JAL-3251 SequenceToSequenceMapping now SequenceMapping, MappingType++

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0dfd383..f1084a7 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -24,7 +24,6 @@ import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
 
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -36,6 +35,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceMapping;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
@@ -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);
@@ -1935,7 +1935,7 @@ public class AlignmentUtils
             .findMappingsForSequence(proteinProduct, mappings);
     for (AlignedCodonFrame acf : mappingsToPeptide)
     {
-      for (SequenceToSequenceMapping map : acf.getMappings())
+      for (SequenceMapping map : acf.getMappings())
       {
         Mapping mapping = map.getMapping();
         if (mapping != aMapping
@@ -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;