Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / analysis / CrossRefTest.java

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 62bcae8..a85dcef 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -80,12 +80,11 @@ public class CrossRefTest
      * Just the protein refs:
      */
     found = DBRefUtils.selectDbRefs(false, refs);
-    assertEquals(5, found.length);
+    assertEquals(4, found.length);
     assertSame(ref1, found[0]);
     assertSame(ref2, found[1]);
-    assertSame(ref3, found[2]);
-    assertSame(ref4, found[3]);
-    assertSame(ref9, found[4]);
+    assertSame(ref4, found[2]);
+    assertSame(ref9, found[3]);
   }
 
   /**
@@ -122,8 +121,9 @@ public class CrossRefTest
     seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
     sources = new CrossRef(new SequenceI[] { seq }, al)
             .findXrefSourcesForSequences(false);
-    assertEquals(4, sources.size());
-    assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+    // method is patched to remove EMBL from the sources to match
+    assertEquals(3, sources.size());
+    assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
 
     /*
      * add a sequence to the alignment which has a dbref to UNIPROT|A1234
@@ -141,8 +141,9 @@ public class CrossRefTest
     al.addSequence(seq2);
     sources = new CrossRef(new SequenceI[] { seq, seq2 }, al)
             .findXrefSourcesForSequences(false);
-    assertEquals(3, sources.size());
-    assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
+    // method removed EMBL from sources to match
+    assertEquals(2, sources.size());
+    assertEquals("[EMBLCDS, GENEDB]", sources.toString());
   }
 
   /**
@@ -250,8 +251,7 @@ public class CrossRefTest
      */
     SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
     Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList(
-            new int[] { 1, 21 }, new int[] {
-        1, 7 }, 3, 1));
+            new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1));
     DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
     dna1.addDBRef(dbref);
     dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
@@ -281,7 +281,7 @@ public class CrossRefTest
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
     found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
             acf, false); // search dataset with a protein xref from a dna
-                          // sequence to locate the protein product
+                         // sequence to locate the protein product
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(pep1, result.get(0));
@@ -295,7 +295,7 @@ public class CrossRefTest
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
     found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
             acf, false); // search dataset with a protein's direct dbref to
-                          // locate dna sequences with matching xref
+                         // locate dna sequences with matching xref
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(dna1, result.get(0));
@@ -403,11 +403,14 @@ public class CrossRefTest
   public void testFindXrefSequences_withFetch()
   {
     SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
-    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
-    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
-    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
     final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
     final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
 
     /*
      * argument false suppresses adding DAS sources
@@ -472,7 +475,7 @@ public class CrossRefTest
      * 'spliced transcript' with CDS ranges
      */
     SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
-    braf002.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
+    braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
     braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
             null));
     braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
@@ -484,8 +487,9 @@ public class CrossRefTest
      * which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl 
      */
     final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
     final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
-
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
     /*
      * argument false suppresses adding DAS sources
      * todo: define an interface type SequenceFetcherI and mock that
@@ -621,7 +625,7 @@ public class CrossRefTest
      */
     final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG");
     DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20");
-    dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+    dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
             new MapList(map2)));
     x07547.addDBRef(dbref7);
     DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");