X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=4ba0ac4dc9f0bb71727f625912969bfd1cd23216;hb=bc7c2cf5500c5a4124a69ef8e7b1374d8997558f;hp=9354d55fa447e8dc43a1b6acdd08ae1fa5cb9329;hpb=ed581b841fe9361bfe80bb006df190a29df264fb;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 9354d55..4ba0ac4 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -710,6 +710,17 @@ public class AlignmentAnnotation
   public AlignmentAnnotation(AlignmentAnnotation annotation)
   {
     setAnnotationId();
+    updateAlignmentAnnotationFrom(annotation);
+  }
+
+  /**
+   * copy attributes and annotation from an existing annotation (used by copy
+   * constructor). This method does not update the unique annotationId
+   * 
+   * @param annotation
+   */
+  public void updateAlignmentAnnotationFrom(AlignmentAnnotation annotation)
+  {
     this.label = new String(annotation.label);
     if (annotation.description != null)
     {
@@ -733,6 +744,9 @@ public class AlignmentAnnotation
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
+    this.bitScore = annotation.bitScore;
+    this.eValue = annotation.eValue;
+
     if (annotation.properties != null)
     {
       properties = new HashMap<>();
@@ -1738,4 +1752,22 @@ public class AlignmentAnnotation
     this.eValue = eValue;
   }
 
+  public static AlignmentAnnotation findFirstAnnotation(
+          Iterable<AlignmentAnnotation> alignmentAnnotation, String name,
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
+  {
+
+    for (AlignmentAnnotation annot : alignmentAnnotation)
+    {
+      if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+              && (calcId == null || annot.getCalcId().equals(calcId))
+              && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+      {
+        return annot;
+      }
+    }
+    return null;
+  }
+
 }