JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index c2954f0..84d31f0 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -389,7 +389,6 @@ public class VamsasAppDatastore
         {
           dssmods.addElement(sequence);
         }
-        ;
       }
       if (dssmods.size() > 0)
       {
@@ -585,7 +584,6 @@ public class VamsasAppDatastore
                           (AlignmentSequence) alsref, aa[i]);
                   break;
                 }
-                ;
               }
             }
           }
@@ -1478,8 +1476,7 @@ public class VamsasAppDatastore
           // active
           if (mappings != null)
           {
-            jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.getInstance())
+            Desktop.getStructureSelectionManager()
                     .registerMappings(mappings);
           }
         }
@@ -2020,17 +2017,17 @@ public class VamsasAppDatastore
   }
 
   // bitfields - should be a template in j1.5
-  private static int HASSECSTR = 0;
+  private static final int HASSECSTR = 0;
 
-  private static int HASVALS = 1;
+  private static final int HASVALS = 1;
 
-  private static int HASHPHOB = 2;
+  private static final int HASHPHOB = 2;
 
-  private static int HASDC = 3;
+  private static final int HASDC = 3;
 
-  private static int HASDESCSTR = 4;
+  private static final int HASDESCSTR = 4;
 
-  private static int HASTWOSTATE = 5; // not used yet.
+  private static final int HASTWOSTATE = 5; // not used yet.
 
   /**
    * parses the AnnotationElements - if they exist - into