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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
RNAStructExportImport.java
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
bc11d2f
..
0a9cb19
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-21,7
+21,6
@@
package jalview.ws.jabaws;
import java.util.Locale;
package jalview.ws.jabaws;
import java.util.Locale;
-
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
@@
-36,8
+35,10
@@
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.project.Jalview2XML;
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.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;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.AutoCalcSetting;
@@
-81,7
+82,7
@@
public class RNAStructExportImport
public static Jws2Instance rnaalifoldws;
public static Jws2Instance rnaalifoldws;
- jalview.ws.jws2.RNAalifoldClient alifoldClient;
+ SeqAnnotationServiceCalcWorker alifoldClient;
public static jalview.gui.AlignFrame af = null;
public static jalview.gui.AlignFrame af = null;
@@
-98,13
+99,13
@@
public class RNAStructExportImport
Thread.sleep(100);
}
Thread.sleep(100);
}
- for (Jws2Instance svc : disc.getServices())
+ for (ServiceWithParameters svc : disc.getServices())
{
if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
.contains("rnaalifoldws"))
{
{
if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
.contains("rnaalifoldws"))
{
- rnaalifoldws = svc;
+ rnaalifoldws = (Jws2Instance) svc;
}
}
}
}
@@
-159,7
+160,8
@@
public class RNAStructExportImport
public void testRNAAliFoldValidStructure()
{
public void testRNAAliFoldValidStructure()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
af.getViewport().getCalcManager().startWorker(alifoldClient);
@@
-192,7
+194,8
@@
public class RNAStructExportImport
public void testRNAStructExport()
{
public void testRNAStructExport()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
af.getViewport().getCalcManager().startWorker(alifoldClient);
@@
-209,7
+212,7
@@
public class RNAStructExportImport
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
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);
}
verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
@@
-278,7
+281,8
@@
public class RNAStructExportImport
opts.add(rg);
}
}
opts.add(rg);
}
}
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+ JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);
af.getViewport().getCalcManager().startWorker(alifoldClient);