JAL-1136 JAL-811 JAL-812 store/recover autocalc alignment annotation based on calcId...

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index d09c41d..7e55e36 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -438,15 +438,17 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * search for or create a specific annotation row on the alignment
-   *
-   * @param method - CalcId for the annotation (must match)
+   * @param name name for annotation (must match)
+   * @param calcId calcId for the annotation (null or must match)
    * @param autoCalc - value of autocalc flag for the annotation
    * @param seqRef - null or specific sequence reference
    * @param groupRef - null or specific group reference
+   * @param method - CalcId for the annotation (must match)
+   *
    * @return existing annotation matching the given attributes
    */
-  public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
-          SequenceI seqRef, SequenceGroup groupRef);
+  public AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+          boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
 
   /**
    * move the given group up or down in the alignment by the given number of rows.