diff -N LCIOCallback.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ LCIOCallback.java	9 Oct 2007 22:56:22 -0000	1.1
@@ -0,0 +1,10 @@

+package org.lcsim.util.lcio;
+
+/**
+ * Allows block handlers to register to be called back at end of event.
+ * @author tonyj
+ */
+interface LCIOCallback
+{
+   void callback();   
+}

diff -N SIOReferencesBlockHandler.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ SIOReferencesBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.1
@@ -0,0 +1,46 @@

+package org.lcsim.util.lcio;
+
+import hep.lcd.io.sio.SIOInputStream;
+import hep.lcd.io.sio.SIOOutputStream;
+import hep.lcd.io.sio.SIORef;
+import java.io.IOException;
+import java.util.ListIterator;
+import org.lcsim.event.MCParticle;
+
+/**
+ *
+ * @author tonyj
+ */
+class SIOReferencesBlockHandler extends AbstractBlockHandler
+{
+   private String type;
+   private Class classForType;
+   SIOReferencesBlockHandler(String type, Class classForType)
+   {
+      this.type = type;
+      this.classForType = classForType;
+   }
+   public String getType() { return type; }
+   public Class getClassForType() { return classForType; }
+   
+   LCIOCallback addCollectionElements(LCIOEvent event, final LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException
+   {
+      for (int i = 0; i < n; i++) collection.add(in.readPntr());
+      return new LCIOCallback()
+      {
+         public void callback()
+         {
+            for (ListIterator iter = collection.listIterator(); iter.hasNext(); )
+            {
+               SIORef ref = (SIORef) iter.next();
+               iter.set(ref.getObject());
+            }
+         }
+      };
+   }
+   
+   void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException
+   {
+      out.writePntr(element);
+   }
+}

diff -u -r1.8 -r1.9
--- LCIOWriter.java	12 Jul 2007 18:01:29 -0000	1.8
+++ LCIOWriter.java	9 Oct 2007 22:56:22 -0000	1.9
@@ -15,9 +15,13 @@

 import org.lcsim.event.EventHeader;
 import org.lcsim.event.EventHeader.LCMetaData;
 

-

 /**

- *

+ * A class for writing out LCIO files
+ * The LCIO writer maintains a list of collections to ignore, and also a list of collections
+ * to write out. If the list of collections to write out is not empty then all collections 
+ * are written out except those in the ignore list. If the list of collections to write out
+ * is not empty, then only the specified collections are written out (and the ignore list is
+ * ignored).

  * @author Tony Johnson
  */
 public class LCIOWriter

@@ -28,6 +32,7 @@

    private int lastRunNumber = -1;
    private String lastDetectorName = "";
    private Set<String> ignore = new HashSet<String>();

+   private Set<String> only = new HashSet<String>();

    
    /**
     * Create a writer for writing LCIO files

@@ -73,6 +78,10 @@

    {
       ignore.add(collection);
    }

+   public void addAllIgnore(Collection<String> collections)
+   {
+      ignore.addAll(collections);
+   }

    /**
     * Remove an entry to the list of collections to ignore (not write out)
     * @param collection The collection to remove

@@ -81,6 +90,38 @@

    {
       ignore.remove(collection);
    }

+   /** Clear the list of ignored collections.
+    */
+   public void clearIgnore()
+   {
+      ignore.clear();
+   }
+   /**
+    * Add an entry to the list of collections to write out
+    * @param collection The collection to tadd
+    */
+   public void addWriteOnly(String collection)
+   {
+      only.add(collection);
+   }
+   public void addAllWriteOnly(Collection<String> collections)
+   {
+      only.addAll(collections);
+   }
+   /**
+    * Remove an entry to the list of collections to write out
+    * @param collection The collection to remove
+    */
+   public void removeWriteOnly(String collection)
+   {
+      only.remove(collection);
+   }
+   /** Clear the list of collections to be written out
+    */
+   public void clearWriteOnly()
+   {
+      only.clear();
+   }

    public void close() throws IOException
    {
       writer.close();

@@ -101,20 +142,27 @@

          for (List<Object> collection : collections)
          {
             LCMetaData md = event.getMetaData(collection);

-            Class type = md.getType();
-            LCIOBlockHandler bh = manager.handlerForClass(type);
-            if (bh == null) log.warning("No handler found for block "+md.getName()+" of class "+type.getName());
-            else if(!ignore.contains(md.getName()))

+            if (!only.isEmpty() && !only.contains(md.getName())) continue;
+            else if (ignore.contains(md.getName())) continue;
+            else

             {

-               if (!isValidCollectionName(md.getName())) throw new IOException("Collection name "+md.getName()+" is invalid for LCIO");
-               blocks.put(md.getName(),bh.getType());

+               Class type = md.getType();
+               LCIOBlockHandler bh = manager.handlerForClass(type,md.getFlags());
+               if (bh == null) log.warning("No handler found for block "+md.getName()+" of class "+type.getName());
+               else
+               {
+                  if (!isValidCollectionName(md.getName())) throw new IOException("Collection name "+md.getName()+" is invalid for LCIO");
+                  blocks.put(md.getName(),bh.getType());
+               }

             }
          }
          
          out.writeInt(blocks.size());
          for (Map.Entry<String,String> entry : blocks.entrySet() )
          {

-            if(!ignore.contains(entry.getKey()))

+            if (!only.isEmpty() && !only.contains(entry.getKey())) continue;
+            else if (ignore.contains(entry.getKey())) continue;
+            else

             {
                out.writeString(entry.getKey());
                out.writeString(entry.getValue());

@@ -131,10 +179,11 @@

          for (List<Object> collection : collections)
          {
             LCMetaData md = event.getMetaData(collection);

-            Class type = md.getType();
-            if(!ignore.contains(md.getName()))

+            if (!only.isEmpty() && !only.contains(md.getName())) continue;
+            else if (ignore.contains(md.getName())) continue;
+            else

             {

-               LCIOBlockHandler bh = manager.handlerForClass(type);

+               LCIOBlockHandler bh = manager.handlerForClass(md.getType(),md.getFlags());

                if (bh != null) bh.writeBlock(writer,collection,md);
             }
          }

diff -u -r1.9 -r1.10
--- LCIOConstants.java	18 Sep 2007 03:46:26 -0000	1.9
+++ LCIOConstants.java	9 Oct 2007 22:56:22 -0000	1.10
@@ -71,10 +71,16 @@

    // LCGenericObject
    int GOBIT_FIXED = 31;
    

+   int BITTransient = 16 ;
+   int BITDefault   = 17 ;
+   int BITSubset    = 18 ;
+   

    String runRecordName = "LCRunHeader";
    String runBlockName = "RunHeader";
    String eventRecordName = "LCEvent";
    String eventBlockName = "Event";
    String eventHeaderRecordName = "LCEventHeader";
    String eventHeaderBlockName = "EventHeader";

+   
+   String references = "_References";

 }

diff -u -r1.3 -r1.4
--- SIOCalorimeterHitBlockHandler.java	5 Apr 2006 18:43:39 -0000	1.3
+++ SIOCalorimeterHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.4
@@ -26,12 +26,13 @@

         return CalorimeterHit.class;
     }
 

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version)

+    LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version)

             throws IOException
     {
         LCMetaData meta = event.getMetaData(collection);
         for (int i = 0; i < n; i++)
             collection.add(new SIOCalorimeterHit(in, collection.getFlags(), version, meta));

+        return null;

     }
 
     void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.2 -r1.3
--- SIOGenericObjectBlockHandler.java	18 Sep 2007 19:04:24 -0000	1.2
+++ SIOGenericObjectBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -14,7 +14,7 @@

 {
    public String getType() { return "LCGenericObject"; }
    public Class getClassForType() { return GenericObject.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       int flags = collection.getFlags();
       if (LCIOUtil.bitTest(flags,LCIOConstants.GOBIT_FIXED))

@@ -30,6 +30,7 @@

          for (int i = 0; i < n; i++)
             collection.add(new SIOGenericObject(in, flags, version));
       }

+      return null;

    }
    
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.4 -r1.5
--- LCIOReader.java	23 Oct 2006 19:42:35 -0000	1.4
+++ LCIOReader.java	9 Oct 2007 22:56:22 -0000	1.5
@@ -7,6 +7,8 @@

 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;

+import java.util.ArrayList;
+import java.util.List;

 import java.util.logging.Logger;
 import org.lcsim.event.EventHeader;
 

@@ -54,15 +56,11 @@

          SIOInputStream in = block.getData();
          LCIOEvent event = new LCIOEvent(in);
          

-         //if( (major<<16 | minor ) > (1<<16|1)  )
-         //{
-         //   parameters = new SIOLCParameters(in) ;
-         //}
-         

          record = reader.readRecord();
          name = record.getRecordName();
          if (!LCIOConstants.eventRecordName.equals(name)) throw new IOException("LCIO record order problem");
          

+         List<LCIOCallback> callbacks = new ArrayList<LCIOCallback>();

          for (;;)
          {
             block = record.getBlock();

@@ -72,10 +70,17 @@

             if (type != null)
             {
                LCIOBlockHandler handler = manager.handlerForType(type);

-               if (handler != null) handler.readBlock(event,block);

+               if (handler != null) 
+               {
+                  LCIOCallback callback = handler.readBlock(event,block);
+                  if (callback != null) callbacks.add(callback);
+               }

                else log.warning("No handler found for "+type);
             }
          }

+         // Give block handlers chance to clean up after entire event is read
+         for (LCIOCallback callback : callbacks) callback.callback();
+         

          return event;
       }
    }

diff -u -r1.2 -r1.3
--- SIOTPCHitBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.2
+++ SIOTPCHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -14,10 +14,11 @@

 {
    public String getType() { return "TPCHit"; }
    public Class getClassForType() { return TPCHit.class; }

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOTPCHit(in, collection.getFlags(), version));

+      return null;

    }
    
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.2 -r1.3
--- SIOTrackerHitBlockHandler.java	2 Aug 2005 17:18:07 -0000	1.2
+++ SIOTrackerHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -15,10 +15,11 @@

 {
    public String getType() { return "TrackerHit"; }
    public Class getClassForType() { return TrackerHit.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOTrackerHit(in, collection.getFlags(), version));

+      return null;

    }
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException
    {

diff -u -r1.4 -r1.5
--- SIOSimCalorimeterHitBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.4
+++ SIOSimCalorimeterHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.5
@@ -16,11 +16,12 @@

 {
    public String getType() { return "SimCalorimeterHit"; }
    public Class getClassForType() { return SimCalorimeterHit.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       LCMetaData meta = event.getMetaData(collection);
       for (int i = 0; i < n; i++)
          collection.add(new SIOSimCalorimeterHit(in, collection.getFlags(), version, meta));

+      return null;

    }
       
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.1 -r1.2
--- LCIOUtil.java	16 Feb 2005 07:28:06 -0000	1.1
+++ LCIOUtil.java	9 Oct 2007 22:56:22 -0000	1.2
@@ -21,5 +21,11 @@

       else flag &= ~mask;
       return flag;
    }

-   

+   /**
+    * Create a bitMask for setting the specified bit
+    */
+   public static int bitMask(int bit)
+   {
+      return 1<<bit;
+   }  

 }

diff -u -r1.13 -r1.14
--- HandlerManager.java	18 Sep 2007 03:46:26 -0000	1.13
+++ HandlerManager.java	9 Oct 2007 22:56:22 -0000	1.14
@@ -47,9 +47,16 @@

    }
    LCIOBlockHandler handlerForType(String type)
    {

-      return handlerForType.get(type);

+      if (type.endsWith(LCIOConstants.references))
+      {
+         String subType = type.substring(0,type.length()-LCIOConstants.references.length());
+         LCIOBlockHandler subHandler = handlerForType.get(subType);
+         if (subHandler == null) return null;
+         else return new SIOReferencesBlockHandler(subType,subHandler.getClassForType());
+      }
+      else return handlerForType.get(type);

    }

-   LCIOBlockHandler handlerForClass(Class type)

+   LCIOBlockHandler handlerForClass(Class type, int flags)

    {
       LCIOBlockHandler handler = handlerForClass.get(type);
 

@@ -65,6 +72,10 @@

             }
          }
       }

-      return handler;

+      if (LCIOUtil.bitTest(flags,LCIOConstants.BITSubset))
+      {
+         return new SIOReferencesBlockHandler(handler.getType()+LCIOConstants.references,type);
+      }
+      else return handler;

    }
 }

diff -u -r1.5 -r1.6
--- SIOSimTrackerHitBlockHandler.java	3 Apr 2006 22:40:20 -0000	1.5
+++ SIOSimTrackerHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.6
@@ -23,12 +23,13 @@

         return SimTrackerHit.class;
     }
 

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version)

+    LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version)

             throws IOException
     {
         LCMetaData meta = event.getMetaData(collection);
         for (int i = 0; i < n; i++)
             collection.add(new SIOSimTrackerHit(in, collection.getFlags(), version, meta));

+        return null;

     }
 
     void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.1 -r1.2
--- SIOTrackerPulseBlockHandler.java	4 Jun 2007 06:50:39 -0000	1.1
+++ SIOTrackerPulseBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.2
@@ -14,10 +14,11 @@

 {
    public String getType() { return "TrackerPulse"; }
    public Class getClassForType() { return TrackerPulse.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOTrackerPulse(in, collection.getFlags(), version));

+      return null;

    }
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException
    {

diff -u -r1.1 -r1.2
--- SIOSiliconTrackerHitBlockHandler.java	19 Jun 2006 19:04:10 -0000	1.1
+++ SIOSiliconTrackerHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.2
@@ -4,8 +4,6 @@

 import hep.lcd.io.sio.SIOOutputStream;
 import java.io.IOException;
 import org.lcsim.event.SiliconTrackerHit;

-
-import org.lcsim.event.TPCHit;

 import org.lcsim.recon.tracking.digitization.SiliconRawHit;
 
 /**

@@ -16,10 +14,11 @@

 {
    public String getType() { return "SiliconRawHit"; }
    public Class getClassForType() { return SiliconRawHit.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOSiliconTrackerHit(in, collection.getFlags(), version));

+      return null;

    }
    
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.7 -r1.8
--- AbstractBlockHandler.java	18 Sep 2007 03:46:26 -0000	1.7
+++ AbstractBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.8
@@ -10,12 +10,13 @@

 import org.lcsim.event.EventHeader.LCMetaData;
 
 /**

- *

+ * A default implementation of LCIOBlockHandler.
+ * This implementation assumes that the block corresponds to a LCIOCollection

  * @author tonyj
  */
 abstract class AbstractBlockHandler implements LCIOBlockHandler
 {

-   public void readBlock(LCIOEvent event, SIOBlock block) throws IOException

+   public LCIOCallback readBlock(LCIOEvent event, SIOBlock block) throws IOException

    {
       int major = block.getMajorVersion();
       int minor = block.getMinorVersion();

@@ -31,9 +32,9 @@

       int n = in.readInt();
       LCIOCollection collection = new LCIOCollection(getClassForType(), flags, n, colParameters);
       event.put(block.getBlockName(),collection);

-      addCollectionElements(event,collection,in,n,version);

+      return addCollectionElements(event,collection,in,n,version);

    }

-   abstract void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException;

+   abstract LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException;

    
    public void writeBlock(SIOWriter writer, List collection, LCMetaData md) throws IOException
    {

diff -u -r1.2 -r1.3
--- SIORawCalorimeterHitBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.2
+++ SIORawCalorimeterHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -10,18 +10,19 @@

  * Block handler for raw calorimeter hits.
  *
  * @author Guilherme Lima

- * @version $Id: SIORawCalorimeterHitBlockHandler.java,v 1.2 2005/08/02 17:18:06 tonyj Exp $

+ * @version $Id: SIORawCalorimeterHitBlockHandler.java,v 1.3 2007/10/09 22:56:22 tonyj Exp $

  */
 class SIORawCalorimeterHitBlockHandler extends AbstractBlockHandler
 {
     public String getType() { return "RawCalorimeterHit"; }
     public Class getClassForType() { return RawCalorimeterHit.class; }

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection,

+    LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection,

 				      SIOInputStream in, int n, int version)
 	throws IOException
     {
       for (int i = 0; i < n; i++)
 	collection.add(new SIORawCalorimeterHit(in, collection.getFlags(), version));

+      return null;

     }
       
     void writeCollectionElement(Object element, SIOOutputStream out, int flags)

diff -u -r1.2 -r1.3
--- SIOClusterBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.2
+++ SIOClusterBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -14,10 +14,11 @@

 {
    public String getType() { return "Cluster"; }
    public Class getClassForType() { return Cluster.class; }

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOCluster(in, collection.getFlags(), version));

+      return null;

    }
    
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.5 -r1.6
--- SIOGenericObject.java	18 Sep 2007 19:04:24 -0000	1.5
+++ SIOGenericObject.java	9 Oct 2007 22:56:22 -0000	1.6
@@ -9,14 +9,10 @@

 /**
  *
  * @author gaede

- * @version $Id: SIOGenericObject.java,v 1.5 2007/09/18 19:04:24 lima Exp $

+ * @version $Id: SIOGenericObject.java,v 1.6 2007/10/09 22:56:22 tonyj Exp $

  */
 class SIOGenericObject implements GenericObject
 {

-   private static int[] nullI = new int[0];
-   private static float[] nullF = new float[0];
-   private static double[] nullD = new double[0];
-   

    private boolean _isFixedSize ;
    private int[] _intVec;
    private float[] _floatVec;

@@ -58,9 +54,7 @@

       {
          _doubleVec[i] = in.readDouble();
       }

-
-      // update pointer table
-      in.readPTag(this);

+      in.readPTag(this); 

    }
    
    static void write(GenericObject object, SIOOutputStream out, int flag) throws IOException

diff -u -r1.2 -r1.3
--- SIOReconstructedParticleBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.2
+++ SIOReconstructedParticleBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -13,10 +13,11 @@

 {
    public String getType() { return "ReconstructedParticle"; }
    public Class getClassForType() { return ReconstructedParticle.class; }

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOReconstructedParticle(in, collection.getFlags(), version));

+      return null;

    }
    
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.2 -r1.3
--- SIOLCRelationBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.2
+++ SIOLCRelationBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -10,18 +10,19 @@

  * Block handler for relation objects.
  *
  * @author Guilherme Lima

- * @version $Id: SIOLCRelationBlockHandler.java,v 1.2 2005/08/02 17:18:06 tonyj Exp $

+ * @version $Id: SIOLCRelationBlockHandler.java,v 1.3 2007/10/09 22:56:22 tonyj Exp $

  */
 class SIOLCRelationBlockHandler extends AbstractBlockHandler
 {
     public String getType() { return "LCRelation"; }
     public Class getClassForType() { return LCRelation.class; }

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection,

+    LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection,

 				      SIOInputStream in, int n, int version)
 	throws IOException
     {
       for (int i = 0; i < n; i++)
 	collection.add(new SIOLCRelation(in, collection.getFlags(), version));

+      return null;

     }
       
     void writeCollectionElement(Object element, SIOOutputStream out, int flags)

diff -u -r1.1 -r1.2
--- SIOTrackerDataBlockHandler.java	4 Jun 2007 06:50:39 -0000	1.1
+++ SIOTrackerDataBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.2
@@ -14,10 +14,11 @@

 {
    public String getType() { return "TrackerData"; }
    public Class getClassForType() { return TrackerData.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOTrackerData(in, collection.getFlags(), version));

+      return null;

    }
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException
    {

diff -u -r1.1 -r1.2
--- SIOVertexBlockHandler.java	18 Sep 2007 03:46:26 -0000	1.1
+++ SIOVertexBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.2
@@ -32,13 +32,15 @@

    { 
       return Vertex.class; 
    }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       String[] typeKeys = collection.getParameters().getStringMap().get(ALGORITHM_TYPES);
       String[] parameterNames = collection.getParameters().getStringMap().get(PARAMETER_NAMES);
       
       for (int i = 0; i < n; i++)
          collection.add(new SIOVertex(in, collection.getFlags(), version, typeKeys, parameterNames));

+      
+      return null;

    }
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException
    {

diff -u -r1.1 -r1.2
--- SIORawTrackerHitBlockHandler.java	24 Oct 2006 19:01:49 -0000	1.1
+++ SIORawTrackerHitBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.2
@@ -22,12 +22,13 @@

         return RawTrackerHit.class;
     }
 

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version)

+    LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version)

             throws IOException
     {
         LCMetaData meta = event.getMetaData(collection);
         for (int i = 0; i < n; i++)
             collection.add(new SIORawTrackerHit(in, collection.getFlags(), version, meta));

+        return null;

     }
 
     void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.4 -r1.5
--- SIOMCParticleBlockHandler.java	2 Aug 2005 17:18:06 -0000	1.4
+++ SIOMCParticleBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.5
@@ -13,12 +13,19 @@

 {
    public String getType() { return "MCParticle"; }
    public Class getClassForType() { return MCParticle.class; }

-    void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, final LCIOCollection collection, SIOInputStream in, final int n, final int version) throws IOException

    {
       for (int i = 0; i < n; i++)
          collection.add(new SIOMCParticle(in, collection.getFlags(), version));

-      for (int i = 0; i < n; i++)
-         ((SIOMCParticle) collection.get(i)).resolve(version);

+
+      return new LCIOCallback()
+      {
+         public void callback()
+         {
+             for (int i = 0; i < n; i++)
+               ((SIOMCParticle) collection.get(i)).resolve(version);
+         }
+      };

    }
    
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException

diff -u -r1.2 -r1.3
--- LCIOBlockHandler.java	16 Feb 2005 07:28:06 -0000	1.2
+++ LCIOBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.3
@@ -14,6 +14,10 @@

 {
    public Class getClassForType();
    public String getType();

-   public void readBlock(LCIOEvent event, SIOBlock block) throws IOException;

+   /** Called by the event reader to read a single block.
+    * It can return an LCIOCallback which will then be called after the entire
+    * event is read, or <code>null</code> if no callback is required.
+    */
+   public LCIOCallback readBlock(LCIOEvent event, SIOBlock block) throws IOException;

    public void writeBlock(SIOWriter out, List collection, LCMetaData md) throws IOException;
 }

diff -u -r1.3 -r1.4
--- SIOTrackBlockHandler.java	11 Sep 2007 18:18:04 -0000	1.3
+++ SIOTrackBlockHandler.java	9 Oct 2007 22:56:22 -0000	1.4
@@ -18,11 +18,12 @@

    private static final Hep3Vector origin = new BasicHep3Vector();
    public String getType() { return "Track"; }
    public Class getClassForType() { return Track.class; }

-   void addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

+   LCIOCallback addCollectionElements(LCIOEvent event, LCIOCollection collection, SIOInputStream in, int n, int version) throws IOException

    {
       double bField = event.getDetector().getFieldMap().getField(origin).z();
       for (int i = 0; i < n; i++)
          collection.add(new SIOTrack(in, collection.getFlags(), version, bField));

+      return null;

    }
    void writeCollectionElement(Object element, SIOOutputStream out, int flags) throws IOException
    {

diff -N ReferenceIOTest.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ ReferenceIOTest.java	9 Oct 2007 22:56:23 -0000	1.1
@@ -0,0 +1,82 @@

+package org.lcsim;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import junit.framework.TestCase;
+import org.freehep.record.loop.LoopException;
+import org.lcsim.event.EventHeader;
+import org.lcsim.event.MCParticle;
+import org.lcsim.util.Driver;
+import org.lcsim.util.cache.FileCache;
+import org.lcsim.util.lcio.*;
+import org.lcsim.util.loop.LCIODriver;
+import org.lcsim.util.loop.LCSimLoop;
+import org.lcsim.util.test.TestUtil.TestOutputFile;
+
+/**
+ *
+ * @author tonyj
+ */
+public class ReferenceIOTest extends TestCase
+{
+   public ReferenceIOTest(String testName)
+   {
+      super(testName);
+   }
+   public void testReferences() throws IOException, LoopException
+   {
+      final String detectorName = "sidaug05";
+      URL url = new URL("ftp://ftp-lcd.slac.stanford.edu/lcd/NewData/NLC500/ZZ/stdhep/pythia/pythiaZZ_nunu_bbbar.stdhep");
+      FileCache cache = new FileCache();
+      File stdhep = cache.getCachedFile(url);
+      
+      File outputFile = new TestOutputFile("reference.slcio");
+      
+      LCSimLoop loop = new LCSimLoop();
+      loop.setStdhepRecordSource(stdhep,detectorName);
+      loop.add(new ReferenceDriver());
+      loop.add(new LCIODriver(outputFile));
+      loop.loop(10, null);
+      assertEquals(10,loop.getTotalCountableSupplied());
+      loop.dispose();
+      
+      // Now read it back in
+      
+      LCSimLoop loop2 = new LCSimLoop();
+      loop2.setLCIORecordSource(outputFile);
+      loop2.loop(0,null);
+      loop.add(new TestReferenceDriver());
+   }
+   class ReferenceDriver extends Driver
+   {
+      protected void process(EventHeader event)
+      {
+         List<MCParticle> particles = event.getMCParticles();
+         List<MCParticle> half = new ArrayList<MCParticle>();
+         int i = 0;
+         for (MCParticle particle : particles)
+         {
+            if (i++ % 2 == 0)
+            {
+               half.add(particle);
+            }
+         }
+         event.put("SomeParticles",half,MCParticle.class,LCIOUtil.bitMask(LCIOConstants.BITSubset));
+      }
+   }
+   class TestReferenceDriver extends Driver
+   {
+      protected void process(EventHeader event)
+      {
+         List<MCParticle> particles = event.getMCParticles();
+         List<MCParticle> half = event.get(MCParticle.class,"SomeParticles");
+         for (int i=0; i<half.size(); i++)
+         {
+            assertEquals(half.get(i),particles.get(2*i));
+         }
+      }
+   }
+}