diff -u -r1.9 -r1.10
--- CommandLineProcessor.java	16 Oct 2006 19:04:42 -0000	1.9
+++ CommandLineProcessor.java	28 Nov 2006 00:53:17 -0000	1.10
@@ -28,7 +28,7 @@

  * Main.
  * 
  * @author Jeremy McCormick

- * @version $Id: CommandLineProcessor.java,v 1.9 2006/10/16 19:04:42 jeremy Exp $

+ * @version $Id: CommandLineProcessor.java,v 1.10 2006/11/28 00:53:17 jeremy Exp $

  */
 public class CommandLineProcessor
 {

@@ -37,7 +37,6 @@

     private Properties _properties = new Properties();
     private UserOptions _userOptions = null;
     private List<File> _infiles = new ArrayList<File>();

-    //private File _outfile = null;

     int _verbosity = 0;
 
     /** Create a CommandLineProcessor where parse will be called later. */

@@ -257,17 +256,14 @@

                 {
                     System.out.println("pattern=" + s);
                 }

-            }
-           
-            System.out.println("user options ...");
-            System.out.println(_userOptions.toString());

+            }           

         }
 
         // There should be some files to process at this point, or the command
         // line arguments did not find any input files.
         if (_infiles.size() == 0)
         {

-            System.err.println("ERROR: No input files were found from command line arguments.");

+            System.err.println("ERROR: No input files were found from arguments.");

             printUsage(true);
         }
 

@@ -294,19 +290,21 @@

         }
         
         // If neither of above 2 are selected for output filename,

-        // the user's outputFile option is kept or the default,
-        // e.g. hard-coded, filename is used.

+        // the user's outputFile option from properties is kept 
+        // or the default, e.g. hard-coded, filename is used.

+        // Print input files and user options after processing.

         if (_verbosity > 0)
         {

-            System.out.println("outputFile=" + _userOptions.getStringOption("outputFile"));
-            

+            System.out.println("--User Options--");
+            System.out.println(_userOptions.toString());
+                        

             int nfiles=0;
             for (File file : _infiles)
             {
                 System.out.println("inputFile["+ nfiles + "]=" + file.getAbsoluteFile());
                 ++nfiles;

-            }                      

+            }                                  

         }
     }
 

diff -u -r1.2 -r1.3
--- MCParticleFlag.java	10 Nov 2006 22:29:15 -0000	1.2
+++ MCParticleFlag.java	28 Nov 2006 00:53:18 -0000	1.3
@@ -4,7 +4,7 @@

  * Combined set of flags for MCParticle statuses, including error conditions.
  * 
  * @author jeremym

- * @version $Id: MCParticleFlag.java,v 1.2 2006/11/10 22:29:15 jeremy Exp $

+ * @version $Id: MCParticleFlag.java,v 1.3 2006/11/28 00:53:18 jeremy Exp $

  */
 enum MCParticleFlag
 {

@@ -34,7 +34,11 @@

     BAD_STAT_DECAYED_CALORIMETER_AND_STOPPED("Bad: Decayed in Calorimeter and Stopped", 23),
     BAD_STAT_LEFT_AND_STOPPED("Bad: Left and Stopped", 24),
     BAD_STAT_SIM_NO_SIM_STATUS("Bad: Sim Particle with no Simulator Status", 25), 

-    BAD_STAT_CHARGE_NAN("Bad: Charge is NaN", 26);

+    BAD_STAT_CHARGE_NAN("Bad: Charge is NaN", 26),
+    ENDPOINT_AT_ORIGIN("Endpoint at (0,0,0)", 27),
+    NO_TRAVEL("Endpoint and Origin are equal", 28),
+    NO_TIME("Time is 0.0", 29),
+    ORIGIN_OUTSIDE_TRACKING_REGION("Bad: Origin Outside Of Tracking Region", 30);

 
     String _descr;
     int _flag;

diff -u -r1.4 -r1.5
--- MCParticleFlags.java	10 Nov 2006 22:59:30 -0000	1.4
+++ MCParticleFlags.java	28 Nov 2006 00:53:18 -0000	1.5
@@ -2,24 +2,34 @@

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

+import java.util.Map;

 
 import org.lcsim.event.MCParticle;
 import org.lcsim.event.util.MCParticleClassifier;
 import org.lcsim.event.util.MCParticleClassifier.MCPClass;

+import org.lcsim.conditions.DetectorLocator;
+import org.lcsim.geometry.Detector;
+import org.lcsim.geometry.compact.Constant;
+import hep.physics.vec.Hep3Vector;

 
 /**
  * A set of MCParticleFlag objects representing the non-exclusive status(es) of
  * an individual MCParticle.
  * 
  * @author jeremym

- * @version $Id: MCParticleFlags.java,v 1.4 2006/11/10 22:59:30 jeremy Exp $

+ * @version $Id: MCParticleFlags.java,v 1.5 2006/11/28 00:53:18 jeremy Exp $

  */
 public class MCParticleFlags
 {

-    List<MCParticleFlag> _flags = new ArrayList<MCParticleFlag>();

+    private List<MCParticleFlag> _flags = new ArrayList<MCParticleFlag>();

 
     private static List<MCParticleFlag> _allFlags;
 

+    public static List<MCParticleFlag> getAllFlags()
+    {
+        return allFlags();
+    }
+    

     public MCParticleFlags(MCParticle particle)
     {
         setMCParticleFlags(particle);

@@ -209,7 +219,13 @@

         {
             add(MCParticleFlag.BAD_STAT_CHARGE_NAN);
         }        

-    }

+        
+        // Check if origin is outside tracking radius.
+        if(MCParticleUtil.isOriginOutsideTrackingRadius(particle)) 
+        {
+            add(MCParticleFlag.ORIGIN_OUTSIDE_TRACKING_REGION);
+        }       
+    }   

 
     /** Check if a particle has an end disposition */
     public boolean hasEndStatus(MCParticle.SimulatorStatus sstat)

diff -u -r1.4 -r1.5
--- MCParticleTypeInfo.java	16 Mar 2006 02:35:22 -0000	1.4
+++ MCParticleTypeInfo.java	28 Nov 2006 00:53:20 -0000	1.5
@@ -9,7 +9,7 @@

  * Information about an MCParticle type, i.e. ones with different PDGIDs.
  * 
  * @author jeremym

- * @version $Id: MCParticleTypeInfo.java,v 1.4 2006/03/16 02:35:22 jeremy Exp $

+ * @version $Id: MCParticleTypeInfo.java,v 1.5 2006/11/28 00:53:20 jeremy Exp $

  */
 class MCParticleTypeInfo
 {

@@ -32,11 +32,19 @@

         
         try {
             _name = mcpLkp.get(pdgid).getName();

+
+            // Replace slashes because they screw
+            // up AIDA directory naming.
+            if (_name.contains("/"))
+            {
+                _name = _name.replaceAll("/","");
+            }
+            

             _charge = mcpLkp.get(pdgid).getCharge();
         }
         catch (Exception e)
         {

-            // Probably an ion, which we flag as Unknown            

+            // Probably an ion, which is flagged as unknown.            

         }
     }
     

diff -u -r1.3 -r1.4
--- MCParticleUtil.java	1 Apr 2006 00:00:02 -0000	1.3
+++ MCParticleUtil.java	28 Nov 2006 00:53:20 -0000	1.4
@@ -6,17 +6,21 @@

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

+import java.util.Map;

+import org.lcsim.conditions.DetectorLocator;

 import org.lcsim.event.EventHeader;
 import org.lcsim.event.MCParticle;
 import org.lcsim.event.SimCalorimeterHit;
 import org.lcsim.event.SimTrackerHit;

+import org.lcsim.geometry.Detector;
+import org.lcsim.geometry.compact.Constant;

 
 /**
  * MCParticle utilities. 
  * 
  * @author jeremym

- * @version $Id: MCParticleUtil.java,v 1.3 2006/04/01 00:00:02 jeremy Exp $

+ * @version $Id: MCParticleUtil.java,v 1.4 2006/11/28 00:53:20 jeremy Exp $

  */
 public final class MCParticleUtil
 {

@@ -93,4 +97,25 @@

         }
         return hits;
     }    

-}

+    
+    public static boolean isOriginOutsideTrackingRadius(MCParticle particle)
+    {                       
+        Detector det = DetectorLocator.getCurrentDetector();
+        Map<String,Constant> constants = det.getConstants();
+    
+        double tracking_radius = constants.get("tracking_region_radius").getValue();
+        double tracking_zmax = constants.get("tracking_region_zmax").getValue();
+    
+        Hep3Vector vtx = particle.getOrigin();
+        double vr = Math.sqrt(vtx.x()*vtx.x()+vtx.y()*vtx.y());
+        double vz = Math.abs(vtx.z());
+    
+        boolean outside=false;
+        if (vr > tracking_radius || vz > tracking_zmax)
+        {
+            outside=true;            
+        }
+        
+        return outside;
+    }    
+}

\ No newline at end of file

diff -u -r1.3 -r1.4
--- UserOptions.java	16 Oct 2006 19:04:44 -0000	1.3
+++ UserOptions.java	28 Nov 2006 00:53:20 -0000	1.4
@@ -10,7 +10,7 @@

  * Represents simple options set from properties file or command-line.
  * 
  * @author Jeremy McCormick

- * @version $Id: UserOptions.java,v 1.3 2006/10/16 19:04:44 jeremy Exp $

+ * @version $Id: UserOptions.java,v 1.4 2006/11/28 00:53:20 jeremy Exp $

  */
 public final class UserOptions
 {    

@@ -97,6 +97,9 @@

         setBooleanOption("genericHitPlots", true);
         setBooleanOption("eventPlots", true);
         

+        setBooleanOption("createGenParticles", true);
+        setBooleanOption("createSimParticles", true);
+        

         setBooleanOption("enableAutoname", true);
         
         // int options

@@ -118,7 +121,10 @@

         parseBooleanOption("calorimeterHitPlots");
         parseBooleanOption("genericHitPlots");
         parseBooleanOption("eventPlots");

-     

+        
+        parseBooleanOption("createGenParticles");
+        parseBooleanOption("createSimParticles");
+         

         parseBooleanOption("enableAutoname");
         
         // int options