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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ee9389c..5f27ea7 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import java.util.Locale;
+
 import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
@@ -280,6 +282,8 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
+  public static final int CUSTOMRENDERER = 4;
+
   public boolean belowAlignment = true;
 
   public SequenceGroup groupRef = null;
@@ -991,7 +995,7 @@ public class AlignmentAnnotation
           seqPos = i + startRes;
         }
 
-        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+        sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
       }
     }
 
@@ -1030,7 +1034,7 @@ public class AlignmentAnnotation
     {
       for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
       {
-        index = new Integer(a);
+        index = Integer.valueOf(a);
         Annotation annot = sequenceMapping.get(index);
         if (annot != null)
         {
@@ -1225,7 +1229,7 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
-      int i = description.toLowerCase().indexOf("<html>");
+      int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
       if (i > -1)
       {
         // move the html tag to before the sequence reference.