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     try
  69     {
  70       // sleep for slow build server to open annotations and viewer windows
  71       Thread.sleep(seqNum * 50 + annNum * 50 + viewerNum * 500);
  72     } catch (InterruptedException e)
  73     {
  74       e.printStackTrace();
  75     }
  76
  77     AlignFrame[] afs = Desktop.getAlignFrames();
  78     Assert.assertNotNull(afs);
  79     Assert.assertTrue(afs.length > 0);
  80
  81     AlignFrame af = afs[0];
  82     Assert.assertNotNull(af);
  83
  84     AlignmentPanel ap = af.alignPanel;
  85     Assert.assertNotNull(ap);
  86
  87     AlignmentI al = ap.getAlignment();
  88     Assert.assertNotNull(al);
  89
  90     List<SequenceI> seqs = al.getSequences();
  91     Assert.assertNotNull(seqs);
  92
  93     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
  94
  95     AlignViewportI av = ap.getAlignViewport();
  96     Assert.assertNotNull(av);
  97
  98     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
  99     int visibleAnn = 0;
 100     int dcount = 0;
 101     for (AlignmentAnnotation aa : aas)
 102     {
 103       if (aa.visible)
 104         visibleAnn++;
 105     }
 106
 107     Assert.assertEquals(visibleAnn, annNum,
 108             "Wrong number of visible annotations");
 109
 110     if (viewerNum > -1)
 111     {
 112       List<StructureViewerBase> openViewers = Desktop.instance
 113               .getStructureViewers(ap, null);
 114       Assert.assertNotNull(openViewers);
 115       int count = 0;
 116       for (StructureViewerBase svb : openViewers)
 117       {
 118         if (svb.isVisible())
 119           count++;
 120       }
 121       Assert.assertEquals(count, viewerNum,
 122               "Wrong number of structure viewers opened");
 123     }
 124   }
 125
 126   @DataProvider(name = "structureOpeningArgsParams")
 127   public Object[][] structureOpeningArgsParams()
 128   {
 129     /*
 130       String cmdLine,
 131       int seqNum,
 132       int annNum,
 133       int structureViewerNum,
 134      */
 135     return new Object[][] {
 136         //
 137         /*
 138          */
 139         { "--gui --nonews --nosplash --debug "
 140                 + "--append=examples/uniref50.fa "
 141                 + "--colour=gecos-flower "
 142                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 143                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 144                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 145             15, 7, 1 },
 146         { "--gui --nonews --nosplash --debug "
 147                 + "--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         { "--gui --nonews --nosplash --debug "
 154                 + "--append=examples/uniref50.fa "
 155                 + "--colour=gecos-flower "
 156                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 157                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 158                 + "--noshowssannotations "
 159                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 160             15, 4, 1 },
 161         { "--gui --nonews --nosplash --debug "
 162                 + "--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                 + "--noshowannotations "
 167                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 168             15, 3, 1 },
 169         { "--gui --nonews --nosplash --debug "
 170                 + "--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                 + "--noshowannotations " + "--noshowssannotations "
 175                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 176             15, 0, 1 },
 177         { "--gui --nonews --nosplash --debug "
 178                 + "--append=examples/uniref50.fa "
 179                 + "--colour=gecos-flower "
 180                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 181                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 182                 + "--noshowannotations " + "--noshowssannotations "
 183                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 184             15, 0, 1 },
 185         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
 186             16, 19, 3 },
 187         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
 188             16, 0, 2 },
 189         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 190                 + "--allstructures "
 191                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 192                 + "--structureviewer=none "
 193                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 194                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 195             16, 10, 0 },
 196         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 197                 + "--allstructures "
 198                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 199                 + "--noallstructures " + "--structureviewer=none "
 200                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 201                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 202             16, 10, 2 },
 203         /*
 204          */
 205         //
 206     };
 207   }
 208 }