Coverage Report
File PhmmerAction.java
Coverage histogram
43% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| PhmmerAction | 27 | 12 | 5 | ||
| PhmmerAction.Builder | 29 | 4 | 2 |
Contributing tests
This file is covered by 37 tests.
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Source view
| 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 | 62 |  private Builder(AlignmentWebServiceClientI client) |
| 34 | { | |
| 35 | 62 | super(); |
| 36 | 62 | Objects.requireNonNull(client); |
| 37 | 62 | this.client = client; |
| 38 | } | |
| 39 | ||
| 40 | 62 | public PhmmerAction build() |
| 41 | { | |
| 42 | 62 | return new PhmmerAction(this); |
| 43 | } | |
| 44 | } | |
| 45 | ||
| 46 | 62 | public static Builder newBuilder(AlignmentWebServiceClientI client) |
| 47 | { | |
| 48 | 62 | return new Builder(client); |
| 49 | } | |
| 50 | ||
| 51 | protected final AlignmentWebServiceClientI client; | |
| 52 | ||
| 53 | 62 | public PhmmerAction(Builder builder) |
| 54 | { | |
| 55 | 62 | super(builder); |
| 56 | 62 | client = builder.client; |
| 57 | } | |
| 58 | ||
| 59 | 0 | public TaskI<AlignmentI> perform(AlignmentViewport viewport, |
| 60 | List<ArgumentI> args, Credentials credentials, | |
| 61 | TaskEventListener<AlignmentI> handler) | |
| 62 | { | |
| 63 | 0 | var task = createTask(viewport, args, credentials); |
| 64 | 0 | task.addTaskEventListener(handler); |
| 65 | 0 | var executor = PollingTaskExecutor.fromPool(viewport.getServiceExecutor()); |
| 66 | 0 | var future = executor.submit(task); |
| 67 | 0 | task.setCancelAction(() -> { future.cancel(true); }); |
| 68 | 0 | return task; |
| 69 | } | |
| 70 | ||
| 71 | 0 | public PhmmerTask createTask(AlignViewportI viewport, |
| 72 | List<ArgumentI> args, Credentials credentials) | |
| 73 | { | |
| 74 | 0 | return new PhmmerTask(client, args, credentials, viewport.getAlignmentView(true)); |
| 75 | } | |
| 76 | ||
| 77 | 0 | @Override |
| 78 | public boolean isActive(AlignmentViewport viewport) | |
| 79 | { | |
| 80 | 0 | return false; |
| 81 | } | |
| 82 | } |