package jalview.ws.sifts;
import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
@BeforeTest(alwaysRun = true)
public void populateExpectedMapping() throws SiftsException
- {
+ {
expectedMapping.put(51, new int[] { 1, 2 });
expectedMapping.put(52, new int[] { 2, 7 });
expectedMapping.put(53, new int[] { 3, 12 });
expectedMapping.put(145, new int[] { 95, 714 });
expectedMapping.put(146, new int[] { 96, 722 });
expectedMapping.put(147, new int[] { 97, 729 });
- }
-
+ }
+
@BeforeTest(alwaysRun = true)
public void setUpSiftsClient() throws SiftsException
{
+ // read test props before manipulating config
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// SIFTs entries are updated weekly - so use saved SIFTs file to enforce
// test reproducibility
new SiftsSettings();
}
}
-
@Test(groups = { "Functional" })
public void getAllMappingAccessionTest()
{
// TODO delete when auto-fetching of DBRefEntry is implemented
DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
- dbRef.setStartRes(1);
- dbRef.setEndRes(147);
testSeq.addDBRef(dbRef);
// testSeq.setSourceDBRef(dbRef);
try
{
HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
- "A", testSeq,
- null);
+ "A", testSeq, null);
Assert.assertEquals(testSeq.getStart(), 1);
Assert.assertEquals(testSeq.getEnd(), 147);
Assert.assertEquals(actualMapping, expectedMapping);
private void populateAtomPositionsNullTest1()
throws IllegalArgumentException, SiftsException
{
- siftsClient.populateAtomPositions(null, null);
+ siftsClient.populateAtomPositions(null, null);
}
@Test(
DBRefEntryI expectedDBRef = new DBRefEntry();
expectedDBRef.setSource(DBRefSource.UNIPROT);
expectedDBRef.setAccessionId("P00221");
- expectedDBRef.setStartRes(1);
- expectedDBRef.setEndRes(147);
expectedDBRef.setVersion("");
Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
} catch (Exception e)
expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionTest() throws SiftsException
{
- SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+ SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
try
{
siftsClient.getValidSourceDBRef(invalidTestSeq);
DBRefEntryI validDBRef = new DBRefEntry();
validDBRef.setSource(DBRefSource.UNIPROT);
validDBRef.setAccessionId("P00221");
- validDBRef.setStartRes(1);
- validDBRef.setEndRes(147);
validDBRef.setVersion("");
Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
}