JAL-2046 simpler deriveSequence - promote to dataset and initSeqFrom or defer to...

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cb3ae70..d9b810d 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -186,12 +186,13 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * Creates a new Sequence object with new features, DBRefEntries,
-   * AlignmentAnnotations, and PDBIds but inherits any existing dataset sequence
-   * reference.
+   * Creates a new Sequence object with new AlignmentAnnotations but inherits
+   * any existing dataset sequence reference. If non exists, everything is
+   * copied.
    * 
    * @param seq
-   *          DOCUMENT ME!
+   *          if seq is a dataset sequence, behaves like a plain old copy
+   *          constructor
    */
   public Sequence(SequenceI seq)
   {
@@ -214,6 +215,16 @@ public class Sequence extends ASequence implements SequenceI
 
   }
 
+  /**
+   * does the heavy lifting when cloning a dataset sequence, or coping data from
+   * dataset to a new derived sequence.
+   * 
+   * @param seq
+   *          - source of attributes.
+   * @param alAnnotation
+   *          - alignment annotation present on seq that should be copied onto
+   *          this sequence
+   */
   protected void initSeqFrom(SequenceI seq,
           AlignmentAnnotation[] alAnnotation)
   {
@@ -226,23 +237,26 @@ public class Sequence extends ASequence implements SequenceI
     description = seq.getDescription();
     sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
             seq.getSourceDBRef());
-    if (seq.getSequenceFeatures() != null)
+    if (seq != datasetSequence)
     {
-      SequenceFeature[] sf = seq.getSequenceFeatures();
-      for (int i = 0; i < sf.length; i++)
-      {
-        addSequenceFeature(new SequenceFeature(sf[i]));
-      }
+      setDatasetSequence(seq.getDatasetSequence());
     }
-    setDatasetSequence(seq.getDatasetSequence());
     if (datasetSequence == null && seq.getDBRefs() != null)
     {
-      // only copy DBRefs if we really are a dataset sequence
+      // only copy DBRefs and seqfeatures if we really are a dataset sequence
       DBRefEntry[] dbr = seq.getDBRefs();
       for (int i = 0; i < dbr.length; i++)
       {
         addDBRef(new DBRefEntry(dbr[i]));
       }
+      if (seq.getSequenceFeatures() != null)
+      {
+        SequenceFeature[] sf = seq.getSequenceFeatures();
+        for (int i = 0; i < sf.length; i++)
+        {
+          addSequenceFeature(new SequenceFeature(sf[i]));
+        }
+      }
     }
     if (seq.getAnnotation() != null)
     {
@@ -1042,31 +1056,24 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    SequenceI seq = new Sequence(this);
-    if (datasetSequence != null)
-    {
-      // duplicate current sequence with same dataset
-      seq.setDatasetSequence(datasetSequence);
-    }
-    else
+    Sequence seq=null;
+    if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
       {
         // Use this as dataset sequence
+        seq = new Sequence(getName(), "", 1, -1);
         seq.setDatasetSequence(this);
+        seq.initSeqFrom(this, getAnnotation());
+        return seq;
       }
       else
       {
         // Create a new, valid dataset sequence
-        SequenceI ds = seq;
-        ds.setSequence(AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars, new String(sequence)));
-        setDatasetSequence(ds);
-        ds.setSequenceFeatures(getSequenceFeatures());
-        seq = this; // and return this sequence as the derived sequence.
+       createDatasetSequence();
       }
     }
-    return seq;
+    return new Sequence(this);
   }
 
   /*