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 387dbfa..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;
                 }
-                ;
               }
             }
           }
@@ -720,9 +718,9 @@ public class VamsasAppDatastore
       // /SAVE THE TREES
       // /////////////////////////////////
       // FIND ANY ASSOCIATED TREES
-      if (Desktop.desktop != null)
+      if (Desktop.getDesktopPane() != null)
       {
-        javax.swing.JInternalFrame[] frames = Desktop.instance
+        javax.swing.JInternalFrame[] frames = Desktop.getInstance()
                 .getAllFrames();
 
         for (int t = 0; t < frames.length; t++)
@@ -1478,8 +1476,7 @@ public class VamsasAppDatastore
           // active
           if (mappings != null)
           {
-            jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance)
+            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
@@ -2248,7 +2245,7 @@ public class VamsasAppDatastore
           Float val = null;
           try
           {
-            val = Float.valueOf(props[p].getContent());
+            val = new Float(props[p].getContent());
           } catch (Exception e)
           {
             Cache.log.warn("Failed to parse threshold property");
@@ -2537,7 +2534,7 @@ public class VamsasAppDatastore
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
           {
-            posList.add(Integer.valueOf(p));
+            posList.add(new Integer(p));
           }
         }
       }
@@ -2548,7 +2545,7 @@ public class VamsasAppDatastore
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(Integer.valueOf(pos));
+          posList.add(new Integer(pos));
         }
       }
     }