fixing patch provided by Tariq

andreasprlic · andreasprlic · commit ab90fce04df3 · 2011-08-03T22:45:38.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9052 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/Alignments.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/Alignments.java
@@ -31,6 +31,7 @@
 import org.biojava3.alignment.template.*;
 import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
 import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava3.core.sequence.compound.DNACompoundSet;
 import org.biojava3.core.sequence.template.Compound;
 import org.biojava3.core.sequence.template.CompoundSet;
 import org.biojava3.core.sequence.template.Sequence;
@@ -144,11 +145,17 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getMulti
             @SuppressWarnings("unchecked") // compound types must be equal since compound sets are equal
             SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>) SubstitutionMatrixHelper.getBlosum62();
             subMatrix = temp;
+        } else if (cs == DNACompoundSet.getDNACompoundSet()) {
+            @SuppressWarnings("unchecked") // compound types must be equal since compound sets are equal
+            SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>) SubstitutionMatrixHelper.getNuc4_4();
+            subMatrix = temp;
+            
         } else if (cs == AmbiguityDNACompoundSet.getDNACompoundSet()) {
             @SuppressWarnings("unchecked") // compound types must be equal since compound sets are equal
             SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>) SubstitutionMatrixHelper.getNuc4_4();
             subMatrix = temp;
-        } 
+            
+        }
         ProfileProfileAlignerType pa = ProfileProfileAlignerType.GLOBAL;
         for (Object o : settings) {
             if (o instanceof PairwiseSequenceScorerType) {
