JAL-1601 Expand secondary structure prediction tests

[jalview.git] / test / jalview / ws2 / actions / secstructpred / SecStructPredTaskTest.java

diff --git a/test/jalview/ws2/actions/secstructpred/SecStructPredTaskTest.java b/test/jalview/ws2/actions/secstructpred/SecStructPredTaskTest.java
deleted file mode 100644 (file)
index 3a79cd4..0000000
--- a/test/jalview/ws2/actions/secstructpred/SecStructPredTaskTest.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package jalview.ws2.actions.secstructpred;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-
-import static jalview.testutils.Matchers.matchesSequenceString;
-import static jalview.testutils.ScopeFunctions.apply;
-import static jalview.testutils.ScopeFunctions.run;
-import org.hamcrest.Matcher;
-import org.hamcrest.Matchers;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.anyList;
-import static org.hamcrest.Matchers.contains;
-
-import static org.mockito.ArgumentMatchers.eq;
-import static org.mockito.Mockito.doAnswer;
-import static org.mockito.Mockito.doThrow;
-import static org.mockito.Mockito.inOrder;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
-import jalview.ws2.api.Credentials;
-import jalview.ws2.client.api.SecStructPredWebServiceClientI;
-
-import static java.lang.String.format;
-
-public class SecStructPredTaskTest
-{
-  protected SecStructPredWebServiceClientI mockClient;
-
-  @BeforeMethod(alwaysRun = true)
-  public void setupMockClient() throws IOException
-  {
-    mockClient = mock(SecStructPredWebServiceClientI.class);
-    when(mockClient.getUrl()).thenReturn("http://example.org");
-    when(mockClient.getClientName()).thenReturn("mock");
-    when(mockClient.getLog(any())).thenReturn("");
-    when(mockClient.getErrorLog(any())).thenReturn("");
-  }
-
-  @DataProvider
-  public Object[][] alignmentWithExpectedInput()
-  {
-    return new Object[][] {
-        {
-            new AlignViewport(createAlignment("AAAAAAAAAAAA", "AAAAAAAAAAAA",
-                "AAAAAAAAAAAA")),
-            List.of("AAAAAAAAAAAA", "AAAAAAAAAAAA", "AAAAAAAAAAAA") },
-        {
-            new AlignViewport(createAlignment("AAAA--NNNNAAAA",
-                "AA--AANNNNAAAA", "AA--AARRRRAAAA")),
-            List.of("AAAA--NNNNAAAA", "AA--AANNNNAAAA", "AA--AARRRRAAAA") },
-        {
-            new AlignViewport(createAlignment("AAAANNNNAAAA--",
-                "AAAARRRRAAAA--", "AAAARRRRAAAA--")),
-            List.of("AAAANNNNAAAA--", "AAAARRRRAAAA--", "AAAARRRRAAAA--") },
-        {
-            new AlignViewport(createAlignment("AAAA--NNNNAAAA",
-                "AAAA--NNNNAAAA", "AAAA--NNNNAAAA")),
-            List.of("AAAA--NNNNAAAA", "AAAA--NNNNAAAA", "AAAA--NNNNAAAA") },
-        {
-            new AlignViewport(createAlignment("AAAACCCCNNNN", "------------",
-                "AAAADDDDNNNN")),
-            List.of("AAAACCCCNNNN", "AAAADDDDNNNN") },
-        {
-            new AlignViewport(createAlignment("AAAACC--NNNN", "AAAACCDDNNNN"),
-                apply(new HiddenColumns(), it -> it.hideColumns(6, 7))),
-            List.of("AAAACCNNNN", "AAAACCNNNN") },
-        {
-            new AlignViewport(
-                createAlignment("CCAAAACC--MMMM", "--AAAAGGGGMMMM"),
-                apply(new HiddenColumns(), it -> {
-                  it.hideColumns(0, 1);
-                  it.hideColumns(8, 9);
-                })),
-            List.of("AAAACCMMMM", "AAAAGGMMMM") },
-        {
-            new AlignViewport(
-                createAlignment("CCAAAACC--MMMM", "CCAAAACC--MMMM"),
-                apply(new HiddenColumns(), it -> it.hideColumns(2, 5))),
-            List.of("CCCC--MMMM", "CCCC--MMMM") } };
-  }
-
-  public static AlignmentI createAlignment(String... sequences)
-  {
-    var seqArray = new Sequence[sequences.length];
-    for (int i = 0; i < sequences.length; i++)
-      seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
-    return new Alignment(seqArray);
-  }
-
-  @Test(groups = { "functional" }, dataProvider = "alignmentWithExpectedInput")
-  public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
-      List<String> expectedInput) throws Exception
-  {
-    var task = new SecStructPredMsaTask(mockClient, List.of(), Credentials.empty(),
-        viewport);
-    var jobs = task.prepareJobs();
-    List<Matcher<? super SequenceI>> seqMatchers = new ArrayList<>(
-        expectedInput.size());
-    for (var seqStr : expectedInput)
-      seqMatchers.add(matchesSequenceString(seqStr));
-    assertThat(jobs.get(0).getInputSequences(),
-        Matchers.<SequenceI> contains(seqMatchers));
-  }
-}