JAL-2110 enable and fix failing tests

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index abe713a..c2d7ca6 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -149,7 +149,7 @@ public class CrossRefTest
    * xref is found - not on the nucleotide sequence but on a peptide sequence in
    * the alignment which which it shares a nucleotide dbref
    */
-  @Test(groups = { "Functional" }, enabled = false)
+  @Test(groups = { "Functional" }, enabled = true)
   public void testFindXrefSequences_indirectDbrefToProtein()
   {
     /*
@@ -180,7 +180,7 @@ public class CrossRefTest
    * xref is found - not on the peptide sequence but on a nucleotide sequence in
    * the alignment which which it shares a protein dbref
    */
-  @Test(groups = { "Functional" }, enabled = false)
+  @Test(groups = { "Functional" }, enabled = true)
   public void testFindXrefSequences_indirectDbrefToNucleotide()
   {
     /*
@@ -193,7 +193,7 @@ public class CrossRefTest
     SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
     emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
     emblSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
-  
+
     /*
      * find EMBL xrefs for peptide sequence - it has no direct
      * dbrefs, but the 'corresponding' nucleotide sequence does, so is returned
@@ -204,9 +204,8 @@ public class CrossRefTest
      * - but nucleotide with matching peptide dbref does, so is returned
      */
     AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
-    Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq },
- al)
-            .findXrefSequences("EMBL", true);
+    Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq }, al)
+            .findXrefSequences("EMBL", false);
     assertEquals(1, xrefs.getHeight());
     assertSame(emblSeq, xrefs.getSequenceAt(0));
   }
@@ -225,7 +224,7 @@ public class CrossRefTest
     SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
     dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
     SequenceI dna2 = new Sequence("AJ307031", "AAACCCTTT");
-  
+
     /*
      * find UNIPROT xrefs for peptide sequence - it has no direct
      * dbrefs, and the other sequence (which has a UNIPROT dbref) is not 
@@ -241,7 +240,7 @@ public class CrossRefTest
    * Tests for the method that searches an alignment (with one sequence
    * excluded) for protein/nucleotide sequences with a given cross-reference
    */
-  @Test(groups = { "Functional" }, enabled = false)
+  @Test(groups = { "Functional" }, enabled = true)
   public void testSearchDataset()
   {
     /*
@@ -274,7 +273,9 @@ public class CrossRefTest
      * search for a protein sequence with dbref UNIPROT:Q9ZTS2
      */
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
-    found = testee.searchDataset(true, dna1, dbref, result, null, true);
+    found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
+            null, false); // search dataset with a protein xref from a dna
+                          // sequence to locate the protein product
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(pep1, result.get(0));
@@ -284,7 +285,9 @@ public class CrossRefTest
      */
     result.clear();
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
-    found = testee.searchDataset(false, pep1, dbref, result, null, false);
+    found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
+            null, false); // search dataset with a protein's direct dbref to
+                          // locate dna sequences with matching xref
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(dna1, result.get(0));