JAL-1796 GeneLociI as distinguished DBRefEntry

[jalview.git] / test / jalview / io / vcf / VCFLoaderTest.java

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index cdfe298..7379ecd 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -4,7 +4,6 @@ import static org.testng.Assert.assertEquals;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.GeneLoci;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -100,8 +99,15 @@ public class VCFLoaderTest
      * verify variant feature(s) computed and added to protein
      * first codon AGC varies to ACC giving S/T
      */
-    SequenceI peptide = al.getSequenceAt(1)
-            .getDBRefs()[0].getMap().getTo();
+    DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs();
+    SequenceI peptide = null;
+    for (DBRefEntry dbref : dbRefs)
+    {
+      if (dbref.getMap().getMap().getFromRatio() == 3)
+      {
+        peptide = dbref.getMap().getTo();
+      }
+    }
     List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
     assertEquals(proteinFeatures.size(), 1);
     sf = proteinFeatures.get(0);
@@ -143,8 +149,7 @@ public class VCFLoaderTest
     SequenceI gene1 = alignment.getSequenceAt(0);
     int[] to = new int[] { 45051610, 45051634 };
     int[] from = new int[] { gene1.getStart(), gene1.getEnd() };
-    gene1.setGeneLoci(new GeneLoci("human", "GRCh38", "17", new MapList(
-            from, to, 1, 1)));
+    gene1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
 
     /*
      * map 'transcript1' to chromosome via 'gene1'
@@ -154,8 +159,8 @@ public class VCFLoaderTest
     to = new int[] { 45051612, 45051619, 45051624, 45051633 };
     SequenceI transcript1 = alignment.getSequenceAt(1);
     from = new int[] { transcript1.getStart(), transcript1.getEnd() };
-    transcript1.setGeneLoci(new GeneLoci("human", "GRCh38", "17",
-            new MapList(from, to, 1, 1)));
+    transcript1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+            1, 1));
 
     /*
      * map gene2 to chromosome reverse strand
@@ -163,8 +168,7 @@ public class VCFLoaderTest
     SequenceI gene2 = alignment.getSequenceAt(2);
     to = new int[] { 45051634, 45051610 };
     from = new int[] { gene2.getStart(), gene2.getEnd() };
-    gene2.setGeneLoci(new GeneLoci("human", "GRCh38", "17", new MapList(
-            from, to, 1, 1)));
+    gene2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
 
     /*
      * map 'transcript2' to chromosome via 'gene2'
@@ -174,8 +178,8 @@ public class VCFLoaderTest
     to = new int[] { 45051633, 45051624, 45051619, 45051612 };
     SequenceI transcript2 = alignment.getSequenceAt(3);
     from = new int[] { transcript2.getStart(), transcript2.getEnd() };
-    transcript2.setGeneLoci(new GeneLoci("human", "GRCh38", "17",
-            new MapList(from, to, 1, 1)));
+    transcript2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+            1, 1));
 
     /*
      * add a protein product as a DBRef on transcript1
@@ -262,7 +266,15 @@ public class VCFLoaderTest
      * verify variant feature(s) computed and added to protein
      * last codon GCT varies to GGT giving A/G in the last peptide position
      */
-    SequenceI peptide = al.getSequenceAt(3).getDBRefs()[0].getMap().getTo();
+    DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs();
+    SequenceI peptide = null;
+    for (DBRefEntry dbref : dbRefs)
+    {
+      if (dbref.getMap().getMap().getFromRatio() == 3)
+      {
+        peptide = dbref.getMap().getTo();
+      }
+    }
     List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
     assertEquals(proteinFeatures.size(), 1);
     sf = proteinFeatures.get(0);