JAL-1270 test coverage TODO Alignment.append(AlignmentI)

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f14539b..0ee0344 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,7 +30,6 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -45,7 +44,7 @@ import java.util.Vector;
  */
 public class Alignment implements AlignmentI
 {
-  protected Alignment dataset;
+  private Alignment dataset;
 
   protected List<SequenceI> sequences;
 
@@ -110,7 +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());
+    }
   }
 
   /**
@@ -987,7 +989,7 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setDataset(Alignment data)
+  public void setDataset(AlignmentI data)
   {
     if (dataset == null && data == null)
     {
@@ -995,7 +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);
@@ -1288,22 +1295,6 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * adds a set of mappings (while ignoring any duplicates)
-   */
-  @Override
-  public void addCodonFrames(Iterable<AlignedCodonFrame> codons)
-  {
-    if (codons != null)
-    {
-      Iterator<AlignedCodonFrame> it = codons.iterator();
-      while (it.hasNext())
-      {
-        addCodonFrame(it.next());
-      }
-    }
-  }
-
   /*
    * (non-Javadoc)
    * 
@@ -1357,6 +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;
   }
 
@@ -1382,7 +1377,7 @@ public class Alignment implements AlignmentI
     {
       System.err.println("Self append may cause a deadlock.");
     }
-    // TODO test this method for a future 2.5 release
+    // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
     boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
@@ -1418,6 +1413,7 @@ public class Alignment implements AlignmentI
       addAnnotation(alan[a]);
     }
 
+    // use add method
     getCodonFrames().addAll(toappend.getCodonFrames());
 
     List<SequenceGroup> sg = toappend.getGroups();
@@ -1708,9 +1704,11 @@ public class Alignment implements AlignmentI
    * Parameters control whether gaps in exon (mapped) and intron (unmapped)
    * regions are preserved. Gaps that connect introns to exons are treated
    * conservatively, i.e. only preserved if both intron and exon gaps are
-   * preserved.
+   * preserved. TODO: check caveats below where the implementation fails
    * 
    * @param al
+   *          - must have same dataset, and sequences in al must have equivalent
+   *          dataset sequence and start/end bounds under given mapping
    * @param preserveMappedGaps
    *          if true, gaps within and between mapped codons are preserved
    * @param preserveUnmappedGaps
@@ -1727,6 +1725,10 @@ public class Alignment implements AlignmentI
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
+    else if (thatIsProtein && thisIsNucleotide)
+    {
+      return AlignmentUtils.alignCdsAsProtein(this, al);
+    }
     return AlignmentUtils.alignAs(this, al);
   }