gracefully cope with non-standard nucleotide or amino acid symbols in pairwise alignment.

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 02776f9..c9ae044 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -113,6 +113,8 @@ public class AlignSeq
 
   String type;
 
+  private  int[] charToInt;
+
   /**
    * Creates a new AlignSeq object.
    * 
@@ -380,11 +382,13 @@ public class AlignSeq
     if (type.equals(AlignSeq.PEP))
     {
       intToStr = pep;
+      charToInt = ResidueProperties.aaIndex;
       defInt = 23;
     }
     else if (type.equals(AlignSeq.DNA))
     {
       intToStr = dna;
+      charToInt = ResidueProperties.nucleotideIndex;
       defInt = 4;
     }
     else
@@ -714,7 +718,7 @@ public class AlignSeq
     {
       E[i][0] = -gapOpen;
       F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
-
+      
       score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
       traceback[i][0] = -1;
     }
@@ -834,33 +838,15 @@ public class AlignSeq
 
       try
       {
-        if (type.equals("pep"))
+        seq1[i] = charToInt[c]; // set accordingly from setType
+        if (seq1[i]<0 || seq1[i] > defInt) // set from setType: 23 for peptides, or 4 for NA.
         {
-          seq1[i] = ResidueProperties.aaIndex[c];
-          if (seq1[i] > 23)
-          {
-            seq1[i] = 23;
-          }
+          seq1[i] = defInt;
         }
-        else if (type.equals("dna"))
-        {
-          seq1[i] = ResidueProperties.nucleotideIndex[c];
-          if (seq1[i] > 4)
-          {
-            seq1[i] = 4;
-          }
-        }
-
+      
       } catch (Exception e)
       {
-        if (type.equals("dna"))
-        {
-          seq1[i] = 4;
-        }
-        else
-        {
-          seq1[i] = 23;
-        }
+        seq1[i] = defInt;
       }
     }