6 import org.testng.Assert;
7 import org.testng.annotations.AfterClass;
8 import org.testng.annotations.AfterMethod;
9 import org.testng.annotations.BeforeClass;
10 import org.testng.annotations.DataProvider;
11 import org.testng.annotations.Test;
13 import jalview.api.AlignViewportI;
14 import jalview.datamodel.AlignmentAnnotation;
15 import jalview.datamodel.AlignmentI;
16 import jalview.datamodel.SequenceI;
17 import jalview.gui.AlignFrame;
18 import jalview.gui.AlignmentPanel;
19 import jalview.gui.Desktop;
20 import jalview.gui.JvOptionPane;
21 import jalview.gui.StructureViewerBase;
24 public class CommandsTest2
26 @BeforeClass(alwaysRun = true)
27 public static void setUpBeforeClass() throws Exception
29 Cache.loadProperties("test/jalview/bin/commandsTest.jvprops");
30 Date oneHourFromNow = new Date(
31 System.currentTimeMillis() + 3600 * 1000);
32 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
33 if (Desktop.instance != null)
34 Desktop.instance.closeAll_actionPerformed(null);
38 @AfterClass(alwaysRun = true)
39 public static void resetProps()
41 Cache.loadProperties("test/jalview/testProps.jvprops");
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51 @AfterMethod(alwaysRun = true)
52 public void tearDown()
54 if (Desktop.instance != null)
55 Desktop.instance.closeAll_actionPerformed(null);
60 { "Functional", "testTask1" },
61 dataProvider = "structureOpeningArgsParams",
62 singleThreaded = true)
63 public void structureOpeningArgsTest(String cmdLine, int seqNum,
64 int annNum, int viewerNum)
66 String[] args = cmdLine.split("\\s+");
71 // sleep for slow build server to open annotations and viewer windows
72 Thread.sleep(seqNum * 50 + annNum * 50 + viewerNum * 500);
73 } catch (InterruptedException e)
78 AlignFrame[] afs = Desktop.getAlignFrames();
79 Assert.assertNotNull(afs);
80 Assert.assertTrue(afs.length > 0);
82 AlignFrame af = afs[0];
83 Assert.assertNotNull(af);
85 AlignmentPanel ap = af.alignPanel;
86 Assert.assertNotNull(ap);
88 AlignmentI al = ap.getAlignment();
89 Assert.assertNotNull(al);
91 List<SequenceI> seqs = al.getSequences();
92 Assert.assertNotNull(seqs);
94 Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
96 AlignViewportI av = ap.getAlignViewport();
97 Assert.assertNotNull(av);
99 AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
102 for (AlignmentAnnotation aa : aas)
108 Assert.assertEquals(visibleAnn, annNum,
109 "Wrong number of visible annotations");
113 List<StructureViewerBase> openViewers = Desktop.instance
114 .getStructureViewers(ap, null);
115 Assert.assertNotNull(openViewers);
117 for (StructureViewerBase svb : openViewers)
122 Assert.assertEquals(count, viewerNum,
123 "Wrong number of structure viewers opened");
127 @DataProvider(name = "structureOpeningArgsParams")
128 public Object[][] structureOpeningArgsParams()
134 int structureViewerNum,
136 return new Object[][] {
140 { "--gui --nonews --nosplash --debug "
141 + "--append=examples/uniref50.fa "
142 + "--colour=gecos-flower "
143 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
144 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
145 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
147 { "--gui --nonews --nosplash --debug "
148 + "--append=examples/uniref50.fa "
149 + "--colour=gecos-flower "
150 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
151 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
152 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
154 { "--gui --nonews --nosplash --debug "
155 + "--append=examples/uniref50.fa "
156 + "--colour=gecos-flower "
157 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
158 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
159 + "--noshowssannotations "
160 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
162 { "--gui --nonews --nosplash --debug "
163 + "--append=examples/uniref50.fa "
164 + "--colour=gecos-flower "
165 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
166 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
167 + "--noshowannotations "
168 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
170 { "--gui --nonews --nosplash --debug "
171 + "--append=examples/uniref50.fa "
172 + "--colour=gecos-flower "
173 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
174 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
175 + "--noshowannotations " + "--noshowssannotations "
176 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
178 { "--gui --nonews --nosplash --debug "
179 + "--append=examples/uniref50.fa "
180 + "--colour=gecos-flower "
181 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
182 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
183 + "--noshowannotations " + "--noshowssannotations "
184 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
186 { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
188 { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
190 { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
192 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
193 + "--structureviewer=none "
194 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
195 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
197 { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
199 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
200 + "--noallstructures " + "--structureviewer=none "
201 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
202 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",