Merge branch 'develop' into feature/JAL-3187linkedFeatures

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0bc8180..4b4e2a7 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1107,7 +1107,7 @@ public class AlignmentUtils
         SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein);
         if (prot != null)
         {
-          Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
+          Mapping seqMap = mapping.getMappingForSequence(dnaSeq, false);
           addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap,
                   alignedCodons);
           unmappedProtein.remove(prot);
@@ -2428,7 +2428,8 @@ public class AlignmentUtils
   static int computePeptideVariants(SequenceI peptide, int peptidePos,
           List<DnaVariant>[] codonVariants)
   {
-    String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
+    String residue = String
+            .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
     int count = 0;
     String base1 = codonVariants[0].get(0).base;
     String base2 = codonVariants[1].get(0).base;