package jalview.util;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DBRefUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the method that selects DBRefEntry items whose source is in a supplied
* list
assertSame(ref2, selected[0]);
assertSame(ref3, selected[1]);
- sources = new String[] { "Uniprot", "EMBLCDS" };
+ sources = new String[] { "EMBLCDS" };
selected = DBRefUtils.selectRefs(dbrefs, sources);
assertNull(selected);
+
+ sources = new String[] { "embl", "uniprot" };
+ selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(3, selected.length);
+ assertSame(ref1, selected[0]);
+ assertSame(ref2, selected[1]);
+ assertSame(ref3, selected[2]);
}
/**
assertEquals("UNIPROTKB/SWISS-CHEESE",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
- }
- @Test(groups = { "Functional" })
- public void testIsDasCoordinateSystem()
- {
- assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
- assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
- assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
- "PDB", "v1", "a1")));
+ // these are not 'known' to Jalview
+ assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+ assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
- assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
- new DBRefEntry("PDB", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
- new DBRefEntry("PDB", "v1", "a1")));
- // "pdb" is converted to upper-case in DBRefEntry constructor
- assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
- new DBRefEntry("pdb", "v1", "a1")));
- assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
- "pdb", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
- "Uniprot", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
- "UNIPROT", "v1", "a1")));
- assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
- new DBRefEntry("pdb", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
- "EMBL", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
- "embl", "v1", "a1")));
}
-
/**
* Test 'parsing' a DBRef - non PDB case
*/