JAL-2046 clarify contract for copy constructor and initSeqFrom implementation

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6f1b403..fbe3670 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -25,6 +25,7 @@ import jalview.api.DBRefEntryI;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -185,12 +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)
   {
@@ -213,31 +215,48 @@ 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)
   {
-    initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+    {
+      char[] oseq = seq.getSequence();
+      initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
+              seq.getStart(),
             seq.getEnd());
+    }
     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)
     {