import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
public class RNAStructExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
public static String testseqs = "examples/RF00031_folded.stk";
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
+ while (disc.isRunning())
+ {
+ // don't get services until discoverer has finished
+ Thread.sleep(100);
+ }
+
for (Jws2Instance svc : disc.getServices())
{
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRNAAliFoldValidStructure()
{
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRNAStructExport()
{
AlignmentI orig_alig = af.getViewport().getAlignment();
- testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+ verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
- public static void testAnnotationFileIO(String testname, AlignmentI al)
+ static void verifyAnnotationFileIO(String testname, AlignmentI al)
{
try
{
// what format would be appropriate for RNAalifold annotations?
- String aligfileout = FileFormat.Pfam.getAlignmentFile().print(
+ String aligfileout = FileFormat.Pfam.getWriter(null).print(
al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRnaalifoldSettingsRecovery()
{
List<Argument> opts = new ArrayList<Argument>();
- for (Argument rg : (List<Argument>) rnaalifoldws
- .getRunnerConfig().getArguments())
+ for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+ .getArguments())
{
if (rg.getDescription().contains("emperature"))
{