JAL-1793 update spike build to latest incl stop and synonymous variants on peptides

[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 e977233..42afa82 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -21,13 +21,12 @@
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import static org.testng.AssertJUnit.assertSame;
 
 import jalview.datamodel.Alignment;
 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;
@@ -37,6 +36,7 @@ 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;
@@ -189,34 +189,6 @@ public class EnsemblSeqProxyTest
 
   }
 
-  @Test(groups = "Functional")
-  public void testIsTranscriptIdentifier()
-  {
-    EnsemblSeqProxy testee = new EnsemblGene();
-    assertFalse(testee.isTranscriptIdentifier(null));
-    assertFalse(testee.isTranscriptIdentifier(""));
-    assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
-    assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
-    assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
-    assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
-    assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
-    assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
-  }
-
-  @Test(groups = "Functional")
-  public void testIsGeneIdentifier()
-  {
-    EnsemblSeqProxy testee = new EnsemblGene();
-    assertFalse(testee.isGeneIdentifier(null));
-    assertFalse(testee.isGeneIdentifier(""));
-    assertFalse(testee.isGeneIdentifier("ENST00000012345"));
-    assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
-    assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
-    assertFalse(testee.isGeneIdentifier("ensg00000012345"));
-    assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
-    assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
-  }
-
   /**
    * Test the method that appends a single allele's reverse complement to a
    * string buffer
@@ -269,15 +241,22 @@ public class EnsemblSeqProxyTest
     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
-    SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
+    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
-    EnsemblSeqProxy.sortFeatures(sfs, true);
-    assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+    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)
-    EnsemblSeqProxy.sortFeatures(sfs, false);
-    assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+    SequenceFeatures.sortFeatures(sfs, false);
+    assertSame(sfs.get(0), sf1);
+    assertSame(sfs.get(1), sf3);
+    assertSame(sfs.get(2), sf2);
+    assertSame(sfs.get(3), sf4);
   }
 }