From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 3 Mar 2016 14:46:00 +0000 (+0000)
Subject: JAL-1919 fixed bug causing PDBfile test failure
X-Git-Tag: Release_2_10_0~293^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f213422632d268e3a2f334255fa705d8e931866f;hp=7d76aa00bf729c0b52e21e6cd5aaae56ebc4909e;p=jalview.git

JAL-1919 fixed bug causing PDBfile test failure
---

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index b927fa5..9415745 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,5 +1,7 @@
 package jalview.api;
 
+import jalview.datamodel.Mapping;
+
 
 public interface DBRefEntryI
 {
@@ -69,4 +71,6 @@ public interface DBRefEntryI
    * @return index of end residue in the source DB
    */
   public int getEndRes();
+
+  public Mapping getMap();
 }
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 0b1fb6d..53642b5 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -37,6 +37,7 @@ public class DBRefEntry implements DBRefEntryI
 
   }
 
+
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -63,13 +64,14 @@ public class DBRefEntry implements DBRefEntryI
     this.map = map;
   }
 
-  public DBRefEntry(DBRefEntry entry)
+  public DBRefEntry(DBRefEntryI entry)
   {
-    this(
-            (entry.source == null ? "" : new String(entry.source)),
-            (entry.version == null ? "" : new String(entry.version)),
-            (entry.accessionId == null ? "" : new String(entry.accessionId)),
-            (entry.map == null ? null : new Mapping(entry.map)));
+    this((entry.getSource() == null ? "" : new String(entry.getSource())),
+            (entry.getVersion() == null ? "" : new String(
+                    entry.getVersion())),
+            (entry.getAccessionId() == null ? "" : new String(
+                    entry.getAccessionId())),
+            (entry.getMap() == null ? null : new Mapping(entry.getMap())));
   }
 
   @Override
@@ -165,6 +167,7 @@ public class DBRefEntry implements DBRefEntryI
   }
 
 
+  @Override
   public Mapping getMap()
   {
     return map;
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d73b283..a2513ba 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -219,7 +219,8 @@ public class Sequence extends ASequence implements SequenceI
     initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
             seq.getEnd());
     description = seq.getDescription();
-    sourceDBRef = seq.getSourceDBRef();
+    sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
+            seq.getSourceDBRef());
     if (seq.getSequenceFeatures() != null)
     {
       SequenceFeature[] sf = seq.getSequenceFeatures();
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index e2b73d1..4ba4c10 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -96,16 +96,11 @@ public abstract class StructureFile extends AlignFile
     sourceDBRef.setStartRes(pdbSequence.getStart());
     sourceDBRef.setEndRes(pdbSequence.getEnd());
 
-    // PDBChain objects maintain reference to dataset
-
-    // SequenceI chainseq = pdbSequence.deriveSequence();
-    // chainseq.setSourceDBRef(sourceDBRef);
-    // chainseq.addPDBId(entry);
-    // chainseq.addDBRef(sourceDBRef);
-    SequenceI chainseq = chain.sequence;
-    chainseq.addPDBId(entry);
+    SequenceI chainseq = pdbSequence.deriveSequence();
     chainseq.setSourceDBRef(sourceDBRef);
+    chainseq.addPDBId(entry);
     chainseq.addDBRef(sourceDBRef);
+
     seqs.addElement(chainseq);
 
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 31c3beb..0fc7d1c 100644
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -83,6 +83,8 @@ public class PDBfileTest
     assertEquals("D", pf.getChains().get(3).id);
 
     PDBChain chainA = pf.getChains().get(0);
+    SequenceI seqA = pf.getSeqs().get(0);
+
     assertEquals(0, chainA.seqstart); // not set
     assertEquals(0, chainA.seqend); // not set
     assertEquals(18, chainA.sequence.getStart());
@@ -91,8 +93,8 @@ public class PDBfileTest
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, chainA.sequence.getAllPDBEntries().size());
-    PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
+    assertEquals(1, seqA.getAllPDBEntries().size());
+    PDBEntry pdb = seqA.getAllPDBEntries().get(0);
     assertEquals("A", pdb.getChainCode());
     assertEquals("PDB", pdb.getType());
     assertEquals("3W5V", pdb.getId());