Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0440b24..2220171 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;
@@ -1870,7 +1870,7 @@ public class AlignmentUtils
       return;
     }
 
-    MapList newMap = targetToFrom.traverse(fromLoci.getMap());
+    MapList newMap = targetToFrom.traverse(fromLoci.getMapping());
 
     if (newMap != null)
     {
@@ -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