JAL-1619 AlignedCodonFrame in new alignment should references realigned

sequences

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 4016ee5..f65f068 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -22,16 +22,16 @@ package jalview.datamodel;
 
 import jalview.util.MapList;
 
-import java.util.Enumeration;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Stores mapping between the columns of a protein alignment and a DNA alignment
  * and a list of individual codon to amino acid mappings between sequences.
  */
-
 public class AlignedCodonFrame
 {
+
   /**
    * array of nucleotide positions for aligned codons at column of aligned
    * proteins.
@@ -44,6 +44,25 @@ public class AlignedCodonFrame
    */
   public int aaWidth = 0;
 
+  /*
+   * TODO: not an ideal solution - we reference the aligned amino acid sequences
+   * in order to make insertions on them Better would be dnaAlignment and
+   * aaAlignment reference....
+   */
+  private List<SequenceI> a_aaSeqs = new ArrayList<SequenceI>();
+
+  /*
+   * tied array of na Sequence objects.
+   */
+  private SequenceI[] dnaSeqs = null;
+
+  /*
+   * tied array of Mappings to protein sequence Objects and SequenceI[]
+   * aaSeqs=null; MapLists where eac maps from the corresponding dnaSeqs element
+   * to corresponding aaSeqs element
+   */
+  private Mapping[] dnaToProt = null;
+
   /**
    * initialise codon frame with a nominal alignment width
    * 
@@ -64,6 +83,41 @@ public class AlignedCodonFrame
   }
 
   /**
+   * Construct a 'near copy' of the given AlignedCodonFrame, that references the
+   * same dataset sequences, but the given protein aligned sequences.
+   * 
+   * @param acf
+   * @param alignment
+   * @throws IllegalStateException
+   *           if the copied mapping references any dataset not in the alignment
+   */
+  public AlignedCodonFrame(AlignedCodonFrame acf, SequenceI[] alignment)
+  {
+    this.codons = acf.codons;
+    this.dnaSeqs = acf.dnaSeqs;
+    this.dnaToProt = acf.dnaToProt;
+
+    for (SequenceI seq : acf.a_aaSeqs)
+    {
+      boolean found = false;
+      for (SequenceI newseq : alignment)
+      {
+        if (seq.getDatasetSequence() == newseq.getDatasetSequence())
+        {
+          this.a_aaSeqs.add(newseq);
+          found = true;
+          break;
+        }
+      }
+      if (!found)
+      {
+        throw new IllegalStateException("Copying codon mapping for"
+                + seq.getSequenceAsString());
+      }
+    }
+  }
+
+  /**
    * ensure that codons array is at least as wide as aslen residues
    * 
    * @param aslen
@@ -94,13 +148,6 @@ public class AlignedCodonFrame
   }
 
   /**
-   * TODO: not an ideal solution - we reference the aligned amino acid sequences
-   * in order to make insertions on them Better would be dnaAlignment and
-   * aaAlignment reference....
-   */
-  Vector a_aaSeqs = new Vector();
-
-  /**
    * increase aaWidth by one and insert a new aligned codon position space at
    * aspos.
    * 
@@ -111,16 +158,13 @@ public class AlignedCodonFrame
     // this aa appears before the aligned codons at aspos - so shift them in
     // each pair of mapped sequences
     aaWidth++;
-    if (a_aaSeqs != null)
+    // we actually have to modify the aligned sequences here, so use the
+    // a_aaSeqs vector
+    for (SequenceI seq : a_aaSeqs)
     {
-      // we actually have to modify the aligned sequences here, so use the
-      // a_aaSeqs vector
-      Enumeration sq = a_aaSeqs.elements();
-      while (sq.hasMoreElements())
-      {
-        ((SequenceI) sq.nextElement()).insertCharAt(aspos, gapCharacter);
-      }
+      seq.insertCharAt(aspos, gapCharacter);
     }
+
     checkCodonFrameWidth(aspos);
     if (aspos < aaWidth)
     {
@@ -137,18 +181,6 @@ public class AlignedCodonFrame
   }
 
   /**
-   * tied array of na Sequence objects.
-   */
-  SequenceI[] dnaSeqs = null;
-
-  /**
-   * tied array of Mappings to protein sequence Objects and SequenceI[]
-   * aaSeqs=null; MapLists where eac maps from the corresponding dnaSeqs element
-   * to corresponding aaSeqs element
-   */
-  Mapping[] dnaToProt = null;
-
-  /**
    * add a mapping between the dataset sequences for the associated dna and
    * protein sequence objects
    * 
@@ -181,7 +213,7 @@ public class AlignedCodonFrame
     // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
     mp.to = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
             .getDatasetSequence();
-    a_aaSeqs.addElement(aaseq);
+    a_aaSeqs.add(aaseq);
     dnaToProt[nlen] = mp;
   }
 
@@ -261,7 +293,7 @@ public class AlignedCodonFrame
         {
           // TODO very fragile - depends on dnaSeqs, dnaToProt, a_aaSeqs moving
           // in parallel; revise data model to guarantee this
-          return (SequenceI) a_aaSeqs.elementAt(ds);
+          return a_aaSeqs.get(ds);
         }
       }
     }

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index edb56a9..7f05e90 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -27,8 +27,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
 import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 
 public abstract class AWSThread extends Thread
@@ -297,10 +297,11 @@ public abstract class AWSThread extends Thread
       {
         for (int i = 0; i < codonframe.length; i++)
         {
-          if (codonframe[i] != null
-                  && codonframe[i].involvesSequence(alignment[sq]))
+          AlignedCodonFrame acf = codonframe[i];
+          final SequenceI seq = alignment[sq];
+          if (acf != null && acf.involvesSequence(seq))
           {
-            al.addCodonFrame(codonframe[i]);
+            al.addCodonFrame(new AlignedCodonFrame(acf, alignment));
             codonframe[i] = null;
             break;
           }