Merge branch 'releases/Release_2_10_0_Branch'

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

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 50f38b6..e1d075d 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -80,11 +80,11 @@ public class CrossRefTest
      * Just the protein refs:
      */
     found = DBRefUtils.selectDbRefs(false, refs);
-    assertEquals(3, found.length);
+    assertEquals(4, found.length);
     assertSame(ref1, found[0]);
     assertSame(ref2, found[1]);
     assertSame(ref4, found[2]);
-    // assertSame(ref9, found[3]); ENSEMBL not protein
+    assertSame(ref9, found[3]);
   }
 
   /**
@@ -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));
@@ -624,7 +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");