Merge branch 'feature/JAL-3954-ebi-phmmer' into mmw/JAL-4199-task-execution-update

[jalview.git] / src / jalview / ws2 / actions / hmmer / PhmmerTask.java

diff --git a/src/jalview/ws2/actions/hmmer/PhmmerTask.java b/src/jalview/ws2/actions/hmmer/PhmmerTask.java
index 8a7a826..ede61d3 100644 (file)
--- a/src/jalview/ws2/actions/hmmer/PhmmerTask.java
+++ b/src/jalview/ws2/actions/hmmer/PhmmerTask.java
@@ -3,7 +3,6 @@ package jalview.ws2.actions.hmmer;
 import static jalview.util.Comparison.GapChars;
 
 import java.io.IOException;
-import java.util.Arrays;
 import java.util.List;
 
 import jalview.analysis.AlignSeq;
@@ -16,30 +15,28 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 import jalview.ws.params.ArgumentI;
-import jalview.ws2.actions.AbstractPollableTask;
 import jalview.ws2.actions.BaseJob;
+import jalview.ws2.actions.BaseTask;
 import jalview.ws2.actions.ServiceInputInvalidException;
-import jalview.ws2.actions.api.TaskEventListener;
 import jalview.ws2.api.Credentials;
 import jalview.ws2.api.JobStatus;
 import jalview.ws2.client.api.AlignmentWebServiceClientI;
 
-class PhmmerTask extends AbstractPollableTask<BaseJob, AlignmentI>
+class PhmmerTask extends BaseTask<BaseJob, AlignmentI>
 {
   private final AlignmentWebServiceClientI client;
   private final AlignmentView view;
 
   PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,
-          Credentials credentials, AlignmentView view,
-          TaskEventListener<AlignmentI> eventListener)
+          Credentials credentials, AlignmentView view)
   {
-    super(client, args, credentials, eventListener);
+    super(client, args, credentials);
     this.client = client;
     this.view = view;
   }
 
   @Override
-  protected List<BaseJob> prepare() throws ServiceInputInvalidException
+  protected List<BaseJob> prepareJobs() throws ServiceInputInvalidException
   {
     Console.info("Preparing sequence for phmmer job");
     var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
@@ -58,9 +55,9 @@ class PhmmerTask extends AbstractPollableTask<BaseJob, AlignmentI>
   }
 
   @Override
-  protected AlignmentI done() throws IOException
+  protected AlignmentI collectResult(List<BaseJob> jobs) throws IOException
   {
-    var job = getSubJobs().get(0);
+    var job = jobs.get(0);
     var status = job.getStatus();
     Console.info(String.format("phmmer finished job \"%s\" with status %s",
             job.getServerJob().getJobId(), status));