Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

[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 c525e95..f9c2c4b 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,13 +1,18 @@
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
 import java.net.MalformedURLException;
@@ -16,6 +21,8 @@ import java.util.Arrays;
 import java.util.List;
 
 import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -101,20 +108,16 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 
-  @DataProvider(name = "queries")
-  public Object[][] createQueryData(Method m)
+  @BeforeClass
+  public void setUp()
   {
-    return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @Test(dataProvider = "queries")
-  public void testIsValidReference(String query) throws Exception
+  @AfterClass
+  public void tearDown()
   {
-    EnsemblSequenceFetcher esq = new EnsemblProtein();
-    Assert.assertTrue(esq.isValidReference(query),
-            "Expected reference string " + query
-                    + " to be valid for regex "
-                    + esq.getAccessionValidator().toString());
+    SequenceOntologyFactory.setInstance(null);
   }
 
   @DataProvider(name = "ens_seqs")
@@ -211,73 +214,37 @@ public class EnsemblSeqProxyTest
                     : "DOWN or unreachable ******************* BAD!"));
   }
 
-  /**
-   * Tests for the method that computes all peptide variants given codon
-   * variants
-   */
   @Test(groups = "Functional")
-  public void testComputePeptideVariants()
+  public void getGenomicRangesFromFeatures()
   {
-    String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
 
-    /*
-     * AGT codes for S - this is not included in the variants returned
-     */
-    List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
-    assertEquals("[]", variants.toString());
-
-    // S is reported if it differs from the current value (A):
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
-    assertEquals("[S]", variants.toString());
-
-    /*
-     * synonymous variant is not reported
-     */
-    codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
-    // AGC and AGT both code for S
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
-    assertEquals("[]", variants.toString());
-
-    /*
-     * equivalent variants are only reported once
-     */
-    codonVariants = new String[][] { { "C" }, { "T" },
-        { "A", "C", "G", "T" } };
-    // CTA CTC CTG CTT all code for L
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
-    assertEquals("[L]", variants.toString());
-
-    /*
-     * vary codons 1 and 2; variant products are sorted and non-redundant
-     */
-    codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
-    // aga ata cga cta code for R, I, R, L
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
-    assertEquals("[I, L, R]", variants.toString());
-
-    /*
-     * vary codons 2 and 3
-     */
-    codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
-    // aga agc ata atc code for R, S, I, I
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
-    assertEquals("[I, R]", variants.toString());
+  }
 
-    /*
-     * vary codons 1 and 3
-     */
-    codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
-    // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
-    assertEquals("[K, N, Y, STOP]", variants.toString());
+  @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"));
+  }
 
-    /*
-     * vary codons 1, 2 and 3
-     */
-    codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
-        { "t", "g" } };
-    // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
-    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
-    assertEquals("[C, R, T, W]", variants.toString());
+  @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"));
   }
 }
\ No newline at end of file