Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 44a73d9..f73ff88 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,25 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-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;
@@ -64,6 +45,25 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+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
@@ -307,7 +307,7 @@ public class AppletJmol extends EmbmenuFrame implements
       else if (protocol == DataSourceType.FILE
               || protocol == DataSourceType.URL)
       {
-        jmb.viewer.openFile(pdbentry.getFile());
+        jmb.jmolViewer.openFile(pdbentry.getFile());
       }
       else
       {
@@ -335,7 +335,7 @@ public class AppletJmol extends EmbmenuFrame implements
             }
             FileParse fp = new FileParse(pdbentry.getFile(), protocol);
             fp.mark();
-            // reader = new MCview.PDBfile(fp);
+            // reader = new mc_view.PDBfile(fp);
             // could set ID, etc.
             // if (!reader.isValid())
             // {
@@ -350,7 +350,7 @@ public class AppletJmol extends EmbmenuFrame implements
             throw new Exception(MessageManager.getString(
                     "exception.invalid_datasource_couldnt_obtain_reader"));
           }
-          jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
+          jmb.jmolViewer.openReader(pdbentry.getFile(), pdbentry.getId(),
                   freader);
         } catch (Exception e)
         {
@@ -394,7 +394,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void centerViewer()
   {
-    Vector<String> toshow = new Vector<>();
+    Vector<String> toHide = new Vector<>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -402,17 +402,17 @@ public class AppletJmol extends EmbmenuFrame implements
         CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
         if (!item.getState())
         {
-          toshow.addElement(item.getLabel());
+          toHide.addElement(item.getLabel());
         }
       }
     }
-    jmb.setChainsToHide(toshow);
+    jmb.setChainsToHide(toHide);
     jmb.centerViewer();
   }
 
   void closeViewer()
   {
-    jmb.closeViewer();
+    jmb.closeViewer(true);
     jmb = null;
     this.setVisible(false);
   }
@@ -456,41 +456,41 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == zappo)
     {
       setEnabled(zappo);
-      jmb.setJalviewColourScheme(new ZappoColourScheme());
+      jmb.colourByJalviewColourScheme(new ZappoColourScheme());
     }
     else if (evt.getSource() == taylor)
     {
       setEnabled(taylor);
-      jmb.setJalviewColourScheme(new TaylorColourScheme());
+      jmb.colourByJalviewColourScheme(new TaylorColourScheme());
     }
     else if (evt.getSource() == hydro)
     {
       setEnabled(hydro);
-      jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+      jmb.colourByJalviewColourScheme(new HydrophobicColourScheme());
     }
     else if (evt.getSource() == helix)
     {
       setEnabled(helix);
-      jmb.setJalviewColourScheme(new HelixColourScheme());
+      jmb.colourByJalviewColourScheme(new HelixColourScheme());
     }
     else if (evt.getSource() == strand)
     {
       setEnabled(strand);
-      jmb.setJalviewColourScheme(new StrandColourScheme());
+      jmb.colourByJalviewColourScheme(new StrandColourScheme());
     }
     else if (evt.getSource() == turn)
     {
       setEnabled(turn);
-      jmb.setJalviewColourScheme(new TurnColourScheme());
+      jmb.colourByJalviewColourScheme(new TurnColourScheme());
     }
     else if (evt.getSource() == buried)
     {
       setEnabled(buried);
-      jmb.setJalviewColourScheme(new BuriedColourScheme());
+      jmb.colourByJalviewColourScheme(new BuriedColourScheme());
     }
     else if (evt.getSource() == purinepyrimidine)
     {
-      jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+      jmb.colourByJalviewColourScheme(new PurinePyrimidineColourScheme());
     }
     else if (evt.getSource() == user)
     {
@@ -659,7 +659,7 @@ public class AppletJmol extends EmbmenuFrame implements
     {
       currentSize = this.getSize();
 
-      if (jmb.viewer == null)
+      if (jmb.jmolViewer == null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
@@ -670,7 +670,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize.width,
+        jmb.jmolViewer.renderScreenImage(g, currentSize.width,
                 currentSize.height);
       }
     }
@@ -694,9 +694,9 @@ public class AppletJmol extends EmbmenuFrame implements
    * 
    * }
    */
-  public void setJalviewColourScheme(UserColourScheme ucs)
+  public void colourByJalviewColourScheme(UserColourScheme ucs)
   {
-    jmb.setJalviewColourScheme(ucs);
+    jmb.colourByJalviewColourScheme(ucs);
   }
 
   public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)