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" },
  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 * 100 + annNum * 200 + viewerNum * 1500);
  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       System.err.println("##### DIAGNOSIS: annotation " + ++dcount
 105               + " is labelled '" + aa.label + "'");
 106       System.err.println("# " + aa.annotationId + ": " + aa.toString());
 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 viewerNum,
 138       String propsFile
 139      */
 140     return new Object[][] {
 141         //
 142         /*
 143          */
 144         { "--nonews --nosplash --debug " + "--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         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 151                 + "--colour=gecos:flower "
 152                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 153                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 154                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
 155             15, 4, 1 },
 156         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 157                 + "--colour=gecos:flower "
 158                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 159                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 160                 + "--nossannotations "
 161                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 162             15, 4, 1 },
 163         { "--nonews --nosplash --debug " + "--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                 + "--noannotations "
 168                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 169             15, 3, 1 },
 170         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 171                 + "--colour=gecos:flower "
 172                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 173                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 174                 + "--noannotations " + "--nossannotations "
 175                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 176             15, 0, 1 },
 177         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 178                 + "--colour=gecos:flower "
 179                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 180                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 181                 + "--noannotations " + "--nossannotations "
 182                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 183             15, 0, 1 },
 184         { "--props=test/jalview/bin/commandsTest2.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
 185             16, 19, 3 },
 186         { "--props=test/jalview/bin/commandsTest2.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
 187             16, 0, 2 },
 188         //
 189     };
 190   }
 191 }