JAL-2110 ensuring mapped dbrefs between protein and cds

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a9b0d53..f5665db 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -44,7 +44,7 @@ import java.util.Vector;
  */
 public class Alignment implements AlignmentI
 {
-  protected Alignment dataset;
+  private Alignment dataset;
 
   protected List<SequenceI> sequences;
 
@@ -109,7 +109,10 @@ public class Alignment implements AlignmentI
     /*
      * Share the same dataset sequence mappings (if any). 
      */
-    this.setCodonFrames(al.getCodonFrames());
+    if (dataset == null && al.getDataset() == null)
+    {
+      this.setCodonFrames(al.getCodonFrames());
+    }
   }
 
   /**
@@ -986,7 +989,7 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setDataset(Alignment data)
+  public void setDataset(AlignmentI data)
   {
     if (dataset == null && data == null)
     {
@@ -994,7 +997,12 @@ public class Alignment implements AlignmentI
     }
     else if (dataset == null && data != null)
     {
-      dataset = data;
+      if (!(data instanceof Alignment))
+      {
+        throw new Error(
+                "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+      }
+      dataset = (Alignment) data;
       for (int i = 0; i < getHeight(); i++)
       {
         SequenceI currentSeq = getSequenceAt(i);
@@ -1340,6 +1348,10 @@ public class Alignment implements AlignmentI
   @Override
   public List<AlignedCodonFrame> getCodonFrames()
   {
+    // TODO: Fix this method to fix failing AlignedCodonFrame tests
+    // this behaviour is currently incorrect. method should return codon frames
+    // for just the alignment,
+    // selected from dataset
     return dataset != null ? dataset.getCodonFrames() : codonFrameList;
   }
 
@@ -1401,6 +1413,7 @@ public class Alignment implements AlignmentI
       addAnnotation(alan[a]);
     }
 
+    // use add method
     getCodonFrames().addAll(toappend.getCodonFrames());
 
     List<SequenceGroup> sg = toappend.getGroups();
@@ -1710,6 +1723,10 @@ public class Alignment implements AlignmentI
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
+    else if (thatIsProtein && thisIsNucleotide)
+    {
+      return AlignmentUtils.alignCdsAsProtein(this, al);
+    }
     return AlignmentUtils.alignAs(this, al);
   }