JAL-1796 GeneLociI as distinguished DBRefEntry

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 6c4526f..78d2ad5 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -11,7 +11,7 @@ import jalview.analysis.Dna;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.GeneLoci;
+import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -199,13 +199,13 @@ public class VCFLoader
           boolean isVcfRefGrch37)
   {
     int count = 0;
-    GeneLoci seqCoords = seq.getGeneLoci();
+    GeneLociI seqCoords = seq.getGeneLoci();
     if (seqCoords == null)
     {
       return 0;
     }
 
-    List<int[]> seqChromosomalContigs = seqCoords.mapping.getToRanges();
+    List<int[]> seqChromosomalContigs = seqCoords.getMap().getToRanges();
     for (int[] range : seqChromosomalContigs)
     {
       count += addVcfVariants(seq, reader, range, isVcfRefGrch37);
@@ -231,11 +231,11 @@ public class VCFLoader
   protected int addVcfVariants(SequenceI seq, VCFReader reader,
           int[] range, boolean isVcfRefGrch37)
   {
-    GeneLoci seqCoords = seq.getGeneLoci();
+    GeneLociI seqCoords = seq.getGeneLoci();
 
-    String chromosome = seqCoords.chromosome;
-    String seqRef = seqCoords.assembly;
-    String species = seqCoords.species;
+    String chromosome = seqCoords.getChromosomeId();
+    String seqRef = seqCoords.getAssemblyId();
+    String species = seqCoords.getSpeciesId();
 
     // TODO handle species properly
     if ("".equals(species))
@@ -273,7 +273,7 @@ public class VCFLoader
      * (convert a reverse strand range to forwards)
      */
     int count = 0;
-    MapList mapping = seqCoords.mapping;
+    MapList mapping = seqCoords.getMap();
 
     int fromLocus = Math.min(range[0], range[1]);
     int toLocus = Math.max(range[0], range[1]);