Merge branch 'develop' into releases/Release_2_11_2_Branch

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

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index c5bc902..c831366 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -21,13 +21,16 @@
 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.Map;
 
+import com.google.common.collect.Lists;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -493,6 +496,7 @@ public class SequenceAnnotationReport
       sb.append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
+    sb.append("\n");
     SequenceI ds = sequence;
     while (ds.getDatasetSequence() != null)
     {
@@ -503,6 +507,7 @@ public class SequenceAnnotationReport
     {
       maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
     }
+    sb.append("\n");
 
     /*
      * add non-positional features if wanted
@@ -534,12 +539,19 @@ public class SequenceAnnotationReport
   protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
           boolean summary)
   {
-    List<DBRefEntry> dbrefs = ds.getDBRefs();
-    if (dbrefs == null)
+    List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
+
+    if (dbrefset == null)
     {
       return 0;
     }
 
+    // PATCH for JAL-3980 defensive copy
+
+    dbrefs = new ArrayList<DBRefEntry>();
+
+    dbrefs.addAll(dbrefset);
+
     // note this sorts the refs held on the sequence!
     dbrefs.sort(comparator);
     boolean ellipsis = false;
@@ -576,7 +588,7 @@ public class SequenceAnnotationReport
       countForSource++;
       if (countForSource == 1 || !summary)
       {
-        sb.append("<br/>");
+        sb.append("<br/>\n");
       }
       if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
@@ -584,7 +596,7 @@ public class SequenceAnnotationReport
         lineLength += accessionId.length() + 1;
         if (countForSource > 1 && summary)
         {
-          sb.append(", ").append(accessionId);
+          sb.append(",\n ").append(accessionId);
           lineLength++;
         }
         else
@@ -602,11 +614,11 @@ public class SequenceAnnotationReport
     }
     if (moreSources)
     {
-      sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
+      sb.append("<br/>\n").append(source).append(COMMA).append(ELLIPSIS);
     }
     if (ellipsis)
     {
-      sb.append("<br/>(");
+      sb.append("<br/>\n(");
       sb.append(MessageManager.getString("label.output_seq_details"));
       sb.append(")");
     }