JAL-2505 remove setters for SequenceFeature.begin,end,type,featureGroup

[jalview.git] / test / jalview / ext / ensembl / EnsemblGeneTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index edecc23..a8c491c 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -211,22 +211,24 @@ public class EnsemblGeneTest
     sf.setValue("ID", "gene:" + geneId);
     assertFalse(testee.retainFeature(sf, geneId));
 
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setType("mature_transcript");
+    sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+            null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+            0f, null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
     sf.setValue("Parent", "gene:XYZ");
     assertFalse(testee.retainFeature(sf, geneId));
 
-    sf.setType("anything");
+    sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, geneId));
   }
 
@@ -253,15 +255,18 @@ public class EnsemblGeneTest
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // gene sub-type with right ID is valid
-    sf.setType("snRNA_gene");
+    sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // transcript not valid:
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
 
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }