X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=d737bd5adace0eb6145e5363526236a0872f1ff6;hb=a24dd1c4927582a629b2ce43c3786abe1c247847;hp=34f8f6edc75ca1b48ad24d53d79f309b83faa125;hpb=36dceb54710feb97a81f4bd69ad051f316141dc3;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 34f8f6e..d737bd5 100755
--- 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;
@@ -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());
+    }
   }
 
   /**
@@ -1293,22 +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)
    * 
@@ -1387,11 +1373,7 @@ public class Alignment implements AlignmentI
   @Override
   public void append(AlignmentI toappend)
   {
-    if (toappend == this)
-    {
-      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();
@@ -1402,6 +1384,8 @@ public class Alignment implements AlignmentI
             .getFullAlignment().getSequences() : toappend.getSequences();
     if (sqs != null)
     {
+      // avoid self append deadlock by
+      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
@@ -1417,9 +1401,13 @@ public class Alignment implements AlignmentI
               }
             }
           }
-          addSequence(addedsq);
+          toappendsq.add(addedsq);
         }
       }
+      for (SequenceI addedsq : toappendsq)
+      {
+        addSequence(addedsq);
+      }
     }
     AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
     for (int a = 0; alan != null && a < alan.length; a++)
@@ -1427,6 +1415,7 @@ public class Alignment implements AlignmentI
       addAnnotation(alan[a]);
     }
 
+    // use add method
     getCodonFrames().addAll(toappend.getCodonFrames());
 
     List<SequenceGroup> sg = toappend.getGroups();
@@ -1717,9 +1706,11 @@ 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
@@ -1736,6 +1727,10 @@ public class Alignment implements AlignmentI
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
+    else if (thatIsProtein && thisIsNucleotide)
+    {
+      return AlignmentUtils.alignCdsAsProtein(this, al);
+    }
     return AlignmentUtils.alignAs(this, al);
   }