src/jalview/ws2/actions/hmmer/PhmmerAction.java

   1 package jalview.ws2.actions.hmmer;
   2
   3 import java.util.List;
   4 import java.util.Objects;
   5
   6 import jalview.api.AlignViewportI;
   7 import jalview.datamodel.AlignmentI;
   8 import jalview.viewmodel.AlignmentViewport;
   9 import jalview.ws.params.ArgumentI;
  10 import jalview.ws2.actions.BaseAction;
  11 import jalview.ws2.actions.PollingTaskExecutor;
  12 import jalview.ws2.actions.api.TaskEventListener;
  13 import jalview.ws2.actions.api.TaskI;
  14 import jalview.ws2.api.Credentials;
  15 import jalview.ws2.client.api.AlignmentWebServiceClientI;
  16 import jalview.ws2.client.api.WebServiceClientI;
  17
  18 /**
  19  * Implementation of the {@link BaseAction} for the phmmer client. This is NOT
  20  * how you should implement it. The action should be more generic and cover
  21  * range of similar services.
  22  *
  23  * @author mmwarowny
  24  *
  25  */
  26 // FIXME: Not an alignment action (temporary hack)
  27 public class PhmmerAction extends BaseAction<AlignmentI>
  28 {
  29   public static class Builder extends BaseAction.Builder<PhmmerAction>
  30   {
  31     protected AlignmentWebServiceClientI client;
  32
  33     private Builder(AlignmentWebServiceClientI client)
  34     {
  35       super();
  36       Objects.requireNonNull(client);
  37       this.client = client;
  38     }
  39
  40     public PhmmerAction build()
  41     {
  42       return new PhmmerAction(this);
  43     }
  44   }
  45
  46   public static Builder newBuilder(AlignmentWebServiceClientI client)
  47   {
  48     return new Builder(client);
  49   }
  50
  51   protected final AlignmentWebServiceClientI client;
  52
  53   public PhmmerAction(Builder builder)
  54   {
  55     super(builder);
  56     client = builder.client;
  57   }
  58
  59   public TaskI<AlignmentI> perform(AlignmentViewport viewport,
  60           List<ArgumentI> args, Credentials credentials,
  61           TaskEventListener<AlignmentI> handler)
  62   {
  63     var task = createTask(viewport, args, credentials);
  64     task.addTaskEventListener(handler);
  65     var executor = PollingTaskExecutor.fromPool(viewport.getServiceExecutor());
  66     var future = executor.submit(task);
  67     task.setCancelAction(() -> { future.cancel(true); });
  68     return task;
  69   }
  70
  71   public PhmmerTask createTask(AlignViewportI viewport,
  72       List<ArgumentI> args, Credentials credentials)
  73   {
  74     return new PhmmerTask(client, args, credentials, viewport.getAlignmentView(true));
  75   }
  76
  77   @Override
  78   public boolean isActive(AlignmentViewport viewport)
  79   {
  80     return false;
  81   }
  82 }