test/jalview/ext/jmol/JmolViewerTest.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.ext.jmol;
  22
  23 import static org.testng.AssertJUnit.assertTrue;
  24
  25 import jalview.api.structures.JalviewStructureDisplayI;
  26 import jalview.bin.Cache;
  27 import jalview.bin.Jalview;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.gui.AlignFrame;
  30 import jalview.gui.JvOptionPane;
  31 import jalview.gui.Preferences;
  32 import jalview.gui.StructureViewer;
  33 import jalview.gui.StructureViewer.ViewerType;
  34 import jalview.io.DataSourceType;
  35
  36 import org.testng.Assert;
  37 import org.testng.annotations.AfterClass;
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.Test;
  40
  41 @Test(singleThreaded = true)
  42 public class JmolViewerTest
  43 {
  44
  45   @BeforeClass(alwaysRun = true)
  46   public void setUpJvOptionPane()
  47   {
  48     JvOptionPane.setInteractiveMode(false);
  49     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  50   }
  51
  52   /**
  53    * @throws java.lang.Exception
  54    */
  55   @BeforeClass(alwaysRun = true)
  56   public static void setUpBeforeClass() throws Exception
  57   {
  58     Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
  59         "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
  60   }
  61
  62   /**
  63    * @throws java.lang.Exception
  64    */
  65   @AfterClass(alwaysRun = true)
  66   public static void tearDownAfterClass() throws Exception
  67   {
  68     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  69   }
  70
  71   @Test(groups = { "Functional" })
  72   public void testSingleSeqViewJMol()
  73   {
  74     Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
  75     String inFile = "examples/1gaq.txt";
  76     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  77             inFile, DataSourceType.FILE);
  78     assertTrue("Didn't read input file " + inFile, af != null);
  79     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  80     {
  81       SequenceI dsq = sq.getDatasetSequence();
  82       while (dsq.getDatasetSequence() != null)
  83       {
  84         dsq = dsq.getDatasetSequence();
  85       }
  86       if (dsq.getAllPDBEntries() != null
  87               && dsq.getAllPDBEntries().size() > 0)
  88       {
  89         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
  90         {
  91           final StructureViewer structureViewer = new StructureViewer(af
  92                   .getViewport().getStructureSelectionManager());
  93           structureViewer.setViewerType(ViewerType.JMOL);
  94           JalviewStructureDisplayI jmolViewer = structureViewer
  95                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
  96                           new SequenceI[] { sq }, af.getCurrentView()
  97                                   .getAlignPanel());
  98           /*
  99            * Wait for viewer load thread to complete
 100            */
 101           try
 102           {
 103             while (!jmolViewer.getBinding().isFinishedInit())
 104             {
 105               Thread.sleep(500);
 106             }
 107           } catch (InterruptedException e)
 108           {
 109           }
 110
 111           jmolViewer.closeViewer(true);
 112           // todo: break here means only once through this loop?
 113           break;
 114         }
 115         break;
 116       }
 117     }
 118   }
 119
 120   @Test(groups = { "Functional, Network" })
 121   public void testStructureLoadingViaURL()
 122   {
 123     Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 124     String inFile = "http://www.jalview.org/builds/develop/examples/3W5V.pdb";
 125     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
 126             inFile, DataSourceType.URL);
 127     assertTrue("Didn't read input file " + inFile, af != null);
 128     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
 129     {
 130       SequenceI dsq = sq.getDatasetSequence();
 131       while (dsq.getDatasetSequence() != null)
 132       {
 133         dsq = dsq.getDatasetSequence();
 134       }
 135       if (dsq.getAllPDBEntries() != null
 136               && dsq.getAllPDBEntries().size() > 0)
 137       {
 138         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
 139         {
 140           final StructureViewer structureViewer = new StructureViewer(af
 141                   .getViewport().getStructureSelectionManager());
 142           structureViewer.setViewerType(ViewerType.JMOL);
 143           JalviewStructureDisplayI jmolViewer = structureViewer
 144                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
 145                           new SequenceI[] { sq }, af.getCurrentView()
 146                                   .getAlignPanel());
 147           /*
 148           * Wait for viewer load thread to complete
 149           */
 150           try
 151           {
 152             while (!jmolViewer.getBinding().isFinishedInit())
 153             {
 154               Thread.sleep(500);
 155             }
 156           } catch (InterruptedException e)
 157           {
 158           }
 159           // System.out.println(">>>>>>>>>>>>>>>>> "
 160           // + jmolViewer.getBinding().getPdbFile());
 161           String[] expectedModelFiles = new String[] { "http://www.jalview.org/builds/develop/examples/3W5V.pdb" };
 162           String[] actualModelFiles = jmolViewer.getBinding().getStructureFiles();
 163           Assert.assertEqualsNoOrder(actualModelFiles, expectedModelFiles);
 164           jmolViewer.closeViewer(true);
 165           // todo: break here means only once through this loop?
 166           break;
 167         }
 168         break;
 169       }
 170     }
 171   }
 172 }