Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef

[jalview.git] / test / jalview / util / DBRefUtilsTest.java

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 7a6dc35..6c39b9b 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -96,6 +96,7 @@ public class DBRefUtilsTest
     assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
     assertEquals("UNIPROTKB/SWISS-CHEESE",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
+    assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
   }
 
   @Test(groups = { "Functional" })
@@ -143,7 +144,7 @@ public class DBRefUtilsTest
     assertEquals("EMBL", ref.getSource());
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
-    assertNull(seq.getAllPDBEntries());
+    assertTrue(seq.getAllPDBEntries().isEmpty());
   }
 
   /**
@@ -229,4 +230,60 @@ public class DBRefUtilsTest
     assertSame(ref1, matches[0]);
     assertSame(ref2, matches[1]);
   }
+
+  /**
+   * Test the method that searches for matching references based on accession id
+   * only
+   */
+  @Test(groups = { "Functional" })
+  public void testSearchRefs_accessionid()
+  {
+  
+    DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
+    DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
+    DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
+    // ref5 matches although it has a mapping - ignored
+    DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
+    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
+        1 }, 1, 1)));
+  
+    DBRefEntry[] dbrefs = new DBRefEntry[] { ref1,
+        ref2, ref3, ref4, ref5 };
+    DBRefEntry[] matches = DBRefUtils.searchRefs(dbrefs, "A1234");
+    assertEquals(3, matches.length);
+    assertSame(ref1, matches[0]);
+    assertSame(ref2, matches[1]);
+    assertSame(ref5, matches[2]);
+  }
+
+  /**
+   * Test the method that searches for matches references - case when we are
+   * matching a reference with null (any) accession id
+   */
+  @Test(groups = { "Functional" })
+  public void testSearchRefs_wildcardAccessionid()
+  {
+    DBRefEntry target = new DBRefEntry("EMBL", "2", null);
+  
+    DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
+    // constructor changes embl to EMBL
+    DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
+    DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
+    // ref5 matches although it has a mapping - ignored
+    DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
+    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
+        1 }, 1, 1)));
+  
+    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
+        ref2, ref3, ref4, ref5 }, target);
+    assertEquals(4, matches.length);
+    assertSame(ref1, matches[0]);
+    assertSame(ref2, matches[1]);
+    assertSame(ref3, matches[2]);
+    assertSame(ref5, matches[3]);
+  }
 }