Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 1a5072d..6936686 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
@@ -238,7 +240,7 @@ public class SequenceAnnotationReport
       {
         if (sb0.length() > 6)
         {
-          sb.append("<br/>");
+          sb.append("<br>");
         }
         sb.append(feature.getType()).append(" ").append(begin).append(":")
                 .append(end);
@@ -248,7 +250,7 @@ public class SequenceAnnotationReport
 
     if (sb0.length() > 6)
     {
-      sb.append("<br/>");
+      sb.append("<br>");
     }
     // TODO: remove this hack to display link only features
     boolean linkOnly = feature.getValue("linkonly") != null;
@@ -274,10 +276,12 @@ public class SequenceAnnotationReport
          * truncate overlong descriptions unless they contain an href
          * before the truncation point (as truncation could leave corrupted html)
          */
-        int linkindex = description.toLowerCase().indexOf("<a ");
+        int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
         boolean hasLink = linkindex > -1
                 && linkindex < MAX_DESCRIPTION_LENGTH;
-        if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+        if (
+                // BH suggestion maxlength == 0 && 
+                description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
         {
           description = description.substring(0, MAX_DESCRIPTION_LENGTH)
                   + ELLIPSIS;
@@ -396,16 +400,16 @@ public class SequenceAnnotationReport
           {
             for (List<String> urllink : createLinksFrom(null, urlstring))
             {
-              sb.append("<br/> <a href=\""
+              sb.append("<br> <a href=\""
                       + urllink.get(3)
                       + "\" target=\""
                       + urllink.get(0)
                       + "\">"
-                      + (urllink.get(0).toLowerCase()
-                              .equals(urllink.get(1).toLowerCase()) ? urllink
+                      + (urllink.get(0).toLowerCase(Locale.ROOT)
+                              .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
                               .get(0) : (urllink.get(0) + ":" + urllink
                                               .get(1)))
-                      + "</a><br/>");
+                      + "</a><br>");
             }
           } catch (Exception x)
           {
@@ -594,7 +598,7 @@ public class SequenceAnnotationReport
       countForSource++;
       if (countForSource == 1 || !summary)
       {
-        sb.append("<br/>");
+        sb.append("<br>");
       }
       if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
@@ -620,11 +624,11 @@ public class SequenceAnnotationReport
     }
     if (moreSources)
     {
-      sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
+      sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
     }
     if (ellipsis)
     {
-      sb.append("<br/>(");
+      sb.append("<br>(");
       sb.append(MessageManager.getString("label.output_seq_details"));
       sb.append(")");
     }