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 c270029..6c39b9b 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -76,6 +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" })
@@ -117,13 +138,13 @@ 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());
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
-    assertNull(seq.getAllPDBEntries());
+    assertTrue(seq.getAllPDBEntries().isEmpty());
   }
 
   /**
@@ -135,7 +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());
@@ -209,4 +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]);
+  }
 }