2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.workers;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.api.AlignCalcManagerI;
28 import jalview.api.AlignCalcWorkerI;
29 import jalview.api.FeatureRenderer;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceI;
36 import jalview.gui.AlignFrame;
38 import java.util.Collections;
39 import java.util.List;
41 import org.testng.annotations.BeforeMethod;
42 import org.testng.annotations.Test;
44 public class AlignCalcManagerTest
46 private AlignFrame alignFrame;
49 * Test the method that removes a worker associated with an annotation,
50 * provided the worker is marked as 'deletable' (some workers should continue
51 * to run even when their results are no longer displayed)
53 @Test(groups = "Functional")
54 public void testRemoveWorkerForAnnotation()
56 AlignCalcManagerI acm = alignFrame.getViewport().getCalcManager();
57 final AlignmentAnnotation ann1 = new AlignmentAnnotation("Ann1",
58 "desc", new Annotation[] {});
59 final AlignmentAnnotation ann2 = new AlignmentAnnotation("Ann2",
60 "desc", new Annotation[] {});
63 * make two workers for ann1, one deletable, one not
64 * and no worker for ann2
66 AlignCalcWorkerI worker1 = makeWorker(ann1, true);
67 AlignCalcWorkerI worker2 = makeWorker(ann1, false);
70 * The new workers will get run each in their own thread.
71 * We can't tell here whether they have finished, or not yet started.
72 * They have to finish to be 'seen' by getRegisteredWorkersOfClass()
73 * registerWorker adds to the 'restartable' list but
74 * getRegisteredWorkers reads from the 'canUpdate' list
75 * (which is only updated after a worker has run) - why?
76 * So just give workers time to start and finish
83 } catch (InterruptedException e)
89 List<AlignCalcWorkerI> workers = acm
90 .getRegisteredWorkersOfClass(worker1.getClass());
91 assertEquals(2, workers.size());
92 assertTrue(workers.contains(worker1));
93 assertTrue(workers.contains(worker2));
94 assertFalse(acm.isDisabled(worker1));
95 assertFalse(acm.isDisabled(worker2));
98 * remove workers for ann2 (there aren't any)
100 acm.removeWorkerForAnnotation(ann2);
101 assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
103 assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
105 assertFalse(acm.isDisabled(worker1));
106 assertFalse(acm.isDisabled(worker2));
109 * remove worker2 for ann1
110 * - should delete worker1 but not worker2
112 acm.removeWorkerForAnnotation(ann1);
113 assertEquals(1, acm.getRegisteredWorkersOfClass(worker1.getClass())
115 assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
117 assertFalse(acm.isDisabled(worker1));
118 assertFalse(acm.isDisabled(worker2));
122 * Make a worker linked to the given annotation
128 AnnotationWorker makeWorker(final AlignmentAnnotation ann,
129 final boolean deletable)
131 AnnotationProviderI annotationProvider = new AnnotationProviderI()
134 public List<AlignmentAnnotation> calculateAnnotation(AlignmentI al,
137 return Collections.singletonList(ann);
140 return new AnnotationWorker(alignFrame.getViewport(),
141 alignFrame.alignPanel, annotationProvider)
144 public boolean isDeletable()
150 public boolean involves(AlignmentAnnotation ann1)
157 @BeforeMethod(alwaysRun = true)
160 AlignmentI al = new Alignment(new SequenceI[] { new Sequence("Seq1",
163 alignFrame = new AlignFrame(al, 3, 1);