X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FDBRefEntryTest.java;h=c8f998b247bc57a9f17d7f4d2e0e94f6d178b684;hb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;hp=8cc31e0778c614931c7df47430685f08e23a43c5;hpb=168ef5a045478ef56a5d9f8c71fbddb53a6b8a58;p=jalview.git

diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index 8cc31e0..c8f998b 100644
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -25,13 +25,22 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.gui.JvOptionPane;
 import jalview.util.MapList;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class DBRefEntryTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Tests for the method that compares equality of reference (but not mapping)
    */
@@ -81,7 +90,7 @@ public class DBRefEntryTest
     assertTrue(ref1.updateFrom(ref2));
     assertEquals("UNIPROT", ref1.getSource()); // unchanged
     assertEquals("V71633", ref1.getAccessionId()); // unchanged
-  
+
     /*
      * ref1 has no mapping, acquires mapping from ref2
      */
@@ -140,39 +149,80 @@ public class DBRefEntryTest
   }
 
   @Test(groups = { "Functional" })
-  public void testIsPrimary()
+  public void testIsPrimaryCandidate()
   {
     DBRefEntry dbr = new DBRefEntry(DBRefSource.UNIPROT, "", "Q12345");
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
+
     /*
-     *  1:1 mapping with shift
+     *  1:1 mapping - ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 5, 9 }, 1,
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
             1));
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
 
     /*
-     *  1:1 mapping with shift and sequenceRef
+     *  1:1 mapping of identical split ranges - not ok
      */
-    dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
-            new int[] { 5, 9 }, 1, 1));
-    assertFalse(dbr.isPrimary());
+    dbr.setMap(new Mapping(null, new int[] { 1, 3, 6, 9 }, new int[] { 1,
+        3, 6, 9 }, 1, 1));
+    assertFalse(dbr.isPrimaryCandidate());
 
     /*
-     * 1:3 mapping with shift (fail)
+     *  1:1 mapping of different ranges - not ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 5, 9 }, 1,
-            3));
-    assertFalse(dbr.isPrimary());
+    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 2, 5 }, 1,
+            1));
+    assertFalse(dbr.isPrimaryCandidate());
+
     /*
-     * 2:2 mapping with shift (expected fail, but maybe not realistic)
+     *  1:1 mapping of 'isoform' ranges - not ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 5, 9 }, 2,
-            2));
-    assertFalse(dbr.isPrimary());
+    dbr.setMap(new Mapping(null, new int[] { 1, 2, 6, 9 }, new int[] { 1,
+        3, 7, 9 }, 1, 1));
+    assertFalse(dbr.isPrimaryCandidate());
+    dbr.setMap(null);
+    assertTrue(dbr.isPrimaryCandidate());
 
+    /*
+     * Version string is prefixed with another dbref source string (fail)
+     */
     dbr.setVersion(DBRefSource.EMBL + ":0");
-    assertFalse(dbr.isPrimary());
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     * Version string is alphanumeric
+     */
+    dbr.setVersion("0.1.b");
+    assertTrue(dbr.isPrimaryCandidate());
 
+    /*
+     * null version string can't be primary ref
+     */
+    dbr.setVersion(null);
+    assertFalse(dbr.isPrimaryCandidate());
+    dbr.setVersion("");
+    assertTrue(dbr.isPrimaryCandidate());
+
+    /*
+     *  1:1 mapping and sequenceRef (fail)
+     */
+    dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
+            new int[] { 1, 3 }, 1, 1));
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     * 1:3 mapping (fail)
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
+            3));
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     * 2:2 mapping with shift (expected fail, but maybe use case for a pass)
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 1, 4 }, 2,
+            2));
+    assertFalse(dbr.isPrimaryCandidate());
   }
 }