Merge branch 'Release_2_9_0b1_Branch'

[jalview.git] / src / jalview / analysis / SeqsetUtils.java

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 27ad577..437ea98 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,9 +20,14 @@
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class SeqsetUtils
 {
@@ -55,8 +60,9 @@ public class SeqsetUtils
       }
     }
     sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
-            : new Vector());
+    sqinfo.put("PdbId",
+            (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+                    : new Vector<PDBEntry>());
     sqinfo.put("datasetSequence",
             (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                     : new Sequence("THISISAPLACEHOLDER", ""));
@@ -84,7 +90,7 @@ public class SeqsetUtils
     Integer start = (Integer) sqinfo.get("Start");
     Integer end = (Integer) sqinfo.get("End");
     Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
-    Vector pdbid = (Vector) sqinfo.get("PdbId");
+    Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)