JAL-2011 adjust method to fix failing unit test

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7264cd2..d93f42f 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -867,6 +867,8 @@ public class AlignmentUtils
    * Realigns the given dna to match the alignment of the protein, using codon
    * mappings to translate aligned peptide positions to codons.
    * 
+   * Always produces a padded CDS alignment.
+   * 
    * @param dna
    *          the alignment whose sequences are realigned by this method
    * @param protein
@@ -883,6 +885,7 @@ public class AlignmentUtils
     // todo: implement this
     List<AlignedCodonFrame> mappings = protein.getCodonFrames();
     int alignedCount = 0;
+    int width = 0; // alignment width for padding CDS
     for (SequenceI dnaSeq : dna.getSequences())
     {
       if (alignCdsSequenceAsProtein(dnaSeq, protein, mappings,
@@ -890,6 +893,17 @@ public class AlignmentUtils
       {
         alignedCount++;
       }
+      width = Math.max(dnaSeq.getLength(), width);
+    }
+    int oldwidth, diff;
+    for (SequenceI dnaSeq : dna.getSequences())
+    {
+      oldwidth = dnaSeq.getLength();
+      diff = width - oldwidth;
+      if (diff > 0)
+      {
+        dnaSeq.insertCharAt(oldwidth, diff, dna.getGapCharacter());
+      }
     }
     return alignedCount;
   }
@@ -2620,11 +2634,16 @@ public class AlignmentUtils
       return false; // should only pass alignments with datasets here
     }
 
-    // map from dataset sequence to alignment sequence
-    Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
+    // map from dataset sequence to alignment sequence(s)
+    Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<SequenceI, List<SequenceI>>();
     for (SequenceI seq : aligned.getSequences())
     {
-      alignedDatasets.put(seq.getDatasetSequence(), seq);
+      SequenceI ds = seq.getDatasetSequence();
+      if (alignedDatasets.get(ds) == null)
+      {
+        alignedDatasets.put(ds, new ArrayList<SequenceI>());
+      }
+      alignedDatasets.get(ds).add(seq);
     }
 
     /*
@@ -2640,15 +2659,22 @@ public class AlignmentUtils
     }
 
     /*
-     * second pass - copy aligned sequences
+     * second pass - copy aligned sequences;
+     * heuristic rule: pair off sequences in order for the case where 
+     * more than one shares the same dataset sequence 
      */
     for (SequenceI seq : unaligned.getSequences())
     {
-      SequenceI alignedSequence = alignedDatasets.get(seq
+      List<SequenceI> alignedSequences = alignedDatasets.get(seq
               .getDatasetSequence());
       // TODO: getSequenceAsString() will be deprecated in the future
       // TODO: need to leave to SequenceI implementor to update gaps
-      seq.setSequence(alignedSequence.getSequenceAsString());
+      seq.setSequence(alignedSequences.get(0).getSequenceAsString());
+      if (alignedSequences.size() > 0)
+      {
+        // pop off aligned sequences (except the last one)
+        alignedSequences.remove(0);
+      }
     }
 
     return true;