import jalview.bin.Cache;
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 jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
+import jalview.project.Jalview2XML;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.AutoCalcSetting;
public static Jws2Instance rnaalifoldws;
- jalview.ws.jws2.RNAalifoldClient alifoldClient;
+ SeqAnnotationServiceCalcWorker alifoldClient;
public static jalview.gui.AlignFrame af = null;
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
- for (Jws2Instance svc : disc.getServices())
+ while (disc.isRunning())
+ {
+ // don't get services until discoverer has finished
+ Thread.sleep(100);
+ }
+
+ for (ServiceWithParameters svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+ if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
{
- rnaalifoldws = svc;
+ rnaalifoldws = (Jws2Instance) svc;
}
}
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
// remove any existing annotation
- List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aal = new ArrayList<>();
for (AlignmentAnnotation rna : af.getViewport().getAlignment()
.getAlignmentAnnotation())
{
public void testRNAAliFoldValidStructure()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
public void testRNAStructExport()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
} 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. bug is JAL-3122
+ verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
- public static void testAnnotationFileIO(String testname, AlignmentI al)
+ static void verifyAnnotationFileIO(String testname, AlignmentI al)
{
try
{
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)
{
@Test(groups = { "Network" })
public void testRnaalifoldSettingsRecovery()
{
- List<Argument> opts = new ArrayList<Argument>();
+ List<Argument> opts = new ArrayList<>();
for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
.getArguments())
{
opts.add(rg);
}
}
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+ JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);