JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 49219b9..2cd9ee5 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
     }
@@ -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)
         {
@@ -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)
@@ -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);
       }
     }