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Merge branch 'develop' into ben/gecos_colour_schemes
[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 2ee4503..f3cdae6 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;
@@ -181,7 +183,8 @@ public class AlignmentAnnotation
     return rnaSecondaryStructureEquivalent(that, true);
   }
 
-  public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
+  public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that,
+          boolean compareType)
   {
     SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
     SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
@@ -194,21 +197,28 @@ public class AlignmentAnnotation
       return false;
     }
     Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
-                                                   // like this
+                                                 // like this
     Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
-                                                   // like this
-    for (int i=0; i < thisSfArray.length; i++) {
+                                                 // like this
+    for (int i = 0; i < thisSfArray.length; i++)
+    {
       SequenceFeature thisSf = thisSfArray[i];
       SequenceFeature thatSf = thatSfArray[i];
-      if (compareType) {
-        if (thisSf.getType() == null || thatSf.getType() == null) {
-          if (thisSf.getType() == null && thatSf.getType() == null) {
+      if (compareType)
+      {
+        if (thisSf.getType() == null || thatSf.getType() == null)
+        {
+          if (thisSf.getType() == null && thatSf.getType() == null)
+          {
             continue;
-          } else {
+          }
+          else
+          {
             return false;
           }
         }
-        if (! thisSf.getType().equals(thatSf.getType())) {
+        if (!thisSf.getType().equals(thatSf.getType()))
+        {
           return false;
         }
       }
@@ -1225,7 +1235,7 @@ 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.