pdb files are global to all alignments with new mapping mechanism.

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b6e6041..eda5eac 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -51,6 +51,10 @@ public class Jalview2XML
   Hashtable annotationIds = new Hashtable();
 
   String uniqueSetSuffix = "";
+  /**
+   * List of pdbfiles added to Jar
+   */
+  Vector pdbfiles = null;
 
   // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
   public void SaveState(File statefile)
@@ -206,7 +210,6 @@ public class Jalview2XML
     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
     JSeq jseq;
-    Vector pdbfiles = null;
 
     //SAVE SEQUENCES
     int id = 0;