X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=371bb91dcd39bdc3ba35850d49325b2b14946602;hb=1d17220cc3868f513b5e310a5d09b0f419f13d84;hp=4a55a0d8e62369a182cd718f1a90924c1ca42119;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 4a55a0d..371bb91 100644
--- 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" })
@@ -137,7 +138,7 @@ public class DBRefUtilsTest
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
-    DBRefEntry[] refs = seq.getDBRef();
+    DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
     assertEquals("EMBL", ref.getSource());
@@ -155,7 +156,7 @@ public class DBRefUtilsTest
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
             "1WRI A; 7-80;");
-    DBRefEntry[] refs = seq.getDBRef();
+    DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
     assertEquals("PDB", ref.getSource());
@@ -229,4 +230,30 @@ 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[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
+        ref2, ref3, ref4, ref5 }, "A1234");
+    assertEquals(3, matches.length);
+    assertSame(ref1, matches[0]);
+    assertSame(ref2, matches[1]);
+    assertSame(ref5, matches[2]);
+  }
 }