JAL-1807 merge from JAL-1759jmolUpdate

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index f54717d..e889467 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,6 +20,23 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
@@ -31,7 +48,6 @@ import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.MenuItem;
 import java.awt.Panel;
-import java.awt.Rectangle;
 import java.awt.TextArea;
 import java.awt.TextField;
 import java.awt.event.ActionEvent;
@@ -44,25 +60,9 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FileParse;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
         KeyListener, ActionListener, ItemListener
@@ -130,7 +130,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
-  ArrayList _aps = new ArrayList();
+  List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+                                                               // added to
 
   String fileLoadingError;
 
@@ -280,7 +281,7 @@ public class AppletJmol extends EmbmenuFrame implements
       dispose();
       return;
     }
-    jmb.newJmolPopup(true, "Jmol", true);
+    // jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -370,7 +371,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector chains)
+  void setChainMenuItems(Vector<String> chains)
   {
     chainMenu.removeAll();
 
@@ -380,10 +381,9 @@ public class AppletJmol extends EmbmenuFrame implements
     chainMenu.add(menuItem);
 
     CheckboxMenuItem menuItemCB;
-    for (int c = 0; c < chains.size(); c++)
+    for (String ch : chains)
     {
-      menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
-              true);
+      menuItemCB = new CheckboxMenuItem(ch, true);
       menuItemCB.addItemListener(this);
       chainMenu.add(menuItemCB);
     }
@@ -393,9 +393,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void centerViewer()
   {
-    Vector toshow = new Vector();
-    String lbl;
-    int mlength, p, mnum;
+    Vector<String> toshow = new Vector<String>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -547,7 +545,7 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      jmb.colourBySequence(ap);
     }
     else if (!allChainsSelected)
     {
@@ -576,8 +574,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    AlignmentPanel panel = (AlignmentPanel) source;
+    jmb.colourBySequence(panel);
   }
 
   public void updateTitleAndMenus()
@@ -588,7 +586,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -643,8 +641,6 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     Dimension currentSize = new Dimension();
 
-    Rectangle rectClip = new Rectangle();
-
     public void update(Graphics g)
     {
       paint(g);
@@ -653,7 +649,6 @@ public class AppletJmol extends EmbmenuFrame implements
     public void paint(Graphics g)
     {
       currentSize = this.getSize();
-      rectClip = g.getClipBounds();
 
       if (jmb.viewer == null)
       {
@@ -666,7 +661,8 @@ public class AppletJmol extends EmbmenuFrame implements
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize.width,
+                currentSize.height);
       }
     }
   }
@@ -698,9 +694,9 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     for (int i = 0; i < _aps.size(); i++)
     {
-      if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+      if (_aps.get(i).av.getAlignment() == alignment)
       {
-        return ((AlignmentPanel) _aps.get(i));
+        return (_aps.get(i));
       }
     }
     return ap;