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     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 viewer window
  72       Thread.sleep(2500);
  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       if (aa.visible)
 107         visibleAnn++;
 108     }
 109
 110     Assert.assertEquals(visibleAnn, annNum,
 111             "Wrong number of visible annotations");
 112
 113     if (viewerNum > -1)
 114     {
 115       List<StructureViewerBase> openViewers = Desktop.instance
 116               .getStructureViewers(ap, null);
 117       Assert.assertNotNull(openViewers);
 118       int count = 0;
 119       for (StructureViewerBase svb : openViewers)
 120       {
 121         if (svb.isVisible())
 122           count++;
 123       }
 124       Assert.assertEquals(count, viewerNum,
 125               "Wrong number of structure viewers opened");
 126     }
 127   }
 128
 129   @DataProvider(name = "structureOpeningArgsParams")
 130   public Object[][] structureOpeningArgsParams()
 131   {
 132     /*
 133       String cmdLine,
 134       int seqNum,
 135       int annNum,
 136       int viewerNum,
 137       String propsFile
 138      */
 139     return new Object[][] {
 140         //
 141         /*
 142          */
 143         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 144                 + "--colour=gecos:flower "
 145                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 146                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 147                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 148             15, 7, 1 },
 149         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 150                 + "--colour=gecos:flower "
 151                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 152                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 153                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
 154             15, 4, 1 },
 155         { "--nonews --nosplash --debug " + "--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                 + "--nossannotations "
 160                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 161             15, 4, 1 },
 162         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 163                 + "--colour=gecos:flower "
 164                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 165                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 166                 + "--noannotations "
 167                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 168             15, 3, 1 },
 169         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 170                 + "--colour=gecos:flower "
 171                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 172                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 173                 + "--noannotations " + "--nossannotations "
 174                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 175             15, 0, 1 },
 176         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
 177                 + "--colour=gecos:flower "
 178                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 179                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 180                 + "--noannotations " + "--nossannotations "
 181                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 182             15, 0, 1 },
 183         { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
 184         { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
 185         //
 186     };
 187   }
 188 }