Commit in GeomConverter/src/org/lcsim on MAIN
detector/DetectorElement.java+2-31.19 -> 1.20
        /GeometryInfo.java+2-81.11 -> 1.12
        /IDetectorElement.java+24-351.15 -> 1.16
        /IDetectorElementContainer.java+5-71.4 -> 1.5
        /IGeometryInfo.java+56-611.11 -> 1.12
        /IPhysicalVolume.java+10-91.6 -> 1.7
        /IPhysicalVolumeNavigator.java+27-241.8 -> 1.9
        /IRotation3D.java+12-121.6 -> 1.7
detector/identifier/ExpandedIdentifier.java+2-21.2 -> 1.3
                   /IExpandedIdentifier.java+7-71.3 -> 1.4
                   /IIdentifierHelper.java+2-21.1 -> 1.2
                   /IdentifierHelper.java+5-51.2 -> 1.3
detector/material/BetheBlochCalculator.java+10-71.2 -> 1.3
geometry/Layered.java+2-21.5 -> 1.6
geometry/subdetector/SiTrackerBarrel.java+3-41.10 -> 1.11
material/Material.java+1-11.21 -> 1.22
        /MaterialCalculator.java+1-11.17 -> 1.18
+171-190
17 modified files
JM: Javadoc fixup.  More to follow.

GeomConverter/src/org/lcsim/detector
DetectorElement.java 1.19 -> 1.20
diff -u -r1.19 -r1.20
--- DetectorElement.java	3 May 2007 21:48:25 -0000	1.19
+++ DetectorElement.java	4 May 2007 10:23:37 -0000	1.20
@@ -361,11 +361,10 @@
     }
     
     /**
-     * Set the {@see IIdentifierHelper} for encoding and decoding
+     * Set the {@link IIdentifierHelper} for encoding and decoding
      * identifiers of this DetectorElement.
      * 
-     * @param helper The {@see IIdentifierHelper} that has a reference 
-     *               to this DetectorElement's {@see IIdentifierDictionary}.
+     * @param helper The IdentifierHelper to be assigned.
      */    
     public void setIdentifierHelper( IIdentifierHelper helper )
     {

GeomConverter/src/org/lcsim/detector
GeometryInfo.java 1.11 -> 1.12
diff -u -r1.11 -r1.12
--- GeometryInfo.java	9 Apr 2007 21:05:27 -0000	1.11
+++ GeometryInfo.java	4 May 2007 10:23:37 -0000	1.12
@@ -228,7 +228,7 @@
 
     /** 
      * 
-     * Check if the point @param globalPoint is inside this volume
+     * Check if the global point is inside this volume
      * by transforming the point from global to local coordinates
      * and seeing if the resulting point is inside this DetectorElement's
      * solid. 
@@ -237,7 +237,6 @@
      * have a corresponding node in the geometry tree, i.e. if it 
      * is a "ghost" that is just a container for other DetectorElements.
      * 
-     * @see org.lcsim.detector.IGeometryInfoTest#isInside(hep.physics.vec.Hep3Vector)
      */
     public boolean isInside(Hep3Vector globalPoint) 
     {
@@ -286,11 +285,6 @@
         return parentToLocal.transformed(parentPoint);		
     }
 
-    public void setPath(IPhysicalVolumePath support) 
-    {
-        setupSupport(support);		
-    }
-
     public boolean isGhost()
     {
         return support == null && logicalVolume == null;
@@ -315,4 +309,4 @@
     {
         return support != null;
     }   
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector
IDetectorElement.java 1.15 -> 1.16
diff -u -r1.15 -r1.16
--- IDetectorElement.java	3 May 2007 21:48:25 -0000	1.15
+++ IDetectorElement.java	4 May 2007 10:23:37 -0000	1.16
@@ -15,19 +15,18 @@
  * for other DetectorElements and need not have a physical
  * representation in the geometry tree.
  * 
- * @see DetectorElement
  * @see IDetectorElementStore
  * @see IDetectorElementContainer
- * @see GeometryInfo
+ * @see IGeometryInfo
  * @see IIdentifiable
  * @see IIdentifier
  * @see INamed
+ * @see IParameters
  * @see IReadout
- * @see Readout
  * 
- * @author Tim Nelson
- * @author Jeremy McCormick
- * @version $Id: IDetectorElement.java,v 1.15 2007/05/03 21:48:25 jeremy Exp $
+ * @author jeremym
+ * @author tknelson
+ * @version $Id: IDetectorElement.java,v 1.16 2007/05/04 10:23:37 jeremy Exp $
  */
 public interface IDetectorElement 
 extends IIdentifiable, INamed
@@ -104,11 +103,9 @@
     /**
      * Locate the deepest DetectorElement containing a global point
      * starting with this DetectorElement and traversing into its children.  
-     * This DetectorElement may be returned if it has geometry that 
-     * contains the point but none of its descendants contain the point.
-     * 
+     *
      * This method can be used from {@link org.lcsim.geometry.Detector}
-     * to find the deepest DetectorElement within the complete detector.
+     * to find the deepest node within the complete detector.
      *   
      * This method is not on {@link GeometryInfo}, because a DetectorElement is
      * allowed to have a <code>null</code> GeometryInfo if it is a simple 
@@ -135,7 +132,7 @@
 
     /**
      * True if this DetectorElement has an {@link IReadout}; 
-     * False if the {@link IReadout} is <code>null</code>
+     * False if the {@link IReadout} is <code>null</code>.
      * 
      * @return True if this DetectorElement has a Readout;
      *         False if there is no Readout.
@@ -143,11 +140,11 @@
     public boolean hasReadout();
     
     /**
-     * The named parameters associated with this {@link DetectorElement}.
+     * The named parameters associated to this instance.
      * 
      * @see org.lcsim.detector.IParameters
      * 
-     * @return An {@link IParameters} object containing the {@link DetectorElement}'s named parameters.
+     * @return An IParameters object containing the DetectorElement's named parameter set.
      */
     public IParameters getParameters();
     
@@ -159,7 +156,7 @@
      * 
      * @see IDetectorElementContainer
      * 
-     * @return A list of ancestors from the top {@link DetectorElement}.
+     * @return A list of ancestors from the top to this node.
      */
     public IDetectorElementContainer getAncestry();
     
@@ -173,31 +170,25 @@
     public void clearReadouts();
     
     /**
-     * True if this DetectorElement is a descendant 
-     * of this one.  False if the {@param de} is not 
-     * contained by this {@link DetectorElement} or if
-     * {@param de} is equal to this DetectorElement.
+     * True if the DetectorElement is a descendant 
+     * of this one.  
      * 
-     * @param de A DetectorElement to search for.
+     * @param de A DetectorElement to search for in descendants.
      * @see IDetectorElement
-     * @see DetectorElement
      * @see IDetectorElementContainer
-     * @return True if {@param de} is a descendant
-     *         of this DetectorElement.
+     * @return True if DetectorElement is a descendant of this one.
      */
     public boolean isDescendant(IDetectorElement de);
           
     /**
-     * Pre-order tree traversal of this and children.
-     * 
-     * @param visitor
+     * Recursive pre-order tree traversal of this {@link IDetectorElement}.
+     * @param visitor A visitor interface to perform some action on the node.
      */
     public void traverseDescendantsPreOrder(IDetectorElementVisitor visitor);
  
     /**
-     * Post-order tree traversal of this and children.
-     * 
-     * @param visitor
+     * Recrusive post-order tree traversal of this {@link IDetectorElement}.
+     * @param visitor A visitor interface to perform some action on the node.
      */
     public void traverseDescendantsPostOrder(IDetectorElementVisitor visitor);    
     
@@ -209,19 +200,17 @@
     public void traverseAncestors(IDetectorElementVisitor visitor);
     
     /**
-     * Find ancestors with class matching {@param klass}.
+     * Find ancestors matching a class.
      * 
      * @param klass Class to match.
      */
     public <T extends IDetectorElement> List<T> getAncestors(Class<T> klass);
     
     /**
-     * Find descendants with class matching {@param klass}.
-     * 
-     * @param <T>
-     * @param klass
-     * @return
+     * Find descendants matching a class.
+     *
+     * @param klass The class of the descendant DetectorElement.
+     * @return Get a list of descendants with matching class.
      */
     public <T extends IDetectorElement> List<T> getDescendants(Class<T> klass);
-    
 }

GeomConverter/src/org/lcsim/detector
IDetectorElementContainer.java 1.4 -> 1.5
diff -u -r1.4 -r1.5
--- IDetectorElementContainer.java	2 May 2007 01:58:18 -0000	1.4
+++ IDetectorElementContainer.java	4 May 2007 10:23:37 -0000	1.5
@@ -15,7 +15,7 @@
  * @see java.util.ArrayList
  * 
  * @author Jeremy McCormick
- * @version $Id: IDetectorElementContainer.java,v 1.4 2007/05/02 01:58:18 jeremy Exp $
+ * @version $Id: IDetectorElementContainer.java,v 1.5 2007/05/04 10:23:37 jeremy Exp $
  */
 public interface IDetectorElementContainer 
 extends List<IDetectorElement>
@@ -24,19 +24,17 @@
      * Get a DetectorElement by name.
      * 
      * @param  name The name of the DetectorElement.
-     * @return      The matching DetectorElement or
-     *              <code>null</code> if none exists
-     *              with matching {@param name}.
+     * @return      The DetectorElement matching name or
+     *              <code>null</code> if none exists.
      */
     public IDetectorElement get(String name);
     
     /**
-     * True if contains a DetectorElement with name {@param name};
-     * False if does not contain.
+     * True if contains a DetectorElement with matching name. 
      * 
      * @param   name The name of the DetectorElement.
      * @return       True if contains a DetectorElement with
      *               matching name; False if it does not.
      */
     public boolean contains(String name);
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector
IGeometryInfo.java 1.11 -> 1.12
diff -u -r1.11 -r1.12
--- IGeometryInfo.java	9 Apr 2007 21:05:27 -0000	1.11
+++ IGeometryInfo.java	4 May 2007 10:23:37 -0000	1.12
@@ -3,26 +3,23 @@
 import hep.physics.vec.Hep3Vector;
 
 /**
- * This interface auto-extracted from first draft of GeometryInfo class.
- * 
- * It provides access to the following information:
+ * IGeometryInfo provides geometry information about an {@link IDetectorElement}.
+ *
+ * This information includes the following:
  * 
  * <ul>
- * <li>logical volume</li>
- * <li>logical volume name</li>
- * <li>global to local transform</li>
- * <li>local to global transform</li>
- * <li>parent to local transform</li>
- * <li>the PhysicalVolumePath associated with this DE</li>
+ * <li>associated {@link ILogicalVolume}</li>
+ * <li>name of associated {@link LogicalVolume}</li>
+ * <li>global to local {@link Transform3D}</li>
+ * <li>local to global {@link Transform3D}</li>
+ * <li>parent to local {@link Transform3D}</li>
+ * <li>{@link PhysicalVolumePath} associated with this {@link DetectorElement}</li>
+ * <li>{@link #isInside(Hep3Vector)} on a global point which checks if the point is inside the leaf geometry node in the path</li>
  * </ul>
  *
- * There are services for transforming global or local points 
- * using the above transforms.
- * 
- * Additionally, the isInside method will check whether
- * a global point is inside the leaf PhysicalVolume in the
- * path, i.e. a specific geometry node associated with 
- * the IGeometryInfo's DetectorElement. 
+ * An {@link IDetectorElement} may have an IGeometryInfo, which means that it has support in the geometry tree.
+ * Those DetectorElements without IGeometryInfo are ghost volumes that have no geometric correspondence, but
+ * fill a logical roll in the detector hierarchy.
  *
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Tim Nelson <[log in to unmask]>
@@ -30,76 +27,74 @@
 public interface IGeometryInfo 
 {
 	/**
-	 * Get an IGeometryInfoContainer with the child DetectorElement's IGeometryInfo objects.
+	 * Get an {@link IGeometryInfoContainer} with the child DetectorElement's IGeometryInfo objects.
 	 * @return Container of IGeometryInfos from the child DetectorElements.
 	 */
 	public IGeometryInfoContainer getChildGeometryInfos();
 
 	/**
-	 * Get the IPhysicalVolumePath from a global point @param globalPoint.
-	 * 
-	 * @param global_point
-	 * @return
+	 * Get the {@link IPhysicalVolumePath} at a global point.
+	 * @param globalPoint A point in global coordinates.
+	 * @return A path of physical volumes at the global point.
 	 */
 	public IPhysicalVolumePath getPath(
 			Hep3Vector globalPoint);
 
 	/**
-	 * Get the associated LogicalVolume.
-	 * @return
+	 * Get the associated {@link ILogicalVolume}.
+	 * @return A LogicalVolume associated with this geometry.
 	 */
 	public ILogicalVolume getLogicalVolume();
 
 	/**
 	 * Get the name of the associated LogicalVolume.
-	 * 
-	 * @return
+	 * @return The name of the associated LogicalVolume.
 	 */
 	public String getLogicalVolumeName();
 
 	/**
-	 * Get the PhysicalVolume at the point @param globalPoint
+	 * Get the PhysicalVolume at the global point
 	 * using the IPhysicalVolumePath of this IGeometryInfo.
-	 * 
-	 * @param globalPoint
-	 * @return
+     *
+	 * @param globalPoint A point in global coordinates.
+	 * @return The PhysicalVolume at the point.
 	 */
 	public IPhysicalVolume getPhysicalVolume(Hep3Vector globalPoint);
 
 	/**
-	 * Get the center position of the DetectorElement.
-	 * @return
+	 * Get the center position of the DetectorElement in global coordinates.
+	 * @return Center position of DetectorElement in global coordinates.
 	 */
 	public Hep3Vector getPosition();
 
 	/**
-	 * Get the IPhysicalVolumePath assigned to this GeometryInfo.
+	 * Get the {@link IPhysicalVolumePath} assigned to this GeometryInfo.
 	 * This path points to a unique node in the geometry tree
 	 * and determines the basic global to local transform
 	 * of the DetectorElement.
 	 * 
-	 * @return
+	 * @return The path of this DetectorElement.
 	 */
 	public IPhysicalVolumePath getPhysicalVolumePath();
 
 	/**
 	 * Get the combined global to local transform.
-	 * @return
+     *
+	 * @return The global to local transform.
 	 */
 	public ITransform3D getGlobalToLocal();
 
 	/**
-	 * Transform the global point @param globalPoint from global
-	 * coordinates to local.
+	 * Transform the global point from global coordinates to local.
 	 * 
-	 * @param global_point
-	 * @return
+	 * @param globalPoint 
+	 * @return Global point transformed to local.
 	 */
 	public Hep3Vector transformGlobalToLocal(Hep3Vector globalPoint);
 
 	/**
 	 * True if this IGeometryInfo has an associated LogicalVolume.
-	 * @return
+	 * @return True if the IGeomInfo has a non-<code>null</code> LogicalVolume.
 	 */
 	public boolean hasLogicalVolume();
 
@@ -107,62 +102,62 @@
 	 * True if this IGeometryInfo has an associated full path
 	 * or geometry node.
 	 * 
-	 * @return
+	 * @return True if this IGeometryInfo has an IPhysicalVolumePath.
 	 */
 	public boolean hasPath();
 
 	/**
-	 * True if the @param globalPoint is inside the DetectorElement.
-	 * @param point
-	 * @return
+	 * True if the global point is inside this DetectorElement
+     * or any of its descendants.
+	 * @param globalPoint A global point.
+	 * @return True if the global point is inside this DetectorElement
+     *         or any of its descendants.
 	 */
 	public boolean isInside(Hep3Vector globalPoint);
 
 	/**
 	 * Get the combined local to global transform.
-	 * @return
+     * @see ITransform3D
+	 * @return The local to global transform.
 	 */
 	public ITransform3D getLocalToGlobal();
 
 	/**
 	 * Get the transformation from parent geometry 
 	 * into local geometry.
-	 * 
-	 * @return
+	 * @return The parent to local transform.
 	 */
 	public ITransform3D getParentToLocal();
 	
 	/**
-	 * Transform the local point @param localPoint from local
-	 * to global coordinates.
-	 * 
-	 * @param localPoint
-	 * @return
+	 * Transform a local point into global coordinates.
+	 * @param localPoint A local point.
+	 * @return Point transformed into global coordinate system.
 	 */
 	public Hep3Vector transformLocalToGlobal(Hep3Vector localPoint);
 
 	/**
 	 * Get the parent DetectorElement's IGeometryInfo.
-	 * @return
+	 * @return The parent's IGeometryInfo or <code>null</code>
+     *         if none exists.
 	 */
 	public IGeometryInfo parentIGeometryInfo();	
 
 	/**
-	 * Transform point in parent geometry @parentPoint into
-	 * local geometry. 
+	 * Transform point in parent geometry to local coordinate system. 
 	 * 
-	 * @param parentPoint
-	 * @return
+	 * @param parentPoint A point in the parent coordinate system.
+	 * @return Point transformed from parent to local coordinates.
 	 */
 	public Hep3Vector transformParentToLocal(Hep3Vector parentPoint);
 	
 	/**
-	 * Set the IPhysicalVolumePath with full geometry information
+	 * Set the {@link IPhysicalVolumePath} with full geometry information
 	 * for this DetectorElement.
 	 * 
-	 * @param path
+	 * @param path The path assigned to this DetectorElement.
 	 */
-	public void setPath(IPhysicalVolumePath path);
+	//public void setPath(IPhysicalVolumePath path);
     
     /**
      * True if the IGeometryInfo does not have an associated path in the geometry tree. 
@@ -171,7 +166,7 @@
     
     /**
      * Return the associated DetectorElement.     
-     * @return
+     * @return The associated DetectorElement.
      */
     public IDetectorElement getDetectorElement();
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector
IPhysicalVolume.java 1.6 -> 1.7
diff -u -r1.6 -r1.7
--- IPhysicalVolume.java	7 Apr 2007 21:40:12 -0000	1.6
+++ IPhysicalVolume.java	4 May 2007 10:23:37 -0000	1.7
@@ -7,44 +7,44 @@
 {
 	/**
 	 * Get the associated LogicalVolume.
-	 * @return
+	 * @return The associated LogicalVolume.
 	 */
 	public ILogicalVolume getLogicalVolume();	
 	
 	/**
 	 * Get the mother's LogicalVolume.
-	 * @return
+	 * @return The mother's LogicalVolume.
 	 */
 	public ILogicalVolume getMotherLogicalVolume();
 	
 	/**
 	 * Get the transformation from mother's coordinate system.
-	 * @return
+	 * @return The transformation from mother's coordinate system.
 	 */
 	public ITransform3D getTransform();
 	
 	/**
 	 * Get the translation component of the coordinate transform.
-	 * @return
+	 * @return The translation component of the coordinate transform.
 	 */
 	public Hep3Vector getTranslation();
 	
 	/**
 	 * Get the rotation component of the coordinate transform.
-	 * @return
+	 * @return The rotation component of the coordinate transform.
 	 */
 	public IRotation3D getRotation();
 	
 	/**
 	 * Get the copy number.
-	 * @return
+	 * @return The copy number of this volume.
 	 */
 	public int getCopyNumber();
 	
 	/**
 	 * Transform a point from parent to this volume.
-	 * @param point
-	 * @return
+	 * @param point A point in parent coordinate system.
+	 * @return Point transformed to local coordinate system.
 	 */
 	public Hep3Vector transformParentToLocal(Hep3Vector point);
     
@@ -52,5 +52,6 @@
      * True if this volume is a sensitive component;
      * False if this volume is not a sensitive component.
      */
+    // FIXME: Move to LogicalVolume or DetectorElement?   Geant4 uses LogicalVolume for this.
     public boolean isSensitive();
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector
IPhysicalVolumeNavigator.java 1.8 -> 1.9
diff -u -r1.8 -r1.9
--- IPhysicalVolumeNavigator.java	17 Mar 2007 00:10:40 -0000	1.8
+++ IPhysicalVolumeNavigator.java	4 May 2007 10:23:37 -0000	1.9
@@ -11,7 +11,7 @@
  * transform of an IPhysicalVolumePath.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
- * @version $Id: IPhysicalVolumeNavigator.java,v 1.8 2007/03/17 00:10:40 jeremy Exp $
+ * @version $Id: IPhysicalVolumeNavigator.java,v 1.9 2007/05/04 10:23:37 jeremy Exp $
  */
 public interface IPhysicalVolumeNavigator 
 extends INamed
@@ -20,7 +20,7 @@
 	 * Get the top physical volume assigned to
 	 * this navigator.
 	 * 
-	 * @return
+	 * @return The top or world volume.
 	 */
 	public IPhysicalVolume getTopPhysicalVolume();
 	
@@ -28,19 +28,21 @@
 	 * Set the top physical volume assigned to 
 	 * this navigator.
 	 * 
-	 * @param physvol
+	 * @param physvol A top volume.
 	 */
 	public void setTopPhysicalVolume(IPhysicalVolume physvol);
 	
 	/**
 	 * 
-	 * Get the full stack of PhysicalVolumes from a path string
-	 * of PhysicalVolume names.
-	 * 
-	 * "/name1/name2/[...]"
-	 * 
-	 * @param path
-	 * @return
+	 * Get the full stack of {@link IPhysicalVolume}s from a path string
+	 * of names.
+     *
+	 * <code>
+	 * getPath("/volume_name/subvolume_name")
+	 * <code> 
+     
+	 * @param path A String with the path name.
+	 * @return IPhysicalVolumePath corresponding to the name.
 	 */
 	public IPhysicalVolumePath getPath(String path);	
 
@@ -49,8 +51,8 @@
 	 * Get the full transformation from the origin of
 	 * the coordinate system to the given path.
 	 * 
-	 * @param path
-	 * @return
+	 * @param path The path of volumes.
+	 * @return Transform from a path.
 	 */
 	public Transform3D getTransform(String path);
 	
@@ -58,33 +60,34 @@
 	 * Get the full transformation from the origin of
 	 * the coordinate system from a stack of physical volumes.
 	 * 
-	 * @param path
-	 * @return
+	 * @param path The path of volumes.
+	 * @return The full transform from the path.
 	 */
 	Transform3D getTransform(IPhysicalVolumePath path);
 
 	/**
 	 * Given a global point, return the full path to
-	 * deepest volume containing this point, not past depth
-	 * of @param level.
+	 * deepest volume containing this point, not past
+     * given depth.
 	 * 
-	 * @param point A point in the global coordinate system.
+	 * @param globalPoint A point in the global coordinate system.
 	 * @param level Max depth.  -1 will go to bottom.
-	 * @return
+	 * @return Path down to the given level.
 	 */
 	public IPhysicalVolumePath getPath(Hep3Vector globalPoint, int level);
 	
 	/**
-	 * Same as above with no depth arg.
+	 * Same as {@link #getPath(Hep3Vector globalPoint, int level)}
+     * with level set to -1.
 	 * 
-	 * @param globalPoint
-	 * @return
+	 * @param globalPoint A point in the global coordinate system.
+	 * @return Path at the point.
 	 */
 	public IPhysicalVolumePath getPath(Hep3Vector globalPoint);	
 	 
 	/**
 	 * Traverse the tree using preorder, calling the visit method 
-	 * of the @param IPhysicalVolumeVisitor.
+	 * of the {@link IPhysicalVolumeVisitor}.
 	 * 
 	 * @param visitor An IPhysicalVolumeVisitor that will be activated
 	 *                at each PhysicalVolume in the tree.
@@ -93,10 +96,10 @@
 	
 	/**
 	 * Traverse the tree using postorder, calling the visit method 
-	 * of the @param IPhysicalVolumeVisitor.
+	 * of the {@link IPhysicalVolumeVisitor}.
 	 * 
 	 * @param visitor An IPhysicalVolumeVisitor that will be activated
 	 *                at each PhysicalVolume in the tree.
 	 */
 	public void traversePostOrder(IPhysicalVolumeVisitor visitor);	
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector
IRotation3D.java 1.6 -> 1.7
diff -u -r1.6 -r1.7
--- IRotation3D.java	2 May 2007 01:58:19 -0000	1.6
+++ IRotation3D.java	4 May 2007 10:23:37 -0000	1.7
@@ -7,16 +7,16 @@
 /**
  * An interface to rotations in 3D space,
  * using interfaces and base classes within
- * the hep.physics.vec package.
+ * the {@link hep.physics.vec} package.
  * 
  * @see hep.physics.vec 
  * @see hep.physics.vec.BasicHep3Matrix
  * @see hep.physics.vec.Hep3Matrix
  * @see hep.physics.vec.Hep3Vector
  * 
- * @author Tim Nelson <[log in to unmask]>
- * @author Jeremy McCormick <[log in to unmask]>
- * @version $Id: IRotation3D.java,v 1.6 2007/05/02 01:58:19 jeremy Exp $
+ * @author tknelson
+ * @author jeremym
+ * @version $Id: IRotation3D.java,v 1.7 2007/05/04 10:23:37 jeremy Exp $
  */
 public interface IRotation3D
 {   
@@ -119,7 +119,7 @@
     
     /**
      * Get the components as an array of length 9.
-     * @return
+     * @return Components in array of length 9.
      */
     public double[] getComponents();
     
@@ -131,13 +131,13 @@
     /**
      * Apply inverse transformation, returning
      * a new IRotation3D, not altering this matrix.
-     * @return
+     * @return A new matrix which is the inverse of this one.
      */
     public IRotation3D inverse();
     
     /**
      * The trace of the matrix.
-     * @return
+     * @return The trace of the matrix.
      */
     public double trace();  
     
@@ -145,15 +145,15 @@
      * Get matrix component by row and column.
      * @param row
      * @param col
-     * @return
+     * @return Matrix component at row and col.
      */
     public double getComponent(int row, int col);
     
     /**
      * Get the ith component. 
      * Use the symbolic constants XX, XY, etc. 
-     * @param i
-     * @return
+     * @param i The ith component to return.
+     * @return The ith component.
      */
     public double getComponent(int i);
 
@@ -164,7 +164,7 @@
     
     /**
      * True if this IRotation3D is equivalent to the identity matrix.
-  	 * @return
+  	 * @return True if this rotation is equal to identity.
      */
     public boolean isIdentity(); 
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector/identifier
ExpandedIdentifier.java 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- ExpandedIdentifier.java	4 May 2007 01:18:21 -0000	1.2
+++ ExpandedIdentifier.java	4 May 2007 10:23:38 -0000	1.3
@@ -4,10 +4,10 @@
 import java.util.List;
 
 /**
- * Implementation of {@see IExpandedIdentifier}.
+ * Implementation of {@link IExpandedIdentifier}.
  *
  * @author Jeremy McCormick
- * @version $Id: ExpandedIdentifier.java,v 1.2 2007/05/04 01:18:21 jeremy Exp $
+ * @version $Id: ExpandedIdentifier.java,v 1.3 2007/05/04 10:23:38 jeremy Exp $
  */
 
 public class ExpandedIdentifier

GeomConverter/src/org/lcsim/detector/identifier
IExpandedIdentifier.java 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- IExpandedIdentifier.java	4 May 2007 01:18:21 -0000	1.3
+++ IExpandedIdentifier.java	4 May 2007 10:23:38 -0000	1.4
@@ -3,14 +3,14 @@
 import java.util.List;
 
 /**
- * An ID that has been unpacked from an {@see org.lcsim.detector.IIdentifier}
+ * An ID that has been unpacked from an {@link org.lcsim.detector.IIdentifier}
  * so that individual field values are available by index.
  *
- * Use the appropriate {@see org.lcsim.detector.IIdentifierDictionary} to
+ * Use the appropriate {@link org.lcsim.detector.IIdentifierDictionary} to
  * see which indices correspond to which field labels.
  * 
  * @author  jeremym
- * @version $Id: IExpandedIdentifier.java,v 1.3 2007/05/04 01:18:21 jeremy Exp $
+ * @version $Id: IExpandedIdentifier.java,v 1.4 2007/05/04 10:23:38 jeremy Exp $
  */
 
 public interface IExpandedIdentifier
@@ -21,7 +21,7 @@
     public void addValue(int value);
 
     /**
-     * Get the field value at index of {@param index}.
+     * Get the field value at an index.
      */
     public int getValue(int index);
 
@@ -36,19 +36,19 @@
     public int size();
 
     /**
-     * Get the maximum index which is {@see #size} - 1 .
+     * Get the maximum index which is {@link #size} - 1 .
      */
     public int getMaxIndex();
 
     /**
      * Clear the identifier of all field values.
-     * The {@see #size} method returns 0 after
+     * The {@link #size} method returns 0 after
      * this method is called.
      */
     public void clear();
 
     /**
-     * True if the {@see IExpandedIdentifier} is in
+     * True if the {@link IExpandedIdentifier} is in
      * a valid state with 1 or more field values;
      * False if there are no values when size is 0. 
      */

GeomConverter/src/org/lcsim/detector/identifier
IIdentifierHelper.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IIdentifierHelper.java	2 May 2007 01:58:19 -0000	1.1
+++ IIdentifierHelper.java	4 May 2007 10:23:38 -0000	1.2
@@ -4,7 +4,7 @@
  * COMMENT
  *
  * @author Jeremy McCormick
- * @version $Id: IIdentifierHelper.java,v 1.1 2007/05/02 01:58:19 jeremy Exp $
+ * @version $Id: IIdentifierHelper.java,v 1.2 2007/05/04 10:23:38 jeremy Exp $
  */
 
 public interface IIdentifierHelper
@@ -14,4 +14,4 @@
     //public IIdentifier pack(IExpandedIdentifier id, int start);
     //public IIdentifier pack(IExpandedIdentifier id, int start, int nfields);
     public IExpandedIdentifier unpack(IIdentifier id);
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector/identifier
IdentifierHelper.java 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- IdentifierHelper.java	2 May 2007 23:46:10 -0000	1.2
+++ IdentifierHelper.java	4 May 2007 10:23:38 -0000	1.3
@@ -1,9 +1,9 @@
 package org.lcsim.detector.identifier;
 
 /**
- * A helper class for packing {@see IExpandedIdentifier} objects
- * and unpacking {@see IIdentifier} objects using information in
- * a {@see IIdentifierDictionary}.
+ * A helper class for packing {@link IExpandedIdentifier} objects
+ * and unpacking {@link IIdentifier} objects using information from
+ * an associated {@link IIdentifierDictionary}.
  * 
  * @see IIdentifierDictionary
  * @see IIdentifier
@@ -11,7 +11,7 @@
  * @see IdentifierUtil
  *
  * @author Jeremy McCormick
- * @version $Id: IdentifierHelper.java,v 1.2 2007/05/02 23:46:10 jeremy Exp $
+ * @version $Id: IdentifierHelper.java,v 1.3 2007/05/04 10:23:38 jeremy Exp $
  */
 
 public class IdentifierHelper
@@ -38,4 +38,4 @@
     {
         return IdentifierUtil.unpack( id, iddict );
     }           
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/detector/material
BetheBlochCalculator.java 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- BetheBlochCalculator.java	3 Mar 2007 13:59:17 -0000	1.2
+++ BetheBlochCalculator.java	4 May 2007 10:23:38 -0000	1.3
@@ -15,10 +15,13 @@
 
 /**
  *
- * A calculator for dEdX using the Bethe-Bloch formula.
+ * A calculator for dEdX using the Bethe-Bloch formula
+ * from the PDG guide.  
  *
- * @author Jeremy McCormick <[log in to unmask]>
- * @author Caroline Milstene <[log in to unmask]>
+ * <a href="http://pdg.lbl.gov/2006/reviews/passagerpp.pdf">Passage of Particles Through Matter</a>
+ *
+ * @author jeremym
+ * @author caroline
  */
 public class BetheBlochCalculator
 {	
@@ -29,7 +32,7 @@
 	 * @param material
 	 * @param particle
 	 * @param distance
-	 * @return
+	 * @return The energy loss in MeV. 
 	 */
 	public static double computeBetheBloch(
 			IMaterial material,
@@ -52,7 +55,7 @@
 	 * @param mass
 	 * @param charge
 	 * @param distance
-	 * @return
+	 * @return The energy loss in MeV.
 	 */
 	public static double computeBetheBloch(
 			IMaterial material,
@@ -90,7 +93,7 @@
 	 * @param mass
 	 * @param charge
 	 * @param distance
-	 * @return
+	 * @return The energy loss in MeV.
 	 */
     public static double computeBetheBloch(
     		double Z,
@@ -271,4 +274,4 @@
         
         return result;
     }   
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/geometry
Layered.java 1.5 -> 1.6
diff -u -r1.5 -r1.6
--- Layered.java	2 May 2007 23:44:34 -0000	1.5
+++ Layered.java	4 May 2007 10:23:38 -0000	1.6
@@ -4,7 +4,7 @@
 
 /**
  *
- * @deprecated Use [log in to unmask]
+ * @deprecated Use {@link org.lcsim.detector.IDetectorElement}.
  *
  * @author jeremym
  */
@@ -12,4 +12,4 @@
 public interface Layered 
 {
     Layering getLayering();
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/geometry/subdetector
SiTrackerBarrel.java 1.10 -> 1.11
diff -u -r1.10 -r1.11
--- SiTrackerBarrel.java	4 May 2007 02:04:49 -0000	1.10
+++ SiTrackerBarrel.java	4 May 2007 10:23:38 -0000	1.11
@@ -10,12 +10,11 @@
 
 /**
  * This is just a bootstrap class for a converter,
- * {@link org.lcsim.detector.converter.compactr.SiTrackerBarrelConverter},
+ * {@link org.lcsim.detector.converter.compact.SiTrackerBarrelConverter},
  * which uses the raw XML from the compact description.
  *
  * This class also allows SiTrackerBarrel to be visualized
- * with other compact {@link org.lcsim.geometry.Subdetector}
- * objects.
+ * with other the other {@link org.lcsim.geometry.Subdetector}s.
  *
  * @see org.lcsim.detector.converter.heprep.DetectorElementToHepRepConverter
  * @see org.lcsim.detector.tracker
@@ -23,7 +22,7 @@
  * @author jeremym 
  * @author tknelson 
  
- * @version $Id: SiTrackerBarrel.java,v 1.10 2007/05/04 02:04:49 jeremy Exp $
+ * @version $Id: SiTrackerBarrel.java,v 1.11 2007/05/04 10:23:38 jeremy Exp $
  */
 public class SiTrackerBarrel extends AbstractTracker
 {

GeomConverter/src/org/lcsim/material
Material.java 1.21 -> 1.22
diff -u -r1.21 -r1.22
--- Material.java	1 May 2007 23:46:21 -0000	1.21
+++ Material.java	4 May 2007 10:23:38 -0000	1.22
@@ -553,4 +553,4 @@
         
         return s;
     }
-}
\ No newline at end of file
+}

GeomConverter/src/org/lcsim/material
MaterialCalculator.java 1.17 -> 1.18
diff -u -r1.17 -r1.18
--- MaterialCalculator.java	2 May 2007 23:44:02 -0000	1.17
+++ MaterialCalculator.java	4 May 2007 10:23:39 -0000	1.18
@@ -12,7 +12,7 @@
 
 /**
  *
- * @deprecated Use [log in to unmask], [log in to unmask]
+ * @deprecated Use {@link org.lcsim.detector.material.IMaterial} and {@link org.lcsim.detector.material.BetheBlocheCalculator}.
  * @author jeremym
  */
 @Deprecated
CVSspam 0.2.8