test/jalview/structure/StructureSelectionManagerTest.java

   1 package jalview.structure;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertTrue;
   5
   6 import jalview.datamodel.AlignedCodonFrame;
   7
   8 import java.util.HashSet;
   9 import java.util.Set;
  10
  11 import org.testng.annotations.BeforeMethod;
  12 import org.testng.annotations.Test;
  13
  14 public class StructureSelectionManagerTest
  15 {
  16   private StructureSelectionManager ssm;
  17
  18  @BeforeMethod(alwaysRun = true)
  19   public void setUp()
  20   {
  21     ssm = new StructureSelectionManager();
  22   }
  23
  24   @Test(groups ={ "Functional" })
  25   public void testAddMapping()
  26   {
  27     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  28     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  29
  30     /*
  31      * One mapping only.
  32      */
  33     ssm.addMapping(acf1);
  34     assertEquals(1, ssm.seqmappings.size());
  35     assertTrue(ssm.seqmappings.contains(acf1));
  36     assertEquals(1, ssm.getMappingReferenceCount(acf1));
  37
  38     /*
  39      * A second mapping.
  40      */
  41     ssm.addMapping(acf2);
  42     assertEquals(2, ssm.seqmappings.size());
  43     assertTrue(ssm.seqmappings.contains(acf1));
  44     assertTrue(ssm.seqmappings.contains(acf2));
  45     assertEquals(1, ssm.getMappingReferenceCount(acf1));
  46     assertEquals(1, ssm.getMappingReferenceCount(acf2));
  47
  48     /*
  49      * A second reference to the first mapping.
  50      */
  51     ssm.addMapping(acf1);
  52     assertEquals(2, ssm.seqmappings.size());
  53     assertTrue(ssm.seqmappings.contains(acf1));
  54     assertTrue(ssm.seqmappings.contains(acf2));
  55     assertEquals(2, ssm.getMappingReferenceCount(acf1));
  56     assertEquals(1, ssm.getMappingReferenceCount(acf2));
  57   }
  58
  59   @Test(groups ={ "Functional" })
  60   public void testAddMappings()
  61   {
  62     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  63     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  64     AlignedCodonFrame acf3 = new AlignedCodonFrame();
  65
  66     Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
  67     set1.add(acf1);
  68     set1.add(acf2);
  69     Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
  70     set2.add(acf2);
  71     set2.add(acf3);
  72
  73     /*
  74      * Adding both sets adds acf2 twice and acf1 and acf3 once each.
  75      */
  76     ssm.addMappings(set1);
  77     ssm.addMappings(set2);
  78
  79     assertEquals(3, ssm.seqmappings.size());
  80     assertTrue(ssm.seqmappings.contains(acf1));
  81     assertTrue(ssm.seqmappings.contains(acf2));
  82     assertTrue(ssm.seqmappings.contains(acf3));
  83     assertEquals(1, ssm.getMappingReferenceCount(acf1));
  84     assertEquals(2, ssm.getMappingReferenceCount(acf2));
  85     assertEquals(1, ssm.getMappingReferenceCount(acf3));
  86   }
  87
  88   @Test(groups ={ "Functional" })
  89   public void testRemoveMapping()
  90   {
  91     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  92     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  93
  94     /*
  95      * Add one and remove it.
  96      */
  97     ssm.addMapping(acf1);
  98     ssm.removeMapping(acf1);
  99     ssm.removeMapping(acf2);
 100     assertEquals(0, ssm.seqmappings.size());
 101     assertEquals(0, ssm.getMappingReferenceCount(acf1));
 102     assertEquals(0, ssm.getMappingReferenceCount(acf2));
 103
 104     /*
 105      * Add one twice and remove it once.
 106      */
 107     ssm.addMapping(acf1);
 108     ssm.addMapping(acf2);
 109     ssm.addMapping(acf1);
 110     ssm.removeMapping(acf1);
 111     assertEquals(2, ssm.seqmappings.size());
 112     assertTrue(ssm.seqmappings.contains(acf1));
 113     assertTrue(ssm.seqmappings.contains(acf2));
 114     assertEquals(1, ssm.getMappingReferenceCount(acf1));
 115     assertEquals(1, ssm.getMappingReferenceCount(acf2));
 116
 117     /*
 118      * Remove both once more to clear the set.
 119      */
 120     ssm.removeMapping(acf1);
 121     ssm.removeMapping(acf2);
 122     assertEquals(0, ssm.seqmappings.size());
 123     assertEquals(0, ssm.getMappingReferenceCount(acf1));
 124     assertEquals(0, ssm.getMappingReferenceCount(acf2));
 125   }
 126
 127   @Test(groups ={ "Functional" })
 128   public void testRemoveMappings()
 129   {
 130     AlignedCodonFrame acf1 = new AlignedCodonFrame();
 131     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 132     AlignedCodonFrame acf3 = new AlignedCodonFrame();
 133
 134     /*
 135      * Initial ref counts are 3/2/1:
 136      */
 137     ssm.addMapping(acf1);
 138     ssm.addMapping(acf1);
 139     ssm.addMapping(acf1);
 140     ssm.addMapping(acf2);
 141     ssm.addMapping(acf2);
 142     ssm.addMapping(acf3);
 143
 144     Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
 145     set1.add(acf1);
 146     set1.add(acf2);
 147     Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
 148     set2.add(acf2);
 149     set2.add(acf3);
 150
 151     /*
 152      * Remove one ref each to acf1, acf2, counts are now 2/1/1:
 153      */
 154     ssm.removeMappings(set1);
 155     assertEquals(3, ssm.seqmappings.size());
 156     assertTrue(ssm.seqmappings.contains(acf1));
 157     assertTrue(ssm.seqmappings.contains(acf2));
 158     assertTrue(ssm.seqmappings.contains(acf3));
 159     assertEquals(2, ssm.getMappingReferenceCount(acf1));
 160     assertEquals(1, ssm.getMappingReferenceCount(acf2));
 161     assertEquals(1, ssm.getMappingReferenceCount(acf3));
 162
 163     /*
 164      * Remove one ref each to acf2, acf3 - they are removed
 165      */
 166     ssm.removeMappings(set2);
 167     assertEquals(1, ssm.seqmappings.size());
 168     assertTrue(ssm.seqmappings.contains(acf1));
 169     assertEquals(2, ssm.getMappingReferenceCount(acf1));
 170   }
 171 }