X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=95d0bc6a8b7e463653f7c569a1b1c1fcc42918ca;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=c8313664c86b70d07679fb7655dab9dd7d0bc019;hpb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index c831366..95d0bc6 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,17 +20,14 @@
  */
 package jalview.io;
 
-import java.util.Locale;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
-import com.google.common.collect.Lists;
-
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -58,7 +55,7 @@ public class SequenceAnnotationReport
 
   private static final int MAX_REFS_PER_SOURCE = 4;
 
-  private static final int MAX_SOURCES = 40;
+  private static final int MAX_SOURCES = 5;
 
   private static String linkImageURL;
 
@@ -82,10 +79,19 @@ public class SequenceAnnotationReport
       {
         return 1;
       }
+
       String s1 = ref1.getSource();
       String s2 = ref2.getSource();
       boolean s1Primary = DBRefSource.isPrimarySource(s1);
       boolean s2Primary = DBRefSource.isPrimarySource(s2);
+      if (ref1.isCanonical() && !ref2.isCanonical())
+      {
+        return -1;
+      }
+      if (!ref1.isCanonical() && ref2.isCanonical())
+      {
+        return 1;
+      }
       if (s1Primary && !s2Primary)
       {
         return -1;
@@ -426,7 +432,7 @@ public class SequenceAnnotationReport
             }
           } catch (Exception x)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "problem when creating links from " + urlstring);
             x.printStackTrace();
           }
@@ -449,7 +455,7 @@ public class SequenceAnnotationReport
     UrlLink urlLink = new UrlLink(link);
     if (!urlLink.isValid())
     {
-      System.err.println(urlLink.getInvalidMessage());
+      jalview.bin.Console.errPrintln(urlLink.getInvalidMessage());
       return null;
     }