JAL-1807 explicit imports (jalview.appletgui)

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 32465c1..c981104 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -48,7 +49,6 @@ 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;
@@ -61,6 +61,7 @@ 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;
 
 public class AppletJmol extends EmbmenuFrame implements
@@ -130,7 +131,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
-  ArrayList _aps = new ArrayList();
+  List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+                                                               // added to
 
   String fileLoadingError;
 
@@ -196,7 +198,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
 
-    if (jalview.bin.JalviewLite.debug)
+    if (JalviewLite.debug)
     {
       System.err
               .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
@@ -280,7 +282,7 @@ public class AppletJmol extends EmbmenuFrame implements
       dispose();
       return;
     }
-    jmb.newJmolPopup(true, "Jmol", true);
+    // jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -317,7 +319,7 @@ public class AppletJmol extends EmbmenuFrame implements
           java.io.Reader freader = null;
           if (reader != null)
           {
-            if (jalview.bin.JalviewLite.debug)
+            if (JalviewLite.debug)
             {
               System.err
                       .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
@@ -327,7 +329,7 @@ public class AppletJmol extends EmbmenuFrame implements
           }
           if (freader == null)
           {
-            if (jalview.bin.JalviewLite.debug)
+            if (JalviewLite.debug)
             {
               System.err
                       .println("AppletJmol:Creating new PDBfile IO parser.");
@@ -361,7 +363,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
 
-    jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
+    JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
   }
 
   public void loadInline(String string)
@@ -370,7 +372,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector chains)
+  void setChainMenuItems(Vector<String> chains)
   {
     chainMenu.removeAll();
 
@@ -380,10 +382,9 @@ 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 +394,7 @@ 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)
@@ -421,7 +420,7 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     if (evt.getSource() == mappingMenuItem)
     {
-      jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(
               false, null);
       Frame frame = new Frame();
       frame.add(cap);
@@ -429,12 +428,7 @@ public class AppletJmol extends EmbmenuFrame implements
       StringBuffer sb = new StringBuffer();
       try
       {
-        for (int s = 0; s < jmb.getPdbCount(); s++)
-        {
-          sb.append(jmb.printMapping(jmb.getPdbEntry(s).getFile()));
-          sb.append("\n");
-        }
-        cap.setText(sb.toString());
+        cap.setText(jmb.printMappings());
       } catch (OutOfMemoryError ex)
       {
         frame.dispose();
@@ -442,7 +436,7 @@ public class AppletJmol extends EmbmenuFrame implements
                 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("label.pdb_sequence_mapping"), 550,
               600);
     }
@@ -552,7 +546,7 @@ 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)
     {
@@ -581,8 +575,8 @@ 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()
@@ -593,7 +587,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -648,8 +642,6 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     Dimension currentSize = new Dimension();
 
-    Rectangle rectClip = new Rectangle();
-
     public void update(Graphics g)
     {
       paint(g);
@@ -658,7 +650,6 @@ public class AppletJmol extends EmbmenuFrame implements
     public void paint(Graphics g)
     {
       currentSize = this.getSize();
-      rectClip = g.getClipBounds();
 
       if (jmb.viewer == null)
       {
@@ -671,7 +662,8 @@ public class AppletJmol extends EmbmenuFrame implements
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize.width,
+                currentSize.height);
       }
     }
   }
@@ -703,9 +695,9 @@ 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;