merge from develop

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c78ec22..19ad30f 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -260,9 +260,9 @@ public class Sequence extends ASequence implements SequenceI
         }
       }
     }
-    if (seq.getPDBId() != null)
+    if (seq.getAllPDBEntries() != null)
     {
-      Vector ids = seq.getPDBId();
+      Vector ids = seq.getAllPDBEntries();
       Enumeration e = ids.elements();
       while (e.hasMoreElements())
       {
@@ -410,7 +410,7 @@ public class Sequence extends ASequence implements SequenceI
    * @return DOCUMENT ME!
    */
   @Override
-  public Vector<PDBEntry> getPDBId()
+  public Vector<PDBEntry> getAllPDBEntries()
   {
     return pdbIds;
   }
@@ -1057,7 +1057,7 @@ public class Sequence extends ASequence implements SequenceI
       // move database references onto dataset sequence
       datasetSequence.setDBRef(getDBRef());
       setDBRef(null);
-      datasetSequence.setPDBId(getPDBId());
+      datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
       datasetSequence.updatePDBIds();
       if (annotation != null)
@@ -1221,9 +1221,9 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     // transfer PDB entries
-    if (entry.getPDBId() != null)
+    if (entry.getAllPDBEntries() != null)
     {
-      Enumeration e = entry.getPDBId().elements();
+      Enumeration e = entry.getAllPDBEntries().elements();
       while (e.hasMoreElements())
       {
         PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -1302,5 +1302,28 @@ public class Sequence extends ASequence implements SequenceI
     return result;
   }
 
+  public String toString()
+  {
+    return getDisplayId(false);
+  }
+
+  @Override
+  public PDBEntry getPDBEntry(String pdbIdStr)
+  {
+    if (getDatasetSequence() == null
+            || getDatasetSequence().getAllPDBEntries() == null)
+    {
+      return null;
+    }
+    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    for (PDBEntry entry : entries)
+    {
+      if (entry.getId().equalsIgnoreCase(pdbIdStr))
+      {
+        return entry;
+      }
+    }
+    return null;
+  }
 
 }