Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

[jalview.git] / src / jalview / analysis / AlignmentAnnotationUtils.java

diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index e02aa9e..f5626ce 100644 (file)
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -1,5 +1,29 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -8,10 +32,6 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-
 public class AlignmentAnnotationUtils
 {
 
@@ -71,9 +91,8 @@ public class AlignmentAnnotationUtils
       {
         continue;
       }
-      if (forSequences != null
-              && (aa.sequenceRef != null && forSequences
-                      .contains(aa.sequenceRef)))
+      if (forSequences != null && (aa.sequenceRef != null
+              && forSequences.contains(aa.sequenceRef)))
       {
         String calcId = aa.getCalcId();
 
@@ -94,8 +113,8 @@ public class AlignmentAnnotationUtils
                   .get(calcId);
           if (groupLabelsForCalcId.containsKey(aa.graphGroup))
           {
-            if (!groupLabelsForCalcId.get(aa.graphGroup).contains(
-                    displayLabel))
+            if (!groupLabelsForCalcId.get(aa.graphGroup)
+                    .contains(displayLabel))
             {
               groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel);
             }