JAL-1705 include stop codons in derived CDS; support ensemblgenomes

[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 7ef8dd7..5d95a3c 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -14,11 +14,11 @@ import jalview.io.FastaFile;
 import jalview.io.FileParse;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
+import jalview.util.MappingUtils;
 
 import java.lang.reflect.Method;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
@@ -309,9 +309,8 @@ public class EnsemblSeqProxyTest
     sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
     ds.addSequenceFeature(sf);
 
-    List<int[]> ranges = new ArrayList<int[]>();
-    int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
-    assertEquals(6, mappedLength);
+    List<int[]> ranges = testee.getCdsRanges(dnaSeq);
+    assertEquals(6, MappingUtils.getLength(ranges));
     assertEquals(2, ranges.size());
     assertEquals(4, ranges.get(0)[0]);
     assertEquals(6, ranges.get(0)[1]);
@@ -347,13 +346,12 @@ public class EnsemblSeqProxyTest
     sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
     ds.addSequenceFeature(sf);
   
-    List<int[]> ranges = new ArrayList<int[]>();
-    int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
+    List<int[]> ranges = testee.getCdsRanges(dnaSeq);
 
     /*
      * check the mapping starts with the first complete codon
      */
-    assertEquals(6, mappedLength);
+    assertEquals(6, MappingUtils.getLength(ranges));
     assertEquals(2, ranges.size());
     assertEquals(7, ranges.get(0)[0]);
     assertEquals(9, ranges.get(0)[1]);
@@ -364,26 +362,28 @@ public class EnsemblSeqProxyTest
   @Test(groups = "Functional")
   public void testIsTranscriptIdentifier()
   {
-    assertFalse(EnsemblSeqProxy.isTranscriptIdentifier(null));
-    assertFalse(EnsemblSeqProxy.isTranscriptIdentifier(""));
-    assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENSG00000012345"));
-    assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENST00000012345"));
-    assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENSMUST00000012345"));
-    assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("enst00000012345"));
-    assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST000000123456"));
-    assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST0000001234"));
+    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()
   {
-    assertFalse(EnsemblSeqProxy.isGeneIdentifier(null));
-    assertFalse(EnsemblSeqProxy.isGeneIdentifier(""));
-    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENST00000012345"));
-    assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSG00000012345"));
-    assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSMUSG00000012345"));
-    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ensg00000012345"));
-    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG000000123456"));
-    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG0000001234"));
+    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"));
   }
 }
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