X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FJabawsCalcWorker.java;h=e01c648a12f2b7ca67eb1c8fec2f28abd9a225b0;hb=665ef865f6e0d245d3dde9082e575ed59f52dbb4;hp=e96688623a9fe72fa525eda90b4450a16a8375ea;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabawsCalcWorker.java b/src/jalview/ws/jws2/JabawsCalcWorker.java
index e966886..e01c648 100644
--- a/src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsCalcWorker.java
@@ -158,6 +158,30 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
     return annotation;
   }
 
+  protected void replaceAnnotationOnAlignmentWith(
+          AlignmentAnnotation newAnnot, String typeName, String calcId,
+          SequenceI aSeq)
+  {
+    SequenceI dsseq = aSeq.getDatasetSequence();
+    while (dsseq.getDatasetSequence() != null)
+    {
+      dsseq = dsseq.getDatasetSequence();
+    }
+    // look for same annotation on dataset and lift this one over
+    List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+            typeName);
+    if (dsan != null && dsan.size() > 0)
+    {
+      for (AlignmentAnnotation dssan : dsan)
+      {
+        dsseq.removeAlignmentAnnotation(dssan);
+      }
+    }
+    AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+    dsseq.addAlignmentAnnotation(dssan);
+    dssan.adjustForAlignment();
+  }
+
   private void constructAnnotationFromScore(AlignmentAnnotation annotation,
           int base, int alWidth, Score scr)
   {