JAL-1705 reworked AlignmentUtils.makeCdsAlignment and associated code

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1134857..d1ea70d 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1704,31 +1704,13 @@ public class Alignment implements AlignmentI
           boolean preserveUnmappedGaps)
   {
     // TODO should this method signature be the one in the interface?
-    int count = 0;
     boolean thisIsNucleotide = this.isNucleotide();
     boolean thatIsProtein = !al.isNucleotide();
     if (!thatIsProtein && !thisIsNucleotide)
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
-
-    char thisGapChar = this.getGapCharacter();
-    String gap = thisIsNucleotide && thatIsProtein ? String
-            .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
-            : String.valueOf(thisGapChar);
-
-    // TODO handle intron regions? Needs a 'holistic' alignment of dna,
-    // not just sequence by sequence. But how to 'gap' intron regions?
-
-    /*
-     * Get mappings from 'that' alignment's sequences to this.
-     */
-    for (SequenceI alignTo : getSequences())
-    {
-      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
-              preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
-    }
-    return count;
+    return AlignmentUtils.alignAs(this, al);
   }
 
   /**