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JAL-3807 - Add single sequence capabilities to jws2.JPredClient
[jalview.git]
/
src
/
jalview
/
ws
/
slivkaws
/
SlivkaJPredServiceInstance.java
diff --git
a/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
b/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
index
b8e4d2f
..
462be28
100644
(file)
--- a/
src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
+++ b/
src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
@@
-8,16
+8,41
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.JPredFile;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.JPredFile;
-import jalview.ws.api.JPredMutlipleAlignmentServiceI;
+import jalview.ws.api.JPredServiceI;
import jalview.ws.api.JobId;
import jalview.ws.api.JobId;
+import jalview.ws.params.ArgumentI;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
public class SlivkaJPredServiceInstance extends SlivkaWSInstance
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
public class SlivkaJPredServiceInstance extends SlivkaWSInstance
- implements JPredMutlipleAlignmentServiceI
+ implements JPredServiceI
{
{
+ private class InputFormatParameter implements ArgumentI
+ {
+ String value = "";
+
+ @Override
+ public String getName()
+ {
+ return "format";
+ }
+
+ @Override
+ public String getValue()
+ {
+ return value;
+ }
+
+ @Override
+ public void setValue(String selectedItem)
+ {
+ value = selectedItem;
+ }
+ }
+
+
public SlivkaJPredServiceInstance(SlivkaClient client,
SlivkaService service, String action)
{
public SlivkaJPredServiceInstance(SlivkaClient client,
SlivkaService service, String action)
{
@@
-26,9
+51,13
@@
public class SlivkaJPredServiceInstance extends SlivkaWSInstance
}
@Override
}
@Override
- public JobId align(List<SequenceI> sequences) throws Throwable
+ public JobId predict(List<SequenceI> sequences, boolean msa) throws Throwable
{
{
- return super.submit(sequences, null, null);
+ // Hack allowing to send both single and msa jobs
+ // until msa and single sequence services are separated.
+ var arg = new InputFormatParameter();
+ arg.setValue(msa ? "fasta" : "seq");
+ return super.submit(sequences, null, List.of(arg));
}
@Override
}
@Override