X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FDBRefEntryTest.java;h=ae6dcdafa92140adc317b9c11b85360b5626e78c;hb=f7d70c3514a06321f07f6cda8dd9d26402f7f577;hp=7e1e9a6756950818080f909c06359a6cd2f34263;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index 7e1e9a6..ae6dcda 100644
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -1,17 +1,41 @@
+/*
+ * 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.datamodel;
 
+import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import jalview.util.MapList;
 
+import org.testng.annotations.Test;
+
 public class DBRefEntryTest
 {
 
   /**
    * Tests for the method that compares equality of reference (but not mapping)
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testEqualRef()
   {
     DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "V71633");
@@ -29,15 +53,89 @@ public class DBRefEntryTest
     assertFalse(ref1.equalRef(new DBRefEntry("UNIPROT", "1", "V71632")));
 
     // presence of or differences in mappings are ignored
-    ref1.setMap(new Mapping(new MapList(new int[]
-    { 1, 3 }, new int[]
-    { 1, 1 }, 3, 1)));
+    ref1.setMap(new Mapping(new MapList(new int[] { 1, 3 }, new int[] { 1,
+        1 }, 3, 1)));
     assertTrue(ref1.equalRef(ref2));
     assertTrue(ref2.equalRef(ref1));
-    ref1.setMap(new Mapping(new MapList(new int[]
-    { 1, 6 }, new int[]
-    { 1, 2 }, 3, 1)));
+    ref1.setMap(new Mapping(new MapList(new int[] { 1, 6 }, new int[] { 1,
+        2 }, 3, 1)));
     assertTrue(ref1.equalRef(ref2));
     assertTrue(ref2.equalRef(ref1));
   }
+
+  /**
+   * Tests for the method that may update a DBRefEntry from another with a
+   * mapping or 'real' version
+   */
+  @Test(groups = { "Functional" })
+  public void testUpdateFrom()
+  {
+    DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "V71633");
+
+    assertFalse(ref1.updateFrom(null));
+
+    /*
+     * equivalent other dbref
+     */
+    DBRefEntry ref2 = new DBRefEntry("uniprot", "1", "v71633");
+    assertTrue(ref1.updateFrom(ref2));
+    assertEquals("UNIPROT", ref1.getSource()); // unchanged
+    assertEquals("V71633", ref1.getAccessionId()); // unchanged
+  
+    /*
+     * ref1 has no mapping, acquires mapping from ref2
+     */
+    Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
+        1, 1 }, 3, 1));
+    ref2.setMap(map);
+    assertTrue(ref1.updateFrom(ref2));
+    assertSame(map, ref1.getMap()); // null mapping updated
+
+    /*
+     * ref1 has a mapping, does not acquire mapping from ref2
+     */
+    ref2.setMap(new Mapping(map));
+    assertTrue(ref1.updateFrom(ref2));
+    assertSame(map, ref1.getMap()); // non-null mapping not updated
+
+    /*
+     * ref2 has a different source, accession or version
+     */
+    ref2.setSource("pdb");
+    assertFalse(ref1.updateFrom(ref2));
+    ref2.setSource(ref1.getSource());
+    ref2.setAccessionId("P12345");
+    assertFalse(ref1.updateFrom(ref2));
+    ref2.setAccessionId(ref1.getAccessionId());
+    ref1.setVersion("2");
+    assertFalse(ref1.updateFrom(ref2));
+
+    /*
+     * a non-null version supersedes "0" or "source:0"
+     */
+    ref2.setVersion(null);
+    assertFalse(ref1.updateFrom(ref2));
+    assertEquals("2", ref1.getVersion());
+    ref2.setVersion("3");
+    ref1.setVersion("0");
+    assertTrue(ref1.updateFrom(ref2));
+    assertEquals("3", ref1.getVersion());
+    ref1.setVersion("UNIPROT:0");
+    assertTrue(ref1.updateFrom(ref2));
+    assertEquals("3", ref1.getVersion());
+
+    /*
+     * version "source:n" with n>0 is not superseded
+     */
+    ref1.setVersion("UNIPROT:1");
+    assertFalse(ref1.updateFrom(ref2));
+    assertEquals("UNIPROT:1", ref1.getVersion());
+
+    /*
+     * version "10" is not superseded
+     */
+    ref1.setVersion("10");
+    assertFalse(ref1.updateFrom(ref2));
+    assertEquals("10", ref1.getVersion());
+  }
 }