package jalview.ws.sifts;
import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.structure.StructureMapping;
+import jalview.xml.binding.sifts.Entry.Entity;
import java.io.File;
import java.io.IOException;
@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();
// 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);
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)
DBRefEntryI validDBRef = new DBRefEntry();
validDBRef.setSource(DBRefSource.UNIPROT);
validDBRef.setAccessionId("P00221");
- validDBRef.setStartRes(1);
- validDBRef.setEndRes(147);
validDBRef.setVersion("");
Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
}
System.out.println("Actual DbVersion: " + actualDbVersion);
Assert.assertEquals(actualDbVersion, "2.0");
}
+
+ @Test(groups = { "Functional" })
+ public void getEntityByMostOptimalMatchedIdTest()
+ {
+ SiftsClient siftsClientX = null;
+ PDBfile pdbFile;
+ try
+ {
+ pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
+ + ".pdb", AppletFormatAdapter.FILE);
+ siftsClientX = new SiftsClient(pdbFile);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
+ Assert.assertEquals(entityA.getEntityId(), "A");
+ Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B");
+ Assert.assertEquals(entityB.getEntityId(), "C");
+ Entity entityC = siftsClientX.getEntityByMostOptimalMatchedId("C");
+ Assert.assertEquals(entityC.getEntityId(), "B");
+ Entity entityD = siftsClientX.getEntityByMostOptimalMatchedId("D");
+ Assert.assertEquals(entityD.getEntityId(), "D");
+
+ }
}