/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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
/*
* 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");
+ }
}