X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=fcd24dd0fa527f7c1009259c0fbef8aadc8147aa;hb=dbcbbb61457cb60da170cf99defec797941015b9;hp=eb32e5d2750761b1601176766485e764586b9d06;hpb=f931c557266d95b3f4ab5b64bd108123c90e85ab;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index eb32e5d..fcd24dd 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -78,7 +78,6 @@ public class SequenceTest
     // change sequence, should trigger an update of cached result
     sq.setSequence("ASDFASDFADSF");
     assertTrue(sq.isProtein());
-
     /*
      * in situ change of sequence doesn't change hashcode :-O
      * (sequence should not expose internal implementation)
@@ -111,8 +110,7 @@ public class SequenceTest
   {
     AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
             1f);
-    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
-            1f);
+    addAnnotation("label2", "desc2", "calcId2", 1f);
     AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
             1f);
     AlignmentAnnotation[] anns = seq.getAnnotation("label1");
@@ -134,16 +132,15 @@ public class SequenceTest
   @Test(groups = { "Functional" })
   public void testGetAlignmentAnnotations_forCalcIdAndLabel()
   {
-    AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
-            1f);
+    addAnnotation("label1", "desc1", "calcId1", 1f);
     AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
             1f);
-    AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
-            1f);
+    addAnnotation("label2", "desc3", "calcId3", 1f);
     AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
             1f);
-    AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
-    AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
+    addAnnotation("label5", "desc3", null, 1f);
+    addAnnotation(null, "desc3", "calcId3", 1f);
+
     List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
             "label2");
     assertEquals(2, anns.size());
@@ -441,36 +438,54 @@ public class SequenceTest
 
     sq.setDescription("Test sequence description..");
     sq.setVamsasId("TestVamsasId");
-    sq.setSourceDBRef(new DBRefEntry("PDB", "version0", "1TST"));
+    sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
 
-    sq.addDBRef(new DBRefEntry("PDB", "version1", "1Tst"));
-    sq.addDBRef(new DBRefEntry("PDB", "version2", "2Tst"));
-    sq.addDBRef(new DBRefEntry("PDB", "version3", "3Tst"));
-    sq.addDBRef(new DBRefEntry("PDB", "version4", "4Tst"));
+    sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
+    sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
+    sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
+    sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
 
     sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
     sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
     sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
     sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+    
+    DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
+    DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
+    List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
+        pdb2pdb });
 
+    sq.getDatasetSequence().addDBRef(pdb1pdb);
+    sq.getDatasetSequence().addDBRef(pdb2pdb);
     sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version1", "1Tst"));
-    sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version2", "2Tst"));
-    sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version3", "3Tst"));
+            new DBRefEntry("PDB", "version3", "3PDB"));
     sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version4", "4Tst"));
-
-    sq.getDatasetSequence().addPDBId(
-            new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
-    sq.getDatasetSequence().addPDBId(
-            new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+            new DBRefEntry("PDB", "version4", "4PDB"));
+    
+    PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
+    PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
+    PDBEntry pdbe2a=new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2");
+    PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2");
     sq.getDatasetSequence().addPDBId(
-            new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+            pdbe1a);
     sq.getDatasetSequence().addPDBId(
-            new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+            pdbe1b);
+    sq.getDatasetSequence().addPDBId(pdbe2a);
+    sq.getDatasetSequence().addPDBId(pdbe2b);
+
+    /*
+     * test we added pdb entries to the dataset sequence
+     */
+    Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
+            .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
+            "PDB Entries were not found on dataset sequence.");
 
+    /*
+     * we should recover a pdb entry that is on the dataset sequence via PDBEntry
+     */
+    Assert.assertEquals(pdbe1a,
+            sq.getDatasetSequence().getPDBEntry("1PDB"),
+            "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
     ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
     System.out.println(">>>>>> " + sq.getSequenceAsString().length());
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
@@ -482,7 +497,7 @@ public class SequenceTest
             new AlignmentAnnotation("Test annot", "Test annot description",
                     annots));
     Assert.assertEquals(sq.getDescription(), "Test sequence description..");
-    Assert.assertEquals(sq.getDBRefs().length, 4);
+    Assert.assertEquals(sq.getDBRefs().length, 5);
     Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(sq.getAnnotation());
     Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
@@ -495,7 +510,7 @@ public class SequenceTest
 
     Assert.assertEquals(derived.getDescription(),
             "Test sequence description..");
-    Assert.assertEquals(derived.getDBRefs().length, 4);
+    Assert.assertEquals(derived.getDBRefs().length, 4); // come from dataset
     Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(derived.getAnnotation());
     Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
@@ -513,6 +528,17 @@ public class SequenceTest
     assertNotNull(sq.getSequenceFeatures());
     assertArrayEquals(sq.getSequenceFeatures(),
             derived.getSequenceFeatures());
+    
+    /*
+     *  verify we have primary db refs *just* for PDB IDs with associated
+     *  PDBEntry objects
+     */
+
+    assertEquals(primRefs, sq.getPrimaryDBRefs());
+    assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
+
+    assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
+
   }
 
   /**