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" },
  61     dataProvider = "structureOpeningArgsParams")
  62   public void structureOpeningArgsTest(String cmdLine, int seqNum,
  63           int annNum, int viewerNum)
  64   {
  65     String[] args = cmdLine.split("\\s+");
  66
  67     Jalview.main(args);
  68     AlignFrame[] afs = Desktop.getAlignFrames();
  69     Assert.assertNotNull(afs);
  70     Assert.assertTrue(afs.length > 0);
  71
  72     AlignFrame af = afs[0];
  73     Assert.assertNotNull(af);
  74
  75     AlignmentPanel ap = af.alignPanel;
  76     Assert.assertNotNull(ap);
  77
  78     AlignmentI al = ap.getAlignment();
  79     Assert.assertNotNull(al);
  80
  81     List<SequenceI> seqs = al.getSequences();
  82     Assert.assertNotNull(seqs);
  83
  84     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
  85
  86     AlignViewportI av = ap.getAlignViewport();
  87     Assert.assertNotNull(av);
  88
  89     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
  90     int visibleAnn = 0;
  91     for (AlignmentAnnotation aa : aas)
  92     {
  93       if (aa.visible)
  94         visibleAnn++;
  95     }
  96
  97     Assert.assertEquals(visibleAnn, annNum,
  98             "Wrong number of visible annotations");
  99
 100     if (viewerNum > -1)
 101     {
 102       try
 103       {
 104         // sleep for slow build server to open viewer window
 105         Thread.sleep(2000);
 106       } catch (InterruptedException e)
 107       {
 108         e.printStackTrace();
 109       }
 110       List<StructureViewerBase> openViewers = Desktop.instance
 111               .getStructureViewers(ap, null);
 112       Assert.assertNotNull(openViewers);
 113       int count = 0;
 114       int dcount = 0;
 115       for (StructureViewerBase svb : openViewers)
 116       {
 117         System.err.println("##### DIAGNOSIS: annotation " + dcount
 118                 + " is called '" + svb.getName() + "'");
 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                 + "--nossannotations "
 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                 + "--noannotations "
 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                 + "--noannotations " + "--nossannotations "
 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                 + "--noannotations " + "--nossannotations "
 179                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 180             15, 0, 1 },
 181         { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
 182         { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
 183         //
 184     };
 185   }
 186 }