From 3293a3287aa25f50577baae4f2373710895bdca2 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 2 Nov 2009 13:25:48 +0000
Subject: [PATCH] gracefully cope with non-standard nucleotide or amino acid
 symbols in pairwise alignment.

---
 src/jalview/analysis/AlignSeq.java |   31 ++++++++-----------------------
 1 file changed, 8 insertions(+), 23 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 49be7f9..999dd07 100755
--- 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
@@ -821,7 +825,6 @@ public class AlignSeq
   public int[] stringToInt(String s, String type)
   {
     int[] seq1 = new int[s.length()];
-
     for (int i = 0; i < s.length(); i++)
     {
       // String ss = s.substring(i, i + 1).toUpperCase();
@@ -834,33 +837,15 @@ public class AlignSeq
 
       try
       {
-        if (type.equals("pep"))
-        {
-          seq1[i] = ResidueProperties.aaIndex[c];
-          if (seq1[i] > 23)
-          {
-            seq1[i] = 23;
-          }
-        }
-        else if (type.equals("dna"))
+        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.nucleotideIndex[c];
-          if (seq1[i] > 4)
-          {
-            seq1[i] = 4;
-          }
+          seq1[i] = defInt;
         }
 
       } catch (Exception e)
       {
-        if (type.equals("dna"))
-        {
-          seq1[i] = 4;
-        }
-        else
-        {
-          seq1[i] = 23;
-        }
+        seq1[i] = defInt;
       }
     }
 
-- 
1.7.10.2