test/jalview/structure/StructureSelectionManagerTest.java

   1 package jalview.structure;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertNotNull;
   5 import static org.testng.AssertJUnit.assertTrue;
   6
   7 import jalview.datamodel.AlignedCodonFrame;
   8 import jalview.gui.AlignFrame;
   9 import jalview.gui.Desktop;
  10 import jalview.io.FileLoader;
  11 import jalview.io.FormatAdapter;
  12
  13 import java.util.HashSet;
  14 import java.util.LinkedHashSet;
  15 import java.util.Set;
  16
  17 import org.testng.annotations.BeforeClass;
  18 import org.testng.annotations.BeforeMethod;
  19 import org.testng.annotations.Test;
  20
  21 public class StructureSelectionManagerTest
  22 {
  23   private StructureSelectionManager ssm;
  24
  25   @BeforeClass(alwaysRun = true)
  26   public static void setUpBeforeClass() throws Exception
  27   {
  28     jalview.bin.Jalview.main(new String[] { "-props",
  29         "test/jalview/testProps.jvprops" });
  30   }
  31
  32  @BeforeMethod(alwaysRun = true)
  33   public void setUp()
  34   {
  35     ssm = new StructureSelectionManager();
  36   }
  37
  38   @Test(groups ={ "Functional" })
  39   public void testRegisterMapping()
  40   {
  41     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  42     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  43
  44     ssm.registerMapping(acf1);
  45     assertEquals(1, ssm.seqmappings.size());
  46     assertTrue(ssm.seqmappings.contains(acf1));
  47
  48     ssm.registerMapping(acf2);
  49     assertEquals(2, ssm.seqmappings.size());
  50     assertTrue(ssm.seqmappings.contains(acf1));
  51     assertTrue(ssm.seqmappings.contains(acf2));
  52
  53     /*
  54      * Re-adding the first mapping does nothing
  55      */
  56     ssm.registerMapping(acf1);
  57     assertEquals(2, ssm.seqmappings.size());
  58     assertTrue(ssm.seqmappings.contains(acf1));
  59     assertTrue(ssm.seqmappings.contains(acf2));
  60   }
  61
  62   @Test(groups ={ "Functional" })
  63   public void testRegisterMappings()
  64   {
  65     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  66     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  67     AlignedCodonFrame acf3 = new AlignedCodonFrame();
  68
  69     Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
  70     set1.add(acf1);
  71     set1.add(acf2);
  72     Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
  73     set2.add(acf2);
  74     set2.add(acf3);
  75
  76     /*
  77      * Add both sets twice; each mapping should be added once only
  78      */
  79     ssm.registerMappings(set1);
  80     ssm.registerMappings(set1);
  81     ssm.registerMappings(set2);
  82     ssm.registerMappings(set2);
  83
  84     assertEquals(3, ssm.seqmappings.size());
  85     assertTrue(ssm.seqmappings.contains(acf1));
  86     assertTrue(ssm.seqmappings.contains(acf2));
  87     assertTrue(ssm.seqmappings.contains(acf3));
  88   }
  89
  90   /**
  91    * Test that a mapping is not deregistered if an alignment holds a reference
  92    * to it
  93    */
  94   @Test(groups ={ "Functional" })
  95   public void testDeregisterMapping_withAlignmentReference()
  96   {
  97     Desktop d = Desktop.instance;
  98     assertNotNull(d);
  99
 100     /*
 101      * alignment with reference to mappings
 102      */
 103     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
 104             ">Seq1\nCAGT\n", FormatAdapter.PASTE);
 105
 106     AlignedCodonFrame acf1 = new AlignedCodonFrame();
 107     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 108
 109     Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
 110     mappings.add(acf1);
 111     mappings.add(acf2);
 112     af1.getViewport().getAlignment().setCodonFrames(mappings);
 113
 114     /*
 115      * Add one and remove it.
 116      */
 117     ssm.registerMapping(acf1);
 118     ssm.deregisterMapping(acf1);
 119     assertEquals(1, ssm.seqmappings.size());
 120     assertTrue(ssm.seqmappings.contains(acf1));
 121   }
 122
 123   /**
 124    * Test that a mapping is deregistered if no alignment holds a reference to it
 125    */
 126   @Test(groups ={ "Functional" })
 127   public void testDeregisterMapping_withNoReference()
 128   {
 129     Desktop d = Desktop.instance;
 130     assertNotNull(d);
 131
 132     /*
 133      * alignment with reference to mappings
 134      */
 135     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
 136             ">Seq1\nCAGT\n", FormatAdapter.PASTE);
 137
 138     AlignedCodonFrame acf1 = new AlignedCodonFrame();
 139     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 140
 141     Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
 142     mappings.add(acf2);
 143     af1.getViewport().getAlignment().setCodonFrames(mappings);
 144
 145     /*
 146      * Add one and remove it.
 147      */
 148     ssm.registerMapping(acf1);
 149     assertEquals(1, ssm.seqmappings.size());
 150     assertTrue(ssm.seqmappings.contains(acf1));
 151     ssm.deregisterMapping(acf1);
 152     assertEquals(0, ssm.seqmappings.size());
 153   }
 154
 155   /**
 156    * Test that a mapping is not deregistered when a second view is closed but
 157    * the first still holds a reference to the mapping
 158    */
 159   @Test(groups ={ "Functional" })
 160   public void testDeregisterMapping_onCloseView()
 161   {
 162     /*
 163      * alignment with reference to mappings
 164      */
 165     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
 166             ">Seq1\nCAGT\n", FormatAdapter.PASTE);
 167
 168     AlignedCodonFrame acf1 = new AlignedCodonFrame();
 169     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 170
 171     Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
 172     mappings.add(acf1);
 173     mappings.add(acf2);
 174     af1.getViewport().getAlignment().setCodonFrames(mappings);
 175     af1.newView_actionPerformed(null);
 176
 177     /*
 178      * Verify that creating the alignment for the new View has registered the
 179      * mappings
 180      */
 181     ssm = StructureSelectionManager
 182             .getStructureSelectionManager(Desktop.instance);
 183     assertEquals(2, ssm.seqmappings.size());
 184     assertTrue(ssm.seqmappings.contains(acf1));
 185     assertTrue(ssm.seqmappings.contains(acf2));
 186
 187     /*
 188      * Close the second view. Verify that mappings are not removed as the first
 189      * view still holds a reference to them.
 190      */
 191     af1.closeMenuItem_actionPerformed(false);
 192     assertEquals(2, ssm.seqmappings.size());
 193     assertTrue(ssm.seqmappings.contains(acf1));
 194     assertTrue(ssm.seqmappings.contains(acf2));
 195   }
 196 }