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     Desktop.closeDesktop();
  55   }
  56
  57   @Test(
  58     groups =
  59     { "Functional", "testTask1" },
  60     dataProvider = "structureOpeningArgsParams",
  61     singleThreaded = true)
  62   public void structureOpeningArgsTest(String cmdLine, int seqNum,
  63           int annNum, int viewerNum)
  64   {
  65     String[] args = cmdLine.split("\\s+");
  66
  67     CommandsTest.callJalviewMain(args);
  68     while (Desktop.instance!=null && Desktop.instance.operationsAreInProgress())
  69     {
  70       try
  71       {
  72         // sleep for slow build server to open annotations and viewer windows
  73         Thread.sleep(viewerNum * 50);
  74       } catch (InterruptedException e)
  75       {
  76         e.printStackTrace();
  77       }
  78     }
  79     ;
  80
  81     AlignFrame[] afs = Desktop.getAlignFrames();
  82     Assert.assertNotNull(afs);
  83     Assert.assertTrue(afs.length > 0);
  84
  85     AlignFrame af = afs[0];
  86     Assert.assertNotNull(af);
  87
  88     AlignmentPanel ap = af.alignPanel;
  89     Assert.assertNotNull(ap);
  90
  91     AlignmentI al = ap.getAlignment();
  92     Assert.assertNotNull(al);
  93
  94     List<SequenceI> seqs = al.getSequences();
  95     Assert.assertNotNull(seqs);
  96
  97     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
  98
  99     AlignViewportI av = ap.getAlignViewport();
 100     Assert.assertNotNull(av);
 101
 102     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
 103     int visibleAnn = 0;
 104     int dcount = 0;
 105     for (AlignmentAnnotation aa : aas)
 106     {
 107       if (aa.visible)
 108         visibleAnn++;
 109     }
 110
 111     Assert.assertEquals(visibleAnn, annNum,
 112             "Wrong number of visible annotations");
 113
 114     if (viewerNum > -1)
 115     {
 116       List<StructureViewerBase> openViewers = Desktop.instance
 117               .getStructureViewers(ap, null);
 118       Assert.assertNotNull(openViewers);
 119       int count = 0;
 120       for (StructureViewerBase svb : openViewers)
 121       {
 122         if (svb.isVisible())
 123           count++;
 124       }
 125       Assert.assertEquals(count, viewerNum,
 126               "Wrong number of structure viewers opened");
 127     }
 128   }
 129
 130   @DataProvider(name = "structureOpeningArgsParams")
 131   public Object[][] structureOpeningArgsParams()
 132   {
 133     /*
 134       String cmdLine,
 135       int seqNum,
 136       int annNum,
 137       int structureViewerNum,
 138      */
 139     return new Object[][] {
 140         //
 141         /*
 142          */
 143         { "--gui --nonews --nosplash --debug "
 144                 + "--append=examples/uniref50.fa "
 145                 + "--colour=gecos-flower "
 146                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 147                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 148                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 149             15, 7, 1 },
 150         { "--gui --nonews --nosplash --debug "
 151                 + "--append=examples/uniref50.fa "
 152                 + "--colour=gecos-flower "
 153                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 154                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 155                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
 156             15, 4, 1 },
 157         { "--gui --nonews --nosplash --debug "
 158                 + "--append=examples/uniref50.fa "
 159                 + "--colour=gecos-flower "
 160                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 161                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 162                 + "--noshowssannotations "
 163                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 164             15, 4, 1 },
 165         { "--gui --nonews --nosplash --debug "
 166                 + "--append=examples/uniref50.fa "
 167                 + "--colour=gecos-flower "
 168                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 169                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 170                 + "--noshowannotations "
 171                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 172             15, 3, 1 },
 173         { "--gui --nonews --nosplash --debug "
 174                 + "--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         { "--gui --nonews --nosplash --debug "
 182                 + "--append=examples/uniref50.fa "
 183                 + "--colour=gecos-flower "
 184                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 185                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 186                 + "--noshowannotations " + "--noshowssannotations "
 187                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 188             15, 0, 1 },
 189         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
 190             16, 19, 3 },
 191         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
 192             16, 0, 2 },
 193         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 194                 + "--allstructures "
 195                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 196                 + "--structureviewer=none "
 197                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 198                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 199             16, 10, 0 },
 200         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 201                 + "--allstructures "
 202                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 203                 + "--noallstructures " + "--structureviewer=none "
 204                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 205                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 206             16, 10, 2 },
 207         /*
 208          */
 209         //
 210     };
 211   }
 212 }