JAL-3285 add unmerged code to AlignmentAnnotation

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ee9389c..6ac5da8 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -584,7 +584,7 @@ public class AlignmentAnnotation
     }
     return null;
   }
-
+  
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -696,7 +696,7 @@ public class AlignmentAnnotation
       }
     }
   }
-
+  
   /**
    * Copy constructor creates a new independent annotation row with the same
    * associated sequenceRef
@@ -960,6 +960,7 @@ public class AlignmentAnnotation
    * @param seqRef
    * @param startRes
    * @param alreadyMapped
+   *          - annotation are at aligned columns
    */
   public void createSequenceMapping(SequenceI seqRef, int startRes,
           boolean alreadyMapped)
@@ -991,7 +992,7 @@ public class AlignmentAnnotation
           seqPos = i + startRes;
         }
 
-        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+        sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
       }
     }
 
@@ -1030,7 +1031,7 @@ 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)
         {
@@ -1161,7 +1162,7 @@ public class AlignmentAnnotation
   {
     return hasScore || !Double.isNaN(score);
   }
-
+  
   /**
    * Score only annotation
    * 
@@ -1192,6 +1193,7 @@ public class AlignmentAnnotation
     makeVisibleAnnotation(hidden);
   }
 
+
   public void setPadGaps(boolean padgaps, char gapchar)
   {
     this.padGaps = padgaps;
@@ -1651,7 +1653,6 @@ public class AlignmentAnnotation
           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
           String label)
   {
-
     ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : list)
     {
@@ -1696,7 +1697,6 @@ public class AlignmentAnnotation
   public static Iterable<AlignmentAnnotation> findAnnotation(
           List<AlignmentAnnotation> list, String calcId)
   {
-
     List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {