X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=a85dcefd55c4af1647b19554180f19fce5a27816;hb=b9867dd3b0aeaa0fcb839b59cadbb1f76309cb5e;hp=24ddb34ce9dd79428ff5e36e815f18bffde10e60;hpb=bf0a46a8e950f4cf270c2f13e0f5bcf9dd206b70;p=jalview.git

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 24ddb34..a85dcef 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -121,8 +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
@@ -140,8 +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());
   }
 
   /**
@@ -249,8 +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"));
@@ -280,7 +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));
@@ -294,7 +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));
@@ -402,11 +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
@@ -471,7 +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,
@@ -483,8 +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
@@ -620,7 +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");