JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 49219b9..1ac3abc 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -134,7 +134,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
-  List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+  List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
                                                                // added to
 
   String fileLoadingError;
@@ -213,7 +213,7 @@ public class AppletJmol extends EmbmenuFrame implements
     {
       reader = StructureSelectionManager
               .getStructureSelectionManager(ap.av.applet)
-              .setMapping(seq, chains, pdbentry.getFile(), protocol);
+              .setMapping(seq, chains, pdbentry.getFile(), protocol, null);
       // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
       // FOR NOW, LETS JUST OPEN A NEW WINDOW
     }
@@ -394,7 +394,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void centerViewer()
   {
-    Vector<String> toshow = new Vector<String>();
+    Vector<String> toshow = new Vector<>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -406,7 +406,8 @@ public class AppletJmol extends EmbmenuFrame implements
         }
       }
     }
-    jmb.centerViewer(toshow);
+    jmb.setChainsToShow(toshow);
+    jmb.centerViewer();
   }
 
   void closeViewer()
@@ -548,7 +549,7 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap);
+      jmb.updateStructureColours(ap);
     }
     else if (!allChainsSelected)
     {
@@ -581,7 +582,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel panel = (AlignmentPanel) source;
-    jmb.colourBySequence(panel);
+    jmb.updateStructureColours(panel);
   }
 
   public void updateTitleAndMenus()
@@ -592,7 +593,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.getChainNames());
-    jmb.colourBySequence(ap);
+    jmb.updateStructureColours(ap);
 
     setTitle(jmb.getViewerTitle());
   }