JAL-2422 pull-up refactoring of structure commands (continued)

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 2cd9ee5..89a912f 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -406,7 +406,7 @@ public class AppletJmol extends EmbmenuFrame implements
         }
       }
     }
-    jmb.centerViewer(toshow);
+    jmb.showChains(toshow);
   }
 
   void closeViewer()
@@ -455,41 +455,41 @@ 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)
     {
@@ -693,9 +693,9 @@ 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)