Merge branch 'develop' into feature/JAL-2422ChimeraX

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3d1442d..89a912f 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -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
       {
@@ -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)
         {
@@ -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)
     {
@@ -658,7 +658,7 @@ 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);
@@ -669,7 +669,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize.width,
+        jmb.jmolViewer.renderScreenImage(g, currentSize.width,
                 currentSize.height);
       }
     }
@@ -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)