X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=8e4e78305e2c41e01d172b21eee8babf757cf1c5;hb=a35bdf653fe2f56b6600c57f53991a0191cb0032;hp=8328e7ab45b64ffa6f5f1efeafd30d52ad203a09;hpb=5a631296dd1dcc1df7b50487a647c27333696c74;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8328e7a..8e4e783 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,7 +20,6 @@
  */
 package jalview.io;
 
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
@@ -58,9 +57,7 @@ public class SequenceAnnotationReport
 
   private static String linkImageURL;
 
-  private static final String[][] PRIMARY_SOURCES = new String[][] {
-      DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
-      DBRefSource.PROTEINDBS };
+ // public static final String[][] PRIMARY_SOURCES  moved to DBRefSource.java
 
   /*
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
@@ -82,8 +79,8 @@ 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;
@@ -104,20 +101,20 @@ 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;
+//    }
   };
 
   private boolean forTooltip;
@@ -216,6 +213,11 @@ public class SequenceAnnotationReport
     {
       beginRange = mf.getMappedPositions(begin, begin);
       endRange = mf.getMappedPositions(end, end);
+      if (beginRange == null || endRange == null)
+      {
+        // something went wrong
+        return false;
+      }
       begin = beginRange[0];
       end = endRange[endRange.length - 1];
     }
@@ -517,14 +519,14 @@ 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;