3253-omnibus save

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

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 72f5a34..a4d6d92 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -21,14 +21,10 @@
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
@@ -36,8 +32,6 @@ import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
-import java.util.Arrays;
-import java.util.List;
 
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
@@ -141,13 +135,13 @@ public class EnsemblSeqProxyTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+    SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
   }
 
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
-    SequenceOntologyFactory.setInstance(null);
+    SequenceOntologyFactory.setSequenceOntology(null);
   }
 
   @DataProvider(name = "ens_seqs")
@@ -225,7 +219,6 @@ public class EnsemblSeqProxyTest
     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
             1, 2, 0f, null);
     sf.setValue("alleles", alleles);
-    sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 
     EnsemblSeqProxy.reverseComplementAlleles(sf);
     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
@@ -233,33 +226,5 @@ public class EnsemblSeqProxyTest
     assertEquals(revcomp, sf.getDescription());
     // verify alleles attribute is updated with reverse complement
     assertEquals(revcomp, sf.getValue("alleles"));
-    // verify attributes string is updated with reverse complement
-    assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
-  }
-
-  @Test(groups = "Functional")
-  public void testSortFeatures()
-  {
-    SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
-    SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
-    SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
-    SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
-    List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
-        sf2, sf3, sf4 });
-
-    // sort by start position ascending (forward strand)
-    // sf2 and sf3 tie and should not be reordered by sorting
-    SequenceFeatures.sortFeatures(sfs, true);
-    assertSame(sfs.get(0), sf2);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf1);
-    assertSame(sfs.get(3), sf4);
-
-    // sort by end position descending (reverse strand)
-    SequenceFeatures.sortFeatures(sfs, false);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf2);
-    assertSame(sfs.get(3), sf4);
   }
 }