From e276157fe1ba0055652596f3e5e2f8a6968e8239 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 21 Jan 2016 17:00:16 +0000
Subject: [PATCH] JAL-1479 JAL-1979 bugfix to check entire annotation property
 of a resDetail object for NOT_OBSERVED rather than just the
 topmost value. Intially thought the multiplicity was 0..1
 rather than 0..* which it turned out to be following the
 N2NScan test

---
 src/jalview/ws/sifts/SiftsClient.java |   19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 9f7bc52..5b03ddb 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -630,16 +630,18 @@ public class SiftsClient implements SiftsClientI
    */
   private boolean isResidueObserved(Residue residue)
   {
-    String annotation = getResidueAnnotaiton(residue,
+    HashSet<String> annotations = getResidueAnnotaitons(residue,
             ResidueDetailType.ANNOTATION);
-    if (annotation == null)
+    if (annotations == null || annotations.isEmpty())
     {
       return true;
     }
-    if (!annotation.equalsIgnoreCase(NOT_FOUND)
-            && annotation.equalsIgnoreCase(NOT_OBSERVED))
+    for (String annotation : annotations)
     {
-      return false;
+      if (annotation.equalsIgnoreCase(NOT_OBSERVED))
+      {
+        return false;
+      }
     }
     return true;
   }
@@ -651,18 +653,19 @@ public class SiftsClient implements SiftsClientI
    * @param type
    * @return
    */
-  private String getResidueAnnotaiton(Residue residue,
+  private HashSet<String> getResidueAnnotaitons(Residue residue,
           ResidueDetailType type)
   {
+    HashSet<String> foundAnnotations = new HashSet<String>();
     List<ResidueDetail> resDetails = residue.getResidueDetail();
     for (ResidueDetail resDetail : resDetails)
     {
       if (resDetail.getProperty().equalsIgnoreCase(type.getCode()))
       {
-        return resDetail.getContent();
+        foundAnnotations.add(resDetail.getContent());
       }
     }
-    return NOT_FOUND;
+    return foundAnnotations;
   }
 
   @Override
-- 
1.7.10.2