update the copy constructor

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 9de07dd..f5d34a6 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -518,6 +518,10 @@ public class AlignmentAnnotation
     this.label = annotation.label;
     this.padGaps = annotation.padGaps;
     this.visible = annotation.visible;
+    this.centreColLabels=annotation.centreColLabels;
+    this.scaleColLabel=annotation.scaleColLabel;
+    this.showAllColLabels=annotation.showAllColLabels;
+    this.calcId = annotation.calcId;
     if (this.hasScore = annotation.hasScore)
     {
       this.score = annotation.score;
@@ -567,6 +571,11 @@ public class AlignmentAnnotation
         }
       }
     }
+    // TODO: check if we need to do this: JAL-952
+    //if (this.isrna=annotation.isrna)
+    {
+      // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+    }
     validateRangeAndDisplay(); // construct hashcodes, etc.
   }