import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.gff.SequenceOntologyLite;
import java.lang.reflect.Method;
-import java.net.MalformedURLException;
-import java.net.URL;
import java.util.Arrays;
-import java.util.List;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
}
}
- @Test(suiteName = "live")
- public void testLiveCheckEnsembl()
- {
- EnsemblRestClient sf = new EnsemblRestClient()
- {
-
- @Override
- public String getDbName()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected URL getUrl(List<String> ids) throws MalformedURLException
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected boolean useGetRequest()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- protected String getRequestMimeType(boolean b)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected String getResponseMimeType()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- };
- boolean isAvailable = sf.isEnsemblAvailable();
- System.out.println("Ensembl is "
- + (isAvailable ? "UP!"
- : "DOWN or unreachable ******************* BAD!"));
- }
-
@Test(groups = "Functional")
public void getGenomicRangesFromFeatures()
{
sb = new StringBuilder();
EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
- assertEquals("aATC-,hgmd_mutation", sb.toString());
+ EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
+ assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
}
/**