JAL-629 More docs. Usage statement. Adjust some logging output to respect --quiet.
[jalview.git] / test / jalview / bin / CommandsTest2.java
1 package jalview.bin;
2
3 import java.util.Date;
4 import java.util.List;
5
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;
12
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;
22
23 @Test
24 public class CommandsTest2
25 {
26   @BeforeClass(alwaysRun = true)
27   public static void setUpBeforeClass() throws Exception
28   {
29     Cache.loadProperties("test/jalview/bin/commandsTest2.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);
35
36   }
37
38   @AfterClass(alwaysRun = true)
39   public static void resetProps()
40   {
41     Cache.loadProperties("test/jalview/testProps.jvprops");
42   }
43
44   @BeforeClass(alwaysRun = true)
45   public void setUpJvOptionPane()
46   {
47     JvOptionPane.setInteractiveMode(false);
48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49   }
50
51   @AfterMethod(alwaysRun = true)
52   public void tearDown()
53   {
54     if (Desktop.instance != null)
55       Desktop.instance.closeAll_actionPerformed(null);
56   }
57
58   @Test(
59     groups =
60     { "Functional", "testTask1" },
61     dataProvider = "structureOpeningArgsParams",
62     singleThreaded = true)
63   public void structureOpeningArgsTest(String cmdLine, int seqNum,
64           int annNum, int viewerNum)
65   {
66     String[] args = cmdLine.split("\\s+");
67
68     Jalview.main(args);
69     try
70     {
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)
74     {
75       e.printStackTrace();
76     }
77
78     AlignFrame[] afs = Desktop.getAlignFrames();
79     Assert.assertNotNull(afs);
80     Assert.assertTrue(afs.length > 0);
81
82     AlignFrame af = afs[0];
83     Assert.assertNotNull(af);
84
85     AlignmentPanel ap = af.alignPanel;
86     Assert.assertNotNull(ap);
87
88     AlignmentI al = ap.getAlignment();
89     Assert.assertNotNull(al);
90
91     List<SequenceI> seqs = al.getSequences();
92     Assert.assertNotNull(seqs);
93
94     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
95
96     AlignViewportI av = ap.getAlignViewport();
97     Assert.assertNotNull(av);
98
99     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
100     int visibleAnn = 0;
101     int dcount = 0;
102     for (AlignmentAnnotation aa : aas)
103     {
104       if (aa.visible)
105         visibleAnn++;
106     }
107
108     Assert.assertEquals(visibleAnn, annNum,
109             "Wrong number of visible annotations");
110
111     if (viewerNum > -1)
112     {
113       List<StructureViewerBase> openViewers = Desktop.instance
114               .getStructureViewers(ap, null);
115       Assert.assertNotNull(openViewers);
116       int count = 0;
117       for (StructureViewerBase svb : openViewers)
118       {
119         if (svb.isVisible())
120           count++;
121       }
122       Assert.assertEquals(count, viewerNum,
123               "Wrong number of structure viewers opened");
124     }
125   }
126
127   @DataProvider(name = "structureOpeningArgsParams")
128   public Object[][] structureOpeningArgsParams()
129   {
130     /*
131       String cmdLine,
132       int seqNum,
133       int annNum,
134       int viewerNum,
135       String propsFile
136      */
137     return new Object[][] {
138         //
139         /*
140          */
141         { "--nonews --nosplash --debug " + "--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 ",
146             15, 7, 1 },
147         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
148                 + "--colour=gecos-flower "
149                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
150                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
151                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
152             15, 4, 1 },
153         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
154                 + "--colour=gecos-flower "
155                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
156                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
157                 + "--noshowssannotations "
158                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
159             15, 4, 1 },
160         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
161                 + "--colour=gecos-flower "
162                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
163                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
164                 + "--noshowannotations "
165                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
166             15, 3, 1 },
167         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
168                 + "--colour=gecos-flower "
169                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
170                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
171                 + "--noshowannotations " + "--noshowssannotations "
172                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
173             15, 0, 1 },
174         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
175                 + "--colour=gecos-flower "
176                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
177                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
178                 + "--noshowannotations " + "--noshowssannotations "
179                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
180             15, 0, 1 },
181         { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
182             16, 19, 3 },
183         { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
184             16, 0, 2 },
185         //
186     };
187   }
188 }