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     while (Desktop.instance != null
  69             && Desktop.instance.operationsAreInProgress())
  70     {
  71       try
  72       {
  73         // sleep for slow build server to open annotations and viewer windows
  74         Thread.sleep(viewerNum * 50);
  75       } catch (InterruptedException e)
  76       {
  77         e.printStackTrace();
  78       }
  79     }
  80     ;
  81
  82     AlignFrame[] afs = Desktop.getAlignFrames();
  83     Assert.assertNotNull(afs);
  84     Assert.assertTrue(afs.length > 0);
  85
  86     AlignFrame af = afs[0];
  87     Assert.assertNotNull(af);
  88
  89     AlignmentPanel ap = af.alignPanel;
  90     Assert.assertNotNull(ap);
  91
  92     AlignmentI al = ap.getAlignment();
  93     Assert.assertNotNull(al);
  94
  95     List<SequenceI> seqs = al.getSequences();
  96     Assert.assertNotNull(seqs);
  97
  98     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
  99
 100     AlignViewportI av = ap.getAlignViewport();
 101     Assert.assertNotNull(av);
 102
 103     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
 104     int visibleAnn = 0;
 105     int dcount = 0;
 106     for (AlignmentAnnotation aa : aas)
 107     {
 108       if (aa.visible)
 109         visibleAnn++;
 110     }
 111
 112     Assert.assertEquals(visibleAnn, annNum,
 113             "Wrong number of visible annotations");
 114
 115     if (viewerNum > -1)
 116     {
 117       List<StructureViewerBase> openViewers = Desktop.instance
 118               .getStructureViewers(ap, null);
 119       Assert.assertNotNull(openViewers);
 120       int count = 0;
 121       for (StructureViewerBase svb : openViewers)
 122       {
 123         if (svb.isVisible())
 124           count++;
 125       }
 126       Assert.assertEquals(count, viewerNum,
 127               "Wrong number of structure viewers opened");
 128     }
 129   }
 130
 131   @DataProvider(name = "structureOpeningArgsParams")
 132   public Object[][] structureOpeningArgsParams()
 133   {
 134     /*
 135       String cmdLine,
 136       int seqNum,
 137       int annNum,
 138       int structureViewerNum,
 139      */
 140     return new Object[][] {
 141         //
 142         /*
 143          */
 144         { "--gui --nonews --nosplash --debug "
 145                 + "--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                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 150             15, 7, 1 },
 151         { "--gui --nonews --nosplash --debug "
 152                 + "--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                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
 157             15, 4, 1 },
 158         { "--gui --nonews --nosplash --debug "
 159                 + "--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                 + "--noshowssannotations "
 164                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 165             15, 4, 1 },
 166         { "--gui --nonews --nosplash --debug "
 167                 + "--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                 + "--noshowannotations "
 172                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 173             15, 3, 1 },
 174         { "--gui --nonews --nosplash --debug "
 175                 + "--append=examples/uniref50.fa "
 176                 + "--colour=gecos-flower "
 177                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 178                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 179                 + "--noshowannotations " + "--noshowssannotations "
 180                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 181             15, 0, 1 },
 182         { "--gui --nonews --nosplash --debug "
 183                 + "--append=examples/uniref50.fa "
 184                 + "--colour=gecos-flower "
 185                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 186                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 187                 + "--noshowannotations " + "--noshowssannotations "
 188                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 189             15, 0, 1 },
 190         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
 191             16, 19, 3 },
 192         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
 193             16, 0, 2 },
 194         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 195                 + "--allstructures "
 196                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 197                 + "--structureviewer=none "
 198                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 199                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 200             16, 10, 0 },
 201         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 202                 + "--allstructures "
 203                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 204                 + "--noallstructures " + "--structureviewer=none "
 205                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 206                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 207             16, 10, 2 },
 208         /*
 209          */
 210         //
 211     };
 212   }
 213 }