translateN.patch

--- src/main/java/org/biojava3/core/sequence/transcription/RNAToAminoAcidTranslator.java.orig	2011-03-09 15:32:39.295875004 -0500
+++ src/main/java/org/biojava3/core/sequence/transcription/RNAToAminoAcidTranslator.java	2011-03-10 08:18:42.525875009 -0500
@@ -85,7 +85,6 @@
             codonL.add(codon);
             
         }
-
         unknownAminoAcidCompound = aminoAcids.getCompoundForString("X");
     }
 
@@ -105,32 +104,32 @@
             new WindowedSequence<NucleotideCompound>(originalSequence, 3);
                 
         for (SequenceView<NucleotideCompound> element : iter) {
-            AminoAcidCompound aminoAcid;
+            AminoAcidCompound aminoAcid = null;
 
             int i =1;
             Table.CaseInsensitiveTriplet triplet = new Table.CaseInsensitiveTriplet(
               element.getCompoundAt(i++), element.getCompoundAt(i++), element.getCompoundAt(i++));
 
-            Codon target;
+            Codon target = null;
 
             int arrayIndex = triplet.intValue();
             //So long as we're within range then access
             if(arrayIndex > -1 && arrayIndex < codonArray.length) {
                 target = codonArray[arrayIndex];
-                aminoAcid = target.getAminoAcid();
+                if (target != null) {
+                    aminoAcid = target.getAminoAcid();
+                }
             }
             //Otherwise we have to use the Map
             else {
                 target = quickLookup.get(triplet);
                 aminoAcid = target.getAminoAcid();
             }
-            
             if(aminoAcid == null && translateNCodons()) {
                 aminoAcid = unknownAminoAcidCompound;
             }
             addCompoundsToList(Arrays.asList(aminoAcid), workingList);
         }
-
         postProcessCompoundLists(workingList);
 
         return workingListToSequences(workingList);
@@ -157,11 +156,13 @@
         AminoAcidCompound initMet = getToCompoundSet().getCompoundForString("M");
         AminoAcidCompound start = sequence.get(0);
         boolean isStart = false;
-        for (Codon c : aminoAcidToCodon.get(start)) {
-            if (c.isStart()) {
-                isStart = true;
-                break;
-            }
+        if (aminoAcidToCodon.containsKey(start)) {
+          for (Codon c : aminoAcidToCodon.get(start)) {
+              if (c.isStart()) {
+                  isStart = true;
+                  break;
+              }
+          }
         }
 
         if (isStart) {
@@ -176,11 +177,13 @@
     protected void trimStop(List<AminoAcidCompound> sequence) {
         AminoAcidCompound stop = sequence.get(sequence.size() - 1);
         boolean isStop = false;
-        for (Codon c : aminoAcidToCodon.get(stop)) {
-            if (c.isStop()) {
-                isStop = true;
-                break;
-            }
+        if (aminoAcidToCodon.containsKey(stop)) {
+          for (Codon c : aminoAcidToCodon.get(stop)) {
+              if (c.isStop()) {
+                  isStop = true;
+                  break;
+              }
+          }
         }
 
         if (isStop) {
--- src/test/java/org/biojava3/core/sequence/TranslationTest.java.orig	2011-03-09 12:14:11.035875001 -0500
+++ src/test/java/org/biojava3/core/sequence/TranslationTest.java	2011-03-10 08:18:27.085875003 -0500
@@ -91,6 +91,21 @@
         assertThat("Initator methionine wrong", initMet.toString(), is("M"));
     }
 
+  @Test
+    public void translateN() {
+        TranscriptionEngine.Builder b = new TranscriptionEngine.Builder();
+        b.translateNCodons(true).initMet(true);
+        TranscriptionEngine e = b.build();
+        DNASequence dna = new DNASequence("ATN");
+        RNASequence rna = dna.getRNASequence(e);
+        ProteinSequence protein = rna.getProteinSequence(e);
+        assertThat("Ambiguous translation problem", protein.toString(), is("X"));
+        DNASequence dna2 = new DNASequence("GTGGTNTAA");
+        RNASequence rna2 = dna2.getRNASequence(e);
+        ProteinSequence protein2 = rna2.getProteinSequence(e);
+        assertThat("Ambiguous translation problem", protein2.toString(), is("VX"));
+    }
+
     @SuppressWarnings("serial")
     @Test
     public void multiFrameTranslation() {