JAL-1152 with sticky annotation sort order that updates as sequences are

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index e7fed8d..f5afa9c 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,13 +20,24 @@
  */
 package jalview.analysis;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
+import jalview.util.Comparison;
+import jalview.util.Format;
+import jalview.util.MapList;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
 
 /**
  * 
@@ -1113,7 +1124,7 @@ public class AlignSeq
               if (removeOldAnnots) {
                 annotations.remove(ap);
               } else {
-                AlignmentAnnotation alan = annotations.get(ap);
+                AlignmentAnnotation alan = annotations.remove(ap);
                 alan.liftOver(sq, sp2sq);
                 alan.setSequenceRef(sq);
                 sq.addAlignmentAnnotation(alan);