import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.io.AnnotationFile;
+import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.Jws2Discoverer;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
public class RNAStructExportImport
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
-
- jalview.bin.Cache.initLogger();
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
for (Jws2Instance svc : disc.getServices())
Assert.fail("no web service");
}
- jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+ FileLoader fl = new FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
// public?
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
if (af != null)
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
- assertTrue(
+ assertNotNull(
"Test "
+ testname
+ "\nAlignment annotation file was not regenerated. Null string",
- anfileout != null);
+ anfileout);
assertTrue(
"Test "
+ testname
@Test(groups = { "Functional" })
public void testRnaalifoldSettingsRecovery()
{
- List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
- for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
- .getRunnerConfig().getArguments())
+ List<Argument> opts = new ArrayList<Argument>();
+ for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+ .getArguments())
{
if (rg.getDescription().contains("emperature"))
{