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/testProps.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     AlignFrame[] afs = Desktop.getAlignFrames();
  70     Assert.assertNotNull(afs);
  71     Assert.assertTrue(afs.length > 0);
  72
  73     AlignFrame af = afs[0];
  74     Assert.assertNotNull(af);
  75
  76     AlignmentPanel ap = af.alignPanel;
  77     Assert.assertNotNull(ap);
  78
  79     AlignmentI al = ap.getAlignment();
  80     Assert.assertNotNull(al);
  81
  82     List<SequenceI> seqs = al.getSequences();
  83     Assert.assertNotNull(seqs);
  84
  85     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
  86
  87     AlignViewportI av = ap.getAlignViewport();
  88     Assert.assertNotNull(av);
  89
  90     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
  91     int visibleAnn = 0;
  92     for (AlignmentAnnotation aa : aas)
  93     {
  94       if (aa.visible)
  95         visibleAnn++;
  96     }
  97
  98     Assert.assertEquals(visibleAnn, annNum,
  99             "Wrong number of visible annotations");
 100
 101     if (viewerNum > -1)
 102     {
 103       try
 104       {
 105         // sleep for slow build server to open viewer window
 106         Thread.sleep(5000);
 107       } catch (InterruptedException e)
 108       {
 109         e.printStackTrace();
 110       }
 111       List<StructureViewerBase> openViewers = Desktop.instance
 112               .getStructureViewers(ap, null);
 113       Assert.assertNotNull(openViewers);
 114       Assert.assertEquals(openViewers.size(), viewerNum,
 115               "Wrong number of structure viewers opened");
 116     }
 117   }
 118
 119   @DataProvider(name = "structureOpeningArgsParams")
 120   public Object[][] structureOpeningArgsParams()
 121   {
 122     /*
 123       String cmdLine,
 124       int seqNum,
 125       int annNum,
 126       int viewerNum,
 127       String propsFile
 128      */
 129     return new Object[][] {
 130         //
 131         /*
 132          */
 133         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 134                 + "--colour=gecos:flower "
 135                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 136                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 137                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 138             15, 7, 1 },
 139         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 140                 + "--colour=gecos:flower "
 141                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 142                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 143                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
 144             15, 4, 1 },
 145         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 146                 + "--colour=gecos:flower "
 147                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 148                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 149                 + "--nossannotations "
 150                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 151             15, 4, 1 },
 152         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 153                 + "--colour=gecos:flower "
 154                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 155                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 156                 + "--noannotations "
 157                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 158             15, 3, 1 },
 159         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 160                 + "--colour=gecos:flower "
 161                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 162                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 163                 + "--noannotations " + "--nossannotations "
 164                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 165             15, 0, 1 },
 166         { "--nonews --nosplash --debug " + "--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                 + "--noannotations " + "--nossannotations "
 171                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 172             15, 0, 1 },
 173         { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
 174         { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
 175         //
 176     };
 177   }
 178 }