test/jalview/bin/CommandsTest2.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.bin;
  22
  23 import java.util.Date;
  24 import java.util.List;
  25
  26 import org.testng.Assert;
  27 import org.testng.annotations.AfterClass;
  28 import org.testng.annotations.AfterMethod;
  29 import org.testng.annotations.BeforeClass;
  30 import org.testng.annotations.DataProvider;
  31 import org.testng.annotations.Test;
  32
  33 import jalview.api.AlignViewportI;
  34 import jalview.datamodel.AlignmentAnnotation;
  35 import jalview.datamodel.AlignmentI;
  36 import jalview.datamodel.SequenceI;
  37 import jalview.gui.AlignFrame;
  38 import jalview.gui.AlignmentPanel;
  39 import jalview.gui.Desktop;
  40 import jalview.gui.JvOptionPane;
  41 import jalview.gui.StructureViewerBase;
  42
  43 @Test
  44 public class CommandsTest2
  45 {
  46   @BeforeClass(alwaysRun = true)
  47   public static void setUpBeforeClass() throws Exception
  48   {
  49     Cache.loadProperties("test/jalview/bin/commandsTest.jvprops");
  50     Date oneHourFromNow = new Date(
  51             System.currentTimeMillis() + 3600 * 1000);
  52     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
  53     if (Desktop.instance != null)
  54       Desktop.instance.closeAll_actionPerformed(null);
  55
  56   }
  57
  58   @AfterClass(alwaysRun = true)
  59   public static void resetProps()
  60   {
  61     Cache.loadProperties("test/jalview/testProps.jvprops");
  62   }
  63
  64   @BeforeClass(alwaysRun = true)
  65   public void setUpJvOptionPane()
  66   {
  67     JvOptionPane.setInteractiveMode(false);
  68     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  69   }
  70
  71   @AfterMethod(alwaysRun = true)
  72   public void tearDown()
  73   {
  74     Desktop.closeDesktop();
  75   }
  76
  77   @Test(
  78     groups =
  79     { "Functional", "testTask1" },
  80     dataProvider = "structureOpeningArgsParams",
  81     singleThreaded = true)
  82   public void structureOpeningArgsTest(String cmdLine, int seqNum,
  83           int annNum, int viewerNum)
  84   {
  85     String[] args = cmdLine.split("\\s+");
  86
  87     CommandsTest.callJalviewMain(args);
  88     while (Desktop.instance != null
  89             && Desktop.instance.operationsAreInProgress())
  90     {
  91       try
  92       {
  93         // sleep for slow build server to open annotations and viewer windows
  94         Thread.sleep(viewerNum * 50);
  95       } catch (InterruptedException e)
  96       {
  97         e.printStackTrace();
  98       }
  99     }
 100     ;
 101
 102     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 103     Assert.assertNotNull(afs);
 104     Assert.assertTrue(afs.length > 0);
 105
 106     AlignFrame af = afs[0];
 107     Assert.assertNotNull(af);
 108
 109     AlignmentPanel ap = af.alignPanel;
 110     Assert.assertNotNull(ap);
 111
 112     AlignmentI al = ap.getAlignment();
 113     Assert.assertNotNull(al);
 114
 115     List<SequenceI> seqs = al.getSequences();
 116     Assert.assertNotNull(seqs);
 117
 118     Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
 119
 120     AlignViewportI av = ap.getAlignViewport();
 121     Assert.assertNotNull(av);
 122
 123     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
 124     int visibleAnn = 0;
 125     int dcount = 0;
 126     for (AlignmentAnnotation aa : aas)
 127     {
 128       if (aa.visible)
 129         visibleAnn++;
 130     }
 131
 132     Assert.assertEquals(visibleAnn, annNum,
 133             "Wrong number of visible annotations");
 134
 135     if (viewerNum > -1)
 136     {
 137       List<StructureViewerBase> openViewers = Desktop.instance
 138               .getStructureViewers(ap, null);
 139       Assert.assertNotNull(openViewers);
 140       int count = 0;
 141       for (StructureViewerBase svb : openViewers)
 142       {
 143         if (svb.isVisible())
 144           count++;
 145       }
 146       Assert.assertEquals(count, viewerNum,
 147               "Wrong number of structure viewers opened");
 148     }
 149   }
 150
 151   @DataProvider(name = "structureOpeningArgsParams")
 152   public Object[][] structureOpeningArgsParams()
 153   {
 154     /*
 155       String cmdLine,
 156       int seqNum,
 157       int annNum,
 158       int structureViewerNum,
 159      */
 160     return new Object[][] {
 161         //
 162         /*
 163          */
 164         { "--gui --nonews --nosplash --debug "
 165                 + "--append=examples/uniref50.fa "
 166                 + "--colour=gecos-flower "
 167                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 168                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 169                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 170             15, 7, 1 },
 171         { "--gui --nonews --nosplash --debug "
 172                 + "--append=examples/uniref50.fa "
 173                 + "--colour=gecos-flower "
 174                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 175                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 176                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
 177             15, 4, 1 },
 178         { "--gui --nonews --nosplash --debug "
 179                 + "--append=examples/uniref50.fa "
 180                 + "--colour=gecos-flower "
 181                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 182                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 183                 + "--noshowssannotations "
 184                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 185             15, 4, 1 },
 186         { "--gui --nonews --nosplash --debug "
 187                 + "--append=examples/uniref50.fa "
 188                 + "--colour=gecos-flower "
 189                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 190                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 191                 + "--noshowannotations "
 192                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 193             15, 3, 1 },
 194         { "--gui --nonews --nosplash --debug "
 195                 + "--append=examples/uniref50.fa "
 196                 + "--colour=gecos-flower "
 197                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 198                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 199                 + "--noshowannotations " + "--noshowssannotations "
 200                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 201             15, 0, 1 },
 202         { "--gui --nonews --nosplash --debug "
 203                 + "--append=examples/uniref50.fa "
 204                 + "--colour=gecos-flower "
 205                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
 206                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 207                 + "--noshowannotations " + "--noshowssannotations "
 208                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
 209             15, 0, 1 },
 210         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
 211             16, 19, 3 },
 212         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
 213             16, 0, 2 },
 214         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 215                 + "--allstructures "
 216                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 217                 + "--structureviewer=none "
 218                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 219                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 220             16, 10, 0 },
 221         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
 222                 + "--allstructures "
 223                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 224                 + "--noallstructures " + "--structureviewer=none "
 225                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
 226                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
 227             16, 10, 2 },
 228         /*
 229          */
 230         //
 231     };
 232   }
 233 }