JAL-3954 Implement phmmer action and task as alignment actions

[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
new file mode 100644 (file)
index 0000000..0565300
--- /dev/null
+++ b/src/jalview/ws2/actions/hmmer/PhmmerTask.java
@@ -0,0 +1,66 @@
+package jalview.ws2.actions.hmmer;
+
+import static jalview.util.Comparison.GapChars;
+
+import java.io.IOException;
+import java.util.List;
+
+import jalview.analysis.AlignSeq;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Sequence;
+import jalview.ws.params.ArgumentI;
+import jalview.ws2.actions.AbstractPollableTask;
+import jalview.ws2.actions.BaseJob;
+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>
+{
+  private final AlignmentWebServiceClientI client;
+  private final AlignmentView view;
+
+  PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,
+          Credentials credentials, AlignmentView view,
+          TaskEventListener<AlignmentI> eventListener)
+  {
+    super(client, args, credentials, eventListener);
+    this.client = client;
+    this.view = view;
+  }
+
+  @Override
+  protected List<BaseJob> prepare() throws ServiceInputInvalidException
+  {
+    Console.info("Preparing sequence for phmmer job");
+    var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
+    var seq = new Sequence(sequence.getName(),
+            AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString()));
+    var job = new BaseJob(List.of(seq))
+    {
+      @Override
+      public boolean isInputValid()
+      {
+        return true;
+      }
+    };
+    job.setStatus(JobStatus.READY);
+    return List.of(job);
+  }
+
+  @Override
+  protected AlignmentI done() throws IOException
+  {
+    var job = getSubJobs().get(0);
+    var jobId = job.getServerJob().getJobId();
+    var status = job.getStatus();
+    Console.info(String.format("phmmer finished job \"%s\" with status %s",
+            jobId, status));
+    return client.getAlignment(job.getServerJob());
+  }
+
+}