import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AADisorderClient;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
import java.util.ArrayList;
import java.util.List;
public static Jws2Discoverer disc;
- public static List<Jws2Instance> iupreds;
+ public static List<ServiceWithParameters> iupreds;
- jalview.ws.jws2.AADisorderClient disorderClient;
+ jalview.ws.jws2.SeqAnnotationServiceCalcWorker disorderClient;
public static jalview.gui.AlignFrame af = null;
// don't get services until discoverer has finished
Thread.sleep(100);
}
-
- iupreds = new ArrayList<Jws2Instance>();
- for (Jws2Instance svc : disc.getServices())
+ SlivkaWSDiscoverer disc2 = SlivkaWSDiscoverer.getInstance();
+ disc2.run();
+ iupreds = new ArrayList<>();
+ for (ServiceWithParameters svc : disc2.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+ if (svc.getNameURI().toLowerCase().contains("iupred"))
{
iupreds.add(svc);
}
@Test(groups = { "External", "Network" })
public void testDisorderAnnotExport()
{
- disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
+ disorderClient = new SeqAnnotationServiceCalcWorker(iupreds.get(0), af, null,
+ null);
af.getViewport().getCalcManager().startWorker(disorderClient);
do
{
AlignmentI orig_alig = af.getViewport().getAlignment();
// NOTE: Consensus annotation row cannot be exported and reimported
// faithfully - so we remove them
- List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> toremove = new ArrayList<>();
for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
{
if (aa.autoCalculated)
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
+ false);
return;
} catch (Exception e)
{