From 4b31a57dbc12d26b92c31186ff3b953f0dd8dfcc Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 17 Nov 2014 14:43:37 +0000
Subject: [PATCH] JAL-1587 propagate results of JABA sequence based predictors
 to dataset

---
 src/jalview/ws/jws2/AADisorderClient.java |   10 ++++++++--
 src/jalview/ws/jws2/JabawsCalcWorker.java |   24 ++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 83eebdf..6c438be 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -279,10 +279,13 @@ public class AADisorderClient extends JabawsCalcWorker implements
               {
                 continue;
               }
+              String typename, calcName;
               AlignmentAnnotation annot = createAnnotationRowsForScores(
                       ourAnnot,
-                      service.serviceType + " (" + scr.getMethod() + ")",
-                      service.getServiceTypeURI() + "/" + scr.getMethod(),
+                      typename = service.serviceType + " ("
+                              + scr.getMethod() + ")",
+                      calcName = service.getServiceTypeURI() + "/"
+                              + scr.getMethod(),
                       aseq, base + 1, scr);
               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 
@@ -333,6 +336,9 @@ public class AADisorderClient extends JabawsCalcWorker implements
                 }
               }
               annot._linecolour = col;
+              // finally, update any dataset annotation
+              replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+                      aseq);
             }
           }
         }
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)
   {
-- 
1.7.10.2