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 6e95633..f73ff88 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -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())
             // {
@@ -394,19 +394,20 @@ 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)
       {
         CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
-        if (item.getState())
+        if (!item.getState())
         {
-          toshow.addElement(item.getLabel());
+          toHide.addElement(item.getLabel());
         }
       }
     }
-    jmb.showChains(toshow);
+    jmb.setChainsToHide(toHide);
+    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());
   }