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/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);
  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 structureViewerNum,
 135      */
 136     return new Object[][] {
 137         //
 138         /*
 139          */
 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 ",
 146             15, 7, 1 },
 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 ",
 153             15, 4, 1 },
 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 ",
 161             15, 4, 1 },
 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 ",
 169             15, 3, 1 },
 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 ",
 177             15, 0, 1 },
 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 ",
 185             15, 0, 1 },
 186         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
 187             16, 19, 3 },
 188         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
 189             16, 0, 2 },
 190         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 191                 + "--allstructures "
 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",
 196             16, 10, 0 },
 197         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 198                 + "--allstructures "
 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",
 203             16, 10, 2 },
 204         /*
 205          */
 206         //
 207     };
 208   }
 209 }