1 package jalview.ws2.actions.secstructpred;
3 import static org.hamcrest.MatcherAssert.assertThat;
5 import static jalview.testutils.Matchers.matchesSequenceString;
6 import static jalview.testutils.ScopeFunctions.apply;
7 import static jalview.testutils.ScopeFunctions.run;
8 import org.hamcrest.Matcher;
9 import org.hamcrest.Matchers;
10 import org.testng.annotations.BeforeMethod;
11 import org.testng.annotations.DataProvider;
12 import org.testng.annotations.Test;
14 import static org.mockito.ArgumentMatchers.any;
15 import static org.mockito.ArgumentMatchers.anyList;
16 import static org.hamcrest.Matchers.contains;
18 import static org.mockito.ArgumentMatchers.eq;
19 import static org.mockito.Mockito.doAnswer;
20 import static org.mockito.Mockito.doThrow;
21 import static org.mockito.Mockito.inOrder;
22 import static org.mockito.Mockito.mock;
23 import static org.mockito.Mockito.verify;
24 import static org.mockito.Mockito.when;
26 import java.io.IOException;
27 import java.util.ArrayList;
28 import java.util.List;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.HiddenColumns;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceI;
35 import jalview.gui.AlignViewport;
36 import jalview.ws2.api.Credentials;
37 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
39 import static java.lang.String.format;
41 public class SecStructPredTaskTest
43 protected SecStructPredWebServiceClientI mockClient;
45 @BeforeMethod(alwaysRun = true)
46 public void setupMockClient() throws IOException
48 mockClient = mock(SecStructPredWebServiceClientI.class);
49 when(mockClient.getUrl()).thenReturn("http://example.org");
50 when(mockClient.getClientName()).thenReturn("mock");
51 when(mockClient.getLog(any())).thenReturn("");
52 when(mockClient.getErrorLog(any())).thenReturn("");
56 public Object[][] alignmentWithExpectedInput()
58 return new Object[][] {
60 new AlignViewport(createAlignment("AAAAAAAAAAAA", "AAAAAAAAAAAA",
62 List.of("AAAAAAAAAAAA", "AAAAAAAAAAAA", "AAAAAAAAAAAA") },
64 new AlignViewport(createAlignment("AAAA--NNNNAAAA",
65 "AA--AANNNNAAAA", "AA--AARRRRAAAA")),
66 List.of("AAAA--NNNNAAAA", "AA--AANNNNAAAA", "AA--AARRRRAAAA") },
68 new AlignViewport(createAlignment("AAAANNNNAAAA--",
69 "AAAARRRRAAAA--", "AAAARRRRAAAA--")),
70 List.of("AAAANNNNAAAA--", "AAAARRRRAAAA--", "AAAARRRRAAAA--") },
72 new AlignViewport(createAlignment("AAAA--NNNNAAAA",
73 "AAAA--NNNNAAAA", "AAAA--NNNNAAAA")),
74 List.of("AAAA--NNNNAAAA", "AAAA--NNNNAAAA", "AAAA--NNNNAAAA") },
76 new AlignViewport(createAlignment("AAAACCCCNNNN", "------------",
78 List.of("AAAACCCCNNNN", "AAAADDDDNNNN") },
80 new AlignViewport(createAlignment("AAAACC--NNNN", "AAAACCDDNNNN"),
81 apply(new HiddenColumns(), it -> it.hideColumns(6, 7))),
82 List.of("AAAACCNNNN", "AAAACCNNNN") },
85 createAlignment("CCAAAACC--MMMM", "--AAAAGGGGMMMM"),
86 apply(new HiddenColumns(), it -> {
90 List.of("AAAACCMMMM", "AAAAGGMMMM") },
93 createAlignment("CCAAAACC--MMMM", "CCAAAACC--MMMM"),
94 apply(new HiddenColumns(), it -> it.hideColumns(2, 5))),
95 List.of("CCCC--MMMM", "CCCC--MMMM") } };
98 public static AlignmentI createAlignment(String... sequences)
100 var seqArray = new Sequence[sequences.length];
101 for (int i = 0; i < sequences.length; i++)
102 seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
103 return new Alignment(seqArray);
106 @Test(groups = { "functional" }, dataProvider = "alignmentWithExpectedInput")
107 public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
108 List<String> expectedInput) throws Exception
110 var task = new SecStructPredMsaTask(mockClient, List.of(), Credentials.empty(),
112 var jobs = task.prepareJobs();
113 List<Matcher<? super SequenceI>> seqMatchers = new ArrayList<>(
114 expectedInput.size());
115 for (var seqStr : expectedInput)
116 seqMatchers.add(matchesSequenceString(seqStr));
117 assertThat(jobs.get(0).getInputSequences(),
118 Matchers.<SequenceI> contains(seqMatchers));