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)
*/
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));
}
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));
+ 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
assertEquals("3", ref1.getVersion());
/*
+ * canonical == false superseded by canonical == true
+ */
+ ref1.setCanonical(false);
+ ref2.setCanonical(true);
+ assertTrue(ref1.updateFrom(ref2));
+ assertTrue(ref1.isCanonical());
+
+ /*
+ * canonical == true NOT superseded by canonical == false
+ */
+ ref1.setCanonical(true);
+ ref2.setCanonical(false);
+ assertFalse(ref1.updateFrom(ref2));
+
+ /*
* version "source:n" with n>0 is not superseded
*/
ref1.setVersion("UNIPROT:1");
}
@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,
- 1));
- assertTrue(dbr.isPrimary());
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 3 }, new int[] { 1, 3 }, 1, 1));
+ 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());
}
}