From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 28 Sep 2016 14:57:58 +0000 (+0100)
Subject: JAL-2210 JAL-2235 fix deriveSequence test for tightened up setDBRefs and addDBRef... 
X-Git-Tag: Release_2_10_0~20^2~25
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9bddf64f7592879716221d69710588aac803c50d;p=jalview.git

JAL-2210 JAL-2235 fix deriveSequence test for tightened up setDBRefs and addDBRef behaviour (always add to dataset sequence if present)
---

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index cfcb9ec..0c401e2 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -460,19 +460,20 @@ public class SequenceTest
     sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
     sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
     
+    // these are the same as ones already added
     DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
-    DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
+    DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
 
     
     List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
         pdb2pdb });
 
-    sq.getDatasetSequence().addDBRef(pdb1pdb);
-    sq.getDatasetSequence().addDBRef(pdb2pdb);
+    sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
+    sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
     sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version3", "3PDB"));
+            new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
     sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version4", "4PDB"));
+            new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
     
     PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
     PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
@@ -509,11 +510,14 @@ public class SequenceTest
             new AlignmentAnnotation("Test annot", "Test annot description",
                     annots));
     Assert.assertEquals(sq.getDescription(), "Test sequence description..");
-    Assert.assertEquals(sq.getDBRefs().length, 5);
+    Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
+                                                   // sequence
     Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(sq.getAnnotation());
     Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
-    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 4);
+    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
+                                                                        // as
+                                                                        // sq.getDBRefs()
     Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
             4);
     Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
@@ -522,11 +526,11 @@ public class SequenceTest
 
     Assert.assertEquals(derived.getDescription(),
             "Test sequence description..");
-    Assert.assertEquals(derived.getDBRefs().length, 4); // come from dataset
+    Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
     Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(derived.getAnnotation());
     Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
-    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 4);
+    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
     Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
             .size(), 4);
     Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());