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
{
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()
{
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
-
- testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+ // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
+ // annotation is mistakenly recognised as an RNA annotation row when read in
+ // as an annotation file.
+ 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()
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
+ "\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>();