JAL-2046 safer createDatasetSequence manipulates private fields and moves sequenceFea...

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7b05649..6f1b403 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -219,7 +219,8 @@ public class Sequence extends ASequence implements SequenceI
     initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
             seq.getEnd());
     description = seq.getDescription();
-    sourceDBRef = seq.getSourceDBRef();
+    sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
+            seq.getSourceDBRef());
     if (seq.getSequenceFeatures() != null)
     {
       SequenceFeature[] sf = seq.getSequenceFeatures();
@@ -420,7 +421,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public Vector<PDBEntry> getAllPDBEntries()
   {
-    return pdbIds;
+    return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
   }
 
   /**
@@ -611,17 +612,15 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
+   * Returns the character of the aligned sequence at the given position (base
+   * zero), or space if the position is not within the sequence's bounds
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public char getCharAt(int i)
   {
-    if (i < sequence.length)
+    if (i >= 0 && i < sequence.length)
     {
       return sequence[i];
     }
@@ -1075,20 +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);