merge from develop
[jalview.git] / test / jalview / structure / StructureSelectionManagerTest.java
index e3612a5..8e3e086 100644 (file)
@@ -4,6 +4,10 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -11,6 +15,8 @@ import java.util.Set;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import MCview.PDBfile;
+
 public class StructureSelectionManagerTest
 {
   private StructureSelectionManager ssm;
@@ -22,45 +28,31 @@ public class StructureSelectionManagerTest
   }
 
   @Test(groups ={ "Functional" })
-  public void testAddMapping()
+  public void testRegisterMapping()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 
-    /*
-     * One mapping only.
-     */
-    ssm.addMapping(acf1);
+    ssm.registerMapping(acf1);
     assertEquals(1, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
-    assertEquals(1, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
 
-    /*
-     * A second mapping.
-     */
-    ssm.addMapping(acf2);
+    ssm.registerMapping(acf2);
     assertEquals(2, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
-    assertEquals(2, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
 
     /*
-     * A second reference to the first mapping.
+     * Re-adding the first mapping does nothing
      */
-    ssm.addMapping(acf1);
+    ssm.registerMapping(acf1);
     assertEquals(2, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
-    assertEquals(2, ssm.seqMappingRefCounts.size());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
   }
 
   @Test(groups ={ "Functional" })
-  public void testAddMappings()
+  public void testRegisterMappings()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
@@ -74,103 +66,58 @@ public class StructureSelectionManagerTest
     set2.add(acf3);
 
     /*
-     * Adding both sets adds acf2 twice and acf1 and acf3 once each.
+     * Add both sets twice; each mapping should be added once only
      */
-    ssm.addMappings(set1);
-    ssm.addMappings(set2);
+    ssm.registerMappings(set1);
+    ssm.registerMappings(set1);
+    ssm.registerMappings(set2);
+    ssm.registerMappings(set2);
 
     assertEquals(3, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
     assertTrue(ssm.seqmappings.contains(acf3));
-    assertEquals(3, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf2).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
   }
 
-  @Test(groups ={ "Functional" })
-  public void testRemoveMapping()
+  /**
+   * Verify that RESNUM sequence features are present after creating a PDB
+   * mapping
+   */
+  @Test(groups = { "Functional" })
+  public void testSetMapping_seqFeatures()
   {
-    AlignedCodonFrame acf1 = new AlignedCodonFrame();
-    AlignedCodonFrame acf2 = new AlignedCodonFrame();
-    ssm.addMapping(acf1);
-
-    /*
-     * Add one and remove it.
-     */
-    ssm.removeMapping(acf1);
-    ssm.removeMapping(acf2);
-    assertEquals(0, ssm.seqmappings.size());
-    assertEquals(0, ssm.seqMappingRefCounts.size());
+    SequenceI seq = new Sequence(
+            "1GAQ|B",
+            "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
+    StructureSelectionManager sm = new StructureSelectionManager();
+    sm.setProcessSecondaryStructure(true);
+    sm.setAddTempFacAnnot(true);
+    PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
+            new String[] { null }, "examples/1gaq.txt",
+            FormatAdapter.FILE);
+    assertTrue(pmap != null);
+
+    assertEquals(3, pmap.getSeqs().size());
+    assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
+    assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
+    assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
 
     /*
-     * Add one twice and remove it once.
+     * Verify a RESNUM sequence feature in the PDBfile sequence
      */
-    ssm.addMapping(acf1);
-    ssm.addMapping(acf2);
-    ssm.addMapping(acf1);
-    ssm.removeMapping(acf1);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
-    assertEquals(2, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+    SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+    assertEquals("RESNUM", sf.getType());
+    assertEquals("1gaq", sf.getFeatureGroup());
+    assertEquals("GLU:  19  1gaqA", sf.getDescription());
 
     /*
-     * Remove both once more to clear the set.
+     * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
+     * sequence
      */
-    ssm.removeMapping(acf1);
-    ssm.removeMapping(acf2);
-    assertEquals(0, ssm.seqmappings.size());
-    assertEquals(0, ssm.seqMappingRefCounts.size());
-  }
-
-  @Test(groups ={ "Functional" })
-  public void testRemoveMappings()
-  {
-    AlignedCodonFrame acf1 = new AlignedCodonFrame();
-    AlignedCodonFrame acf2 = new AlignedCodonFrame();
-    AlignedCodonFrame acf3 = new AlignedCodonFrame();
-
-    /*
-     * Initial ref counts are 3/2/1:
-     */
-    ssm.addMapping(acf1);
-    ssm.addMapping(acf1);
-    ssm.addMapping(acf1);
-    ssm.addMapping(acf2);
-    ssm.addMapping(acf2);
-    ssm.addMapping(acf3);
-
-    Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
-    set1.add(acf1);
-    set1.add(acf2);
-    Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
-    set2.add(acf2);
-    set2.add(acf3);
-
-    /*
-     * Remove one ref each to acf1, acf2, counts are now 2/1/1:
-     */
-    ssm.removeMappings(set1);
-    assertEquals(3, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
-    assertTrue(ssm.seqmappings.contains(acf3));
-    assertEquals(3, ssm.seqMappingRefCounts.size());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
-
-    /*
-     * Remove one ref each to acf2, acf3 - they are removed
-     */
-    ssm.removeMappings(set2);
-    assertEquals(1, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertEquals(1, ssm.seqMappingRefCounts.size());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+    StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
+    sf = map.sequence.getSequenceFeatures()[0];
+    assertEquals("RESNUM", sf.getType());
+    assertEquals("1gaq", sf.getFeatureGroup());
+    assertEquals("ALA:   1  1gaqB", sf.getDescription());
   }
 }