JAL-2106 rejig test to minimally verify patch that getPDBEntry can be called on local...

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index eb32e5d..1fed98b 100644 (file)
--- 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)
@@ -441,36 +440,54 @@ 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));