From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 5 Apr 2016 17:12:59 +0000 (+0100)
Subject: JAL-2046 safer createDatasetSequence manipulates private fields and moves sequenceFea... 
X-Git-Tag: Release_2_10_0~249^2~31^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=cf8e8c6b06fc4272ef915b061ffb12ce555a9bb8;p=jalview.git

JAL-2046 safer createDatasetSequence manipulates private fields and moves sequenceFeatures to dataset
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6c8cbc0..6f1b403 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1074,20 +1074,27 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (datasetSequence == null)
     {
-      datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
+      Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
               jalview.util.Comparison.GapChars, getSequenceAsString()),
               getStart(), getEnd());
-      datasetSequence.setSequenceFeatures(getSequenceFeatures());
-      datasetSequence.setDescription(getDescription());
-      setSequenceFeatures(null);
-      // move database references onto dataset sequence
-      datasetSequence.setDBRefs(getDBRefs());
-      setDBRefs(null);
-      datasetSequence.setPDBId(getAllPDBEntries());
-      setPDBId(null);
+
+      datasetSequence = dsseq;
+
+      dsseq.setDescription(description);
+      // move features and database references onto dataset sequence
+      dsseq.sequenceFeatures = sequenceFeatures;
+      sequenceFeatures=null;
+      dsseq.dbrefs = dbrefs;
+      dbrefs=null;
+      // TODO: search and replace any references to this sequence with
+      // references to the dataset sequence in Mappings on dbref
+      dsseq.pdbIds = pdbIds;
+      pdbIds = null;
       datasetSequence.updatePDBIds();
       if (annotation != null)
       {
+        // annotation is cloned rather than moved, to preserve what's currently
+        // on the alignment
         for (AlignmentAnnotation aa : annotation)
         {
           AlignmentAnnotation _aa = new AlignmentAnnotation(aa);