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 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.io.FormatAdapter;
  11
  12 import java.util.HashSet;
  13 import java.util.Set;
  14
  15 import org.testng.annotations.BeforeMethod;
  16 import org.testng.annotations.Test;
  17
  18 import MCview.PDBfile;
  19
  20 public class StructureSelectionManagerTest
  21 {
  22   private StructureSelectionManager ssm;
  23
  24  @BeforeMethod(alwaysRun = true)
  25   public void setUp()
  26   {
  27     ssm = new StructureSelectionManager();
  28   }
  29
  30   @Test(groups ={ "Functional" })
  31   public void testRegisterMapping()
  32   {
  33     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  34     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  35
  36     ssm.registerMapping(acf1);
  37     assertEquals(1, ssm.seqmappings.size());
  38     assertTrue(ssm.seqmappings.contains(acf1));
  39
  40     ssm.registerMapping(acf2);
  41     assertEquals(2, ssm.seqmappings.size());
  42     assertTrue(ssm.seqmappings.contains(acf1));
  43     assertTrue(ssm.seqmappings.contains(acf2));
  44
  45     /*
  46      * Re-adding the first mapping does nothing
  47      */
  48     ssm.registerMapping(acf1);
  49     assertEquals(2, ssm.seqmappings.size());
  50     assertTrue(ssm.seqmappings.contains(acf1));
  51     assertTrue(ssm.seqmappings.contains(acf2));
  52   }
  53
  54   @Test(groups ={ "Functional" })
  55   public void testRegisterMappings()
  56   {
  57     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  58     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  59     AlignedCodonFrame acf3 = new AlignedCodonFrame();
  60
  61     Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
  62     set1.add(acf1);
  63     set1.add(acf2);
  64     Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
  65     set2.add(acf2);
  66     set2.add(acf3);
  67
  68     /*
  69      * Add both sets twice; each mapping should be added once only
  70      */
  71     ssm.registerMappings(set1);
  72     ssm.registerMappings(set1);
  73     ssm.registerMappings(set2);
  74     ssm.registerMappings(set2);
  75
  76     assertEquals(3, ssm.seqmappings.size());
  77     assertTrue(ssm.seqmappings.contains(acf1));
  78     assertTrue(ssm.seqmappings.contains(acf2));
  79     assertTrue(ssm.seqmappings.contains(acf3));
  80   }
  81
  82   /**
  83    * Verify that RESNUM sequence features are present after creating a PDB
  84    * mapping
  85    */
  86   @Test(groups = { "Functional" })
  87   public void testSetMapping_seqFeatures()
  88   {
  89     SequenceI seq = new Sequence(
  90             "1GAQ|B",
  91             "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
  92     StructureSelectionManager sm = new StructureSelectionManager();
  93     sm.setProcessSecondaryStructure(true);
  94     sm.setAddTempFacAnnot(true);
  95     PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
  96             new String[] { null }, "examples/1gaq.txt",
  97             FormatAdapter.FILE);
  98     assertTrue(pmap != null);
  99
 100     assertEquals(3, pmap.getSeqs().size());
 101     assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
 102     assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
 103     assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
 104
 105     /*
 106      * Verify a RESNUM sequence feature in the PDBfile sequence
 107      */
 108     SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
 109     assertEquals("RESNUM", sf.getType());
 110     assertEquals("1gaq", sf.getFeatureGroup());
 111     assertEquals("GLU:  19  1gaqA", sf.getDescription());
 112
 113     /*
 114      * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
 115      * sequence
 116      */
 117     StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
 118     sf = map.sequence.getSequenceFeatures()[0];
 119     assertEquals("RESNUM", sf.getType());
 120     assertEquals("1gaq", sf.getFeatureGroup());
 121     assertEquals("ALA:   1  1gaqB", sf.getDescription());
 122   }
 123 }