vector otherJmols = new Vector();
-    // Now this AppJmol is mapped to new sequences. We must add them to
-    // the exisiting array
+    Vector result = new Vector();
     JInternalFrame[] frames = Desktop.instance.getAllFrames();
 
-    for (int i = 0; i < frames.length; i++)
+    for (JInternalFrame frame : frames)
     {
-      if (frames[i] instanceof AppJmol)
+      if (frame instanceof AppJmol)
       {
-        AppJmol topJmol = ((AppJmol) frames[i]);
-        if (topJmol.isLinkedWith(ap2))
+        if (((AppJmol) frame).isLinkedWith(apanel))
         {
-          otherJmols.addElement(topJmol);
+          result.addElement(frame);
         }
       }
     }
-    return otherJmols;
+    return result;
   }
 
   void initJmol(String command)
@@ -927,6 +933,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     worker = null;
   }
 
+  @Override
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -964,6 +971,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
   }
 
+  @Override
   public void viewMapping_actionPerformed(ActionEvent actionEvent)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
@@ -987,23 +995,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
             600);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
+  @Override
   public void eps_actionPerformed(ActionEvent e)
   {
     makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
+  @Override
   public void png_actionPerformed(ActionEvent e)
   {
     makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
@@ -1045,15 +1043,17 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
   }
 
-  public void jmolColour_actionPerformed(ActionEvent actionEvent)
+  @Override
+  public void viewerColour_actionPerformed(ActionEvent actionEvent)
   {
-    if (jmolColour.isSelected())
+    if (viewerColour.isSelected())
     {
       // disable automatic sequence colouring.
       jmb.setColourBySequence(false);
     }
   }
 
+  @Override
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
     jmb.setColourBySequence(seqColour.isSelected());
@@ -1079,71 +1079,83 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
   }
 
+  @Override
   public void chainColour_actionPerformed(ActionEvent actionEvent)
   {
     chainColour.setSelected(true);
     jmb.colourByChain();
   }
 
+  @Override
   public void chargeColour_actionPerformed(ActionEvent actionEvent)
   {
     chargeColour.setSelected(true);
     jmb.colourByCharge();
   }
 
+  @Override
   public void zappoColour_actionPerformed(ActionEvent actionEvent)
   {
     zappoColour.setSelected(true);
     jmb.setJalviewColourScheme(new ZappoColourScheme());
   }
 
+  @Override
   public void taylorColour_actionPerformed(ActionEvent actionEvent)
   {
     taylorColour.setSelected(true);
     jmb.setJalviewColourScheme(new TaylorColourScheme());
   }
 
+  @Override
   public void hydroColour_actionPerformed(ActionEvent actionEvent)
   {
     hydroColour.setSelected(true);
     jmb.setJalviewColourScheme(new HydrophobicColourScheme());
   }
 
+  @Override
   public void helixColour_actionPerformed(ActionEvent actionEvent)
   {
     helixColour.setSelected(true);
     jmb.setJalviewColourScheme(new HelixColourScheme());
   }
 
+  @Override
   public void strandColour_actionPerformed(ActionEvent actionEvent)
   {
     strandColour.setSelected(true);
     jmb.setJalviewColourScheme(new StrandColourScheme());
   }
 
+  @Override
   public void turnColour_actionPerformed(ActionEvent actionEvent)
   {
     turnColour.setSelected(true);
     jmb.setJalviewColourScheme(new TurnColourScheme());
   }
 
+  @Override
   public void buriedColour_actionPerformed(ActionEvent actionEvent)
   {
     buriedColour.setSelected(true);
     jmb.setJalviewColourScheme(new BuriedColourScheme());
   }
 
+  @Override
   public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
   {
     setJalviewColourScheme(new PurinePyrimidineColourScheme());
   }
 
+  @Override
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {
     userColour.setSelected(true);
     new UserDefinedColours(this, null);
   }
 
+  @Override
   public void backGround_actionPerformed(ActionEvent actionEvent)
   {
     java.awt.Color col = JColorChooser.showDialog(this,
@@ -1154,7 +1166,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
   }
 
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  @Override
+  public void showHelp_actionPerformed(ActionEvent actionEvent)
   {
     try
     {
@@ -1274,7 +1287,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     this.setTitle(jmb.getViewerTitle());
     if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
     {
-      jmolActionMenu.setVisible(true);
+      viewerActionMenu.setVisible(true);
     }
     if (!jmb.isLoadingFromArchive())
     {
@@ -1293,11 +1306,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
       _alignwith.add(ap);
     }
     ;
-    for (Component c : jmolActionMenu.getMenuComponents())
+    for (Component c : viewerActionMenu.getMenuComponents())
     {
       if (c != alignStructs)
       {
-        jmolActionMenu.remove((JMenuItem) c);
+        viewerActionMenu.remove((JMenuItem) c);
       }
     }
     final ItemListener handler;