Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalv...

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7386d4b..cea1c5b 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -525,6 +525,17 @@ public interface AlignmentI extends AnnotatedCollectionI
           boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
 
   /**
+   * like findOrCreateAnnotation - looks for an existing alignment annotation
+   * row with matching name, calcId, sequenceRef, groupRef and autoCalculated
+   * flag and updates it from the annotation. If none is found the annotation is
+   * added directly.
+   * 
+   * @param ala
+   * @return ala or the annotation row that was updated.
+   */
+  AlignmentAnnotation updateFromOrCopyAnnotation(AlignmentAnnotation ala);
+
+  /**
    * move the given group up or down in the alignment by the given number of
    * rows. Implementor assumes given group is already present on alignment - no
    * recalculations are triggered.