JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

[jalview.git] / src / jalview / gui / CrossRefAction.java

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 85f2498..51ac2ee 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -356,12 +356,12 @@ public class CrossRefAction implements Runnable
             seq.getLength());
     if (geneLoci != null)
     {
-      MapList map = geneLoci.getMap();
+      MapList map = geneLoci.getMapping();
       int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
       if (mappedFromLength == seq.getLength())
       {
         seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
-                geneLoci.getChromosomeId(), geneLoci.getMap());
+                geneLoci.getChromosomeId(), map);
         retrievedLoci.put(dbref, geneLoci);
         return true;
       }
@@ -374,12 +374,12 @@ public class CrossRefAction implements Runnable
             seq.getLength());
     if (geneLoci != null)
     {
-      MapList map = geneLoci.getMap();
+      MapList map = geneLoci.getMapping();
       int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
       if (mappedFromLength == seq.getLength())
       {
         seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
-                geneLoci.getChromosomeId(), geneLoci.getMap());
+                geneLoci.getChromosomeId(), map);
         retrievedLoci.put(dbref, geneLoci);
         return true;
       }