Merge branch 'features/JAL-2349_matrixvis' into merge/develop_JAL-2340_matrixvis

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ee9389c..5708f01 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -280,6 +280,8 @@ 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 +993,7 @@ public class AlignmentAnnotation
           seqPos = i + startRes;
         }
 
-        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+        sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
       }
     }
 
@@ -1030,7 +1032,7 @@ 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)
         {