X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=5451a205d3af149deaa049505eb0a301eba2ab2b;hb=ce0d0a188dc7362f95bb966dc4634d58aee8eb28;hp=f2f0657e60b85d32bb1aeac893304a68cea17337;hpb=e51f922b88b1f316e27cf4c19eef437ff592d74d;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index f2f0657..5451a20 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -54,9 +54,7 @@ public class SequenceAnnotationReport
 
   private static final int MAX_SOURCES = 40;
 
-  private static final String[][] PRIMARY_SOURCES = new String[][] {
-      DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
-      DBRefSource.PROTEINDBS };
+ // public static final String[][] PRIMARY_SOURCES  moved to DBRefSource.java
 
   final String linkImageURL;
 
@@ -64,7 +62,7 @@ public class SequenceAnnotationReport
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
    * with 'Primary' sources placed before others, and 'chromosome' first of all
    */
-  private static Comparator<DBRefEntry> comparator = new Comparator<>()
+  private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
   {
 
     @Override
@@ -80,8 +78,8 @@ public class SequenceAnnotationReport
       }
       String s1 = ref1.getSource();
       String s2 = ref2.getSource();
-      boolean s1Primary = isPrimarySource(s1);
-      boolean s2Primary = isPrimarySource(s2);
+      boolean s1Primary = DBRefSource.isPrimarySource(s1);
+      boolean s2Primary = DBRefSource.isPrimarySource(s2);
       if (s1Primary && !s2Primary)
       {
         return -1;
@@ -102,20 +100,20 @@ public class SequenceAnnotationReport
       return comp;
     }
 
-    private boolean isPrimarySource(String source)
-    {
-      for (String[] primary : PRIMARY_SOURCES)
-      {
-        for (String s : primary)
-        {
-          if (source.equals(s))
-          {
-            return true;
-          }
-        }
-      }
-      return false;
-    }
+//    private boolean isPrimarySource(String source)
+//    {
+//      for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+//      {
+//        for (String s : primary)
+//        {
+//          if (source.equals(s))
+//          {
+//            return true;
+//          }
+//        }
+//      }
+//      return false;
+//    }
   };
 
   public SequenceAnnotationReport(String linkURL)
@@ -420,14 +418,14 @@ public class SequenceAnnotationReport
   protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
           boolean summary)
   {
-    DBRefEntry[] dbrefs = ds.getDBRefs();
+    List<DBRefEntry> dbrefs = ds.getDBRefs();
     if (dbrefs == null)
     {
       return 0;
     }
 
     // note this sorts the refs held on the sequence!
-    Arrays.sort(dbrefs, comparator);
+    dbrefs.sort(comparator);
     boolean ellipsis = false;
     String source = null;
     String lastSource = null;