From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 28 Aug 2012 09:31:50 +0000 (+0100)
Subject: JAL-1148 reinstate sequence references for annotation regardless of whether they... 
X-Git-Tag: Jalview_2_9~394
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e4d3bc400c467cf2547a1c99e9c73ab19fddd015;p=jalview.git

JAL-1148 reinstate sequence references for annotation regardless of whether they are autocalculated or not (patch not checked for regressions!)
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ea5d5a7..6acd421 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2306,24 +2306,20 @@ public class Jalview2XML
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
         }
-        if (autoForView)
+        // register new annotation
+        if (an[i].getId() != null)
         {
-          // register new annotation
-          if (an[i].getId() != null)
-          {
-            annotationIds.put(an[i].getId(), jaa);
-            jaa.annotationId = an[i].getId();
-          }
-          // recover sequence association
-          if (an[i].getSequenceRef() != null)
+          annotationIds.put(an[i].getId(), jaa);
+          jaa.annotationId = an[i].getId();
+        }
+        // recover sequence association
+        if (an[i].getSequenceRef() != null)
+        {
+          if (al.findName(an[i].getSequenceRef()) != null)
           {
-            if (al.findName(an[i].getSequenceRef()) != null)
-            {
-              jaa.createSequenceMapping(
-                      al.findName(an[i].getSequenceRef()), 1, true);
-              al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(
-                      jaa);
-            }
+            jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+                    1, true);
+            al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
           }
         }
         // and make a note of any group association