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  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.ws2.actions.secstructpred

File SecStructPredMsaTaskTest.java

 

Code metrics

2
50
6
1
194
176
7
0.14
8.33
6
1.17

Classes

Class Line # Actions
SecStructPredMsaTaskTest 40 50 7
1.0100%
 

Contributing tests

This file is covered by 10 tests. .

Source view

1    package jalview.ws2.actions.secstructpred;
2   
3    import jalview.datamodel.Alignment;
4    import jalview.datamodel.AlignmentAnnotation;
5    import jalview.datamodel.AlignmentI;
6    import jalview.datamodel.HiddenColumns;
7    import jalview.datamodel.Sequence;
8    import jalview.datamodel.SequenceI;
9    import jalview.gui.AlignViewport;
10    import jalview.io.DataSourceType;
11    import jalview.io.FastaFile;
12    import jalview.io.JPredFile;
13    import jalview.ws2.api.Credentials;
14    import jalview.ws2.api.JobStatus;
15    import jalview.ws2.api.WebServiceJobHandle;
16    import jalview.ws2.client.api.SecStructPredWebServiceClientI;
17    import org.hamcrest.Matcher;
18    import org.hamcrest.Matchers;
19    import org.testng.annotations.BeforeMethod;
20    import org.testng.annotations.DataProvider;
21    import org.testng.annotations.Test;
22   
23    import java.io.IOException;
24    import java.util.ArrayList;
25    import java.util.List;
26   
27    import static jalview.testutils.Matchers.matchesAnnotations;
28    import static jalview.testutils.Matchers.matchesSequenceString;
29    import static jalview.testutils.ScopeFunctions.apply;
30    import static java.lang.String.format;
31    import static org.hamcrest.MatcherAssert.assertThat;
32    import static org.hamcrest.Matchers.allOf;
33    import static org.hamcrest.Matchers.containsInAnyOrder;
34    import static org.hamcrest.Matchers.equalTo;
35    import static org.hamcrest.Matchers.hasProperty;
36    import static org.mockito.ArgumentMatchers.any;
37    import static org.mockito.Mockito.mock;
38    import static org.mockito.Mockito.when;
39   
 
40    public class SecStructPredMsaTaskTest
41    {
42    protected SecStructPredWebServiceClientI mockClient;
43   
 
44  10 toggle @BeforeMethod(alwaysRun = true)
45    public void setupMockClient() throws IOException
46    {
47  10 mockClient = mock(SecStructPredWebServiceClientI.class);
48  10 when(mockClient.getUrl()).thenReturn("http://example.org");
49  10 when(mockClient.getClientName()).thenReturn("mock");
50  10 when(mockClient.submit(any(), any(), any()))
51    .thenReturn(new WebServiceJobHandle("mock", "mock",
52    "http://example.org", "0"));
53  10 when(mockClient.getLog(any())).thenReturn("");
54  10 when(mockClient.getErrorLog(any())).thenReturn("");
55  10 when(mockClient.getStatus(any())).thenReturn(JobStatus.COMPLETED);
56    }
57   
 
58  1 toggle @DataProvider
59    public Object[][] alignmentWithExpectedInput()
60    {
61  1 return new Object[][] { {
62    new AlignViewport(createAlignment("AAAAAAAAAAAA", "AAAAAAAAAAAA",
63    "AAAAAAAAAAAA")),
64    List.of("AAAAAAAAAAAA", "AAAAAAAAAAAA", "AAAAAAAAAAAA") },
65    { new AlignViewport(createAlignment("AAAA--NNNNAAAA",
66    "AA--AANNNNAAAA", "AA--AARRRRAAAA")),
67    List.of("AAAA--NNNNAAAA", "AA--AANNNNAAAA", "AA--AARRRRAAAA") },
68    { new AlignViewport(createAlignment("AAAANNNNAAAA--",
69    "AAAARRRRAAAA--", "AAAARRRRAAAA--")),
70    List.of("AAAANNNNAAAA--", "AAAARRRRAAAA--", "AAAARRRRAAAA--") },
71    { new AlignViewport(createAlignment("AAAA--NNNNAAAA",
72    "AAAA--NNNNAAAA", "AAAA--NNNNAAAA")),
73    List.of("AAAA--NNNNAAAA", "AAAA--NNNNAAAA", "AAAA--NNNNAAAA") },
74    { new AlignViewport(createAlignment("AAAACCCCNNNN", "------------",
75    "AAAADDDDNNNN")),
76    List.of("AAAACCCCNNNN", "AAAADDDDNNNN") },
77    { new AlignViewport(createAlignment("AAAACC--NNNN", "AAAACCDDNNNN"),
78    apply(new HiddenColumns(), it -> it.hideColumns(6, 7))),
79    List.of("AAAACCNNNN", "AAAACCNNNN") },
80    { new AlignViewport(
81    createAlignment("CCAAAACC--MMMM", "--AAAAGGGGMMMM"),
82    apply(new HiddenColumns(), it -> {
83  1 it.hideColumns(0, 1);
84  1 it.hideColumns(8, 9);
85    })),
86    List.of("AAAACCMMMM", "AAAAGGMMMM") },
87    { new AlignViewport(
88    createAlignment("CCAAAACC--MMMM", "CCAAAACC--MMMM"),
89    apply(new HiddenColumns(), it -> it.hideColumns(2, 5))),
90    List.of("CCCC--MMMM", "CCCC--MMMM") } };
91    }
92   
 
93  8 toggle public static AlignmentI createAlignment(String... sequences)
94    {
95  8 var seqArray = new Sequence[sequences.length];
96  29 for (int i = 0; i < sequences.length; i++)
97  21 seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
98  8 return new Alignment(seqArray);
99    }
100   
 
101  8 toggle @Test(
102    groups =
103    { "Functional" },
104    dataProvider = "alignmentWithExpectedInput")
105    public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
106    List<String> expectedInput) throws Exception
107    {
108  8 var task = new SecStructPredMsaTask(mockClient, List.of(),
109    Credentials.empty(), viewport);
110  8 var jobs = task.prepareJobs();
111  8 List<Matcher<? super SequenceI>> seqMatchers = new ArrayList<>(
112    expectedInput.size());
113  8 for (var seqStr : expectedInput)
114  20 seqMatchers.add(matchesSequenceString(seqStr));
115  8 assertThat(jobs.get(0).getInputSequences(),
116    Matchers.<SequenceI> contains(seqMatchers));
117    }
118   
 
119  1 toggle @DataProvider
120    public Object[][] viewportWithServiceOutput() throws IOException
121    {
122   
123  1 return new Object[][] {
124    {
125    new AlignViewport(new Alignment(new FastaFile(
126    "examples/testdata/secstrpred/alignment0_aln.fa",
127    DataSourceType.FILE).getSeqsAsArray())),
128    "examples/testdata/secstrpred/alignment0.fa",
129    "examples/testdata/secstrpred/alignment0.concise"
130    },
131    {
132    new AlignViewport(new Alignment(new FastaFile(
133    "examples/testdata/secstrpred/alignment0a_aln.fa",
134    DataSourceType.FILE).getSeqsAsArray()),
135    apply(new HiddenColumns(), it -> it.hideColumns(3, 7))),
136    "examples/testdata/secstrpred/alignment0.fa",
137    "examples/testdata/secstrpred/alignment0.concise"
138    }
139    };
140    }
141   
 
142  2 toggle @Test(groups = "Functional", dataProvider = "viewportWithServiceOutput")
143    public void testCollectResults(AlignViewport viewport, String alnFileName, String predFileName) throws Exception
144    {
145  2 var alnFile = new FastaFile(alnFileName, DataSourceType.FILE);
146  2 var predFile = new JPredFile(predFileName, DataSourceType.FILE);
147  2 when(mockClient.getPredictionFile(any())).thenReturn(predFile);
148  2 when(mockClient.getAlignmentFile(any())).thenReturn(alnFile);
149   
150  2 var task = new SecStructPredMsaTask(mockClient, List.of(),
151    Credentials.empty(), viewport);
152  2 task.init();
153  2 task.poll();
154  2 task.complete();
155  2 var resultAlignment = task.getResult();
156  2 var sequences = resultAlignment.getSequences();
157   
158    // Test output alignment matches original
159    {
160  2 List<Matcher<? super SequenceI>> matchers = new ArrayList<>();
161  2 for (var seq : viewport.getAlignment().getSequences())
162  6 matchers.add(matchesSequenceString(seq));
163  2 assertThat(sequences, Matchers.contains(matchers));
164    }
165    // Test output sequence names match original
166    {
167  2 List<Matcher<? super SequenceI>> matchers = new ArrayList<>();
168  2 for (var seq : viewport.getAlignment().getSequences())
169  6 matchers.add(hasProperty("name", equalTo(seq.getName())));
170  2 assertThat(sequences, Matchers.contains(matchers));
171    }
172    // Test hidden columns
173    {
174  2 var originalHidden = viewport.getAlignment().getHiddenColumns();
175  2 var resultHidden = resultAlignment.getHiddenColumns();
176  2 assertThat(resultHidden, equalTo(originalHidden));
177    }
178    // Test annotations present on the alignment
179    {
180  2 var hiddenColumns = viewport.getAlignment().getHiddenColumns();
181  2 List<Matcher<? super AlignmentAnnotation>> matchers = new ArrayList<>();
182  2 for (var annot : predFile.getAnnotations())
183  18 matchers.add(allOf(
184    hasProperty("label", equalTo(annot.label)),
185    hasProperty("annotations", matchesAnnotations(annot.annotations))
186    ));
187  2 List<AlignmentAnnotation> annotations = new ArrayList<>();
188  2 for (var annot : resultAlignment.getAlignmentAnnotation())
189  18 annotations.add(new AlignmentAnnotation(annot, hiddenColumns));
190  2 assertThat(annotations, containsInAnyOrder(matchers));
191    }
192   
193    }
194    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
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