JAL-4028 experiment - THISISAPLACEHOLDER sequences get additional sequence data ...

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index f8e70b1..1563dff 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,14 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.features.SequenceFeatures;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.StringUtils;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -39,6 +31,13 @@ import java.util.ListIterator;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
 
 /**
  * 
@@ -1602,33 +1601,46 @@ public class Sequence extends ASequence implements SequenceI
               getStart(), getEnd());
 
       datasetSequence = dsseq;
+      updateDatasetFrom(dsseq, this);
+    }
+    return datasetSequence;
+  }
 
-      dsseq.setDescription(description);
-      // move features and database references onto dataset sequence
-      dsseq.sequenceFeatureStore = sequenceFeatureStore;
-      sequenceFeatureStore = 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)
+  /**
+   * used by createDatasetSequence - transfers dataset-only properties to dsseq
+   * from sequence2
+   * 
+   * @param dsseq
+   *          - newly created dataset sequenceI for sequence
+   * @param sequence2
+   *          - sequence object that needs a dataset
+   */
+  protected void updateDatasetFrom(Sequence dsseq, Sequence sequence2)
+  {
+    dsseq.setDescription(description);
+    // move features and database references onto dataset sequence
+    dsseq.sequenceFeatureStore = sequenceFeatureStore;
+    sequenceFeatureStore = 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)
       {
-        // annotation is cloned rather than moved, to preserve what's currently
-        // on the alignment
-        for (AlignmentAnnotation aa : annotation)
-        {
-          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
-          _aa.sequenceRef = datasetSequence;
-          _aa.adjustForAlignment(); // uses annotation's own record of
-                                    // sequence-column mapping
-          datasetSequence.addAlignmentAnnotation(_aa);
-        }
+        AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+        _aa.sequenceRef = datasetSequence;
+        _aa.adjustForAlignment(); // uses annotation's own record of
+                                  // sequence-column mapping
+        datasetSequence.addAlignmentAnnotation(_aa);
       }
     }
-    return datasetSequence;
   }
 
   /*