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.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
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;
+ AbstractJabaCalcWorker alifoldClient;
public static jalview.gui.AlignFrame af = null;
public void testRNAAliFoldValidStructure()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
public void testRNAStructExport()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
AlignmentI orig_alig = af.getViewport().getAlignment();
// 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.
+ // as an annotation file. bug is JAL-3122
verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
opts.add(rg);
}
}
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+ alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);