import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.structure.StructureImportSettings;
import java.io.IOException;
import java.util.List;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBfileTest
assertEquals("D", pf.getChains().get(3).id);
PDBChain chainA = pf.getChains().get(0);
+ SequenceI seqA = pf.getSeqs().get(0);
+
assertEquals(0, chainA.seqstart); // not set
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
- assertEquals(1, chainA.sequence.getAllPDBEntries().size());
- PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
+ assertEquals(1, seqA.getAllPDBEntries().size());
+ PDBEntry pdb = seqA.getAllPDBEntries().get(0);
assertEquals("A", pdb.getChainCode());
assertEquals("PDB", pdb.getType());
assertEquals("3W5V", pdb.getId());
/*
* PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
*/
- assertEquals("Secondary Structure for 3W5VA", anns[0].description);
- assertEquals("Secondary Structure for 3W5VB", anns[2].description);
- assertEquals("Secondary Structure for 3W5VC", anns[4].description);
- assertEquals("Secondary Structure for 3W5VD", anns[6].description);
+ assertEquals("Secondary Structure for 3w5vA", anns[0].description);
+ assertEquals("Secondary Structure for 3w5vB", anns[2].description);
+ assertEquals("Secondary Structure for 3w5vC", anns[4].description);
+ assertEquals("Secondary Structure for 3w5vD", anns[6].description);
/*
* Verify SS annotations are linked to respective sequences (chains)
pf.addAnnotations(al);
return al.getAlignmentAnnotation();
}
+
+ // @formatter:on
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ }
}