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"));
+
+ // these are not 'known' to Jalview
+ assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+ assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
+
}
@Test(groups = { "Functional" })
1 }, 1, 1)));
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3, ref4, ref5 }, target);
+ ref1, ref2, ref3, ref4, ref5 }, target);
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
ref3.setMap(map3);
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3 }, target);
+ ref1, ref2, ref3 }, target);
assertEquals(2, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
@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 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[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
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
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
+
List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
- ref1,
- ref2, ref3, ref4, ref5 }, target);
+ ref1, ref2, ref3, ref4, ref5 }, target);
assertEquals(4, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));