Commit in lcdd on MAIN
include/lcdd/detectors/CellReadout.hh+2-21.4 -> 1.5
                      /CellReadout2D.hh+2-21.4 -> 1.5
include/lcdd/geant4/LCDDHeaderRecord.hh+153-471.2 -> 1.3
                   /PhysVolId.hh+47-151.2 -> 1.3
                   /PhysVolIdMap.hh+19-111.3 -> 1.4
                   /PhysicsLimitSet.hh+85-181.1 -> 1.2
                   /UserRegionInformation.hh+55-121.1 -> 1.2
include/lcdd/hits/CalorimeterHit.hh+108-91.1 -> 1.2
                 /HitContribution.hh+2-21.1 -> 1.2
                 /TrackInformation.hh+150-221.2 -> 1.3
                 /TrackerHit.hh+108-11.1 -> 1.2
include/lcdd/id/Id64bit.hh+32-31.1 -> 1.2
               /IdComparator.hh+20-31.3 -> 1.4
               /IdFactory.hh+57-251.2 -> 1.3
               /IdField.hh+64-191.1 -> 1.2
               /IdManager.hh+75-121.1 -> 1.2
               /IdSpec.hh+102-301.1 -> 1.2
               /IdVec.hh+65-291.1 -> 1.2
src/lcdd/bfield/Cartesian3DMagneticFieldMap.cc+11.1 -> 1.2
src/lcdd/detectors/CalorimeterSD.cc+2-21.2 -> 1.3
                  /OpticalCalorimeterSD.cc+2-21.1 -> 1.2
                  /UnsegmentedCalorimeterSD.cc+2-21.1 -> 1.2
src/lcdd/geant4/PhysicsLimitSet.cc+19-191.1 -> 1.2
src/lcdd/hits/CalorimeterHit.cc+2-21.1 -> 1.2
src/lcdd/id/IdFactory.cc+2-21.2 -> 1.3
           /IdSpec.cc+3-31.1 -> 1.2
           /IdVec.cc+13-81.1 -> 1.2
+1192-302
27 modified files
add yet more doxygen doc; some method and variable renaming

lcdd/include/lcdd/detectors
CellReadout.hh 1.4 -> 1.5
diff -u -r1.4 -r1.5
--- CellReadout.hh	2 Jul 2013 21:19:44 -0000	1.4
+++ CellReadout.hh	3 Jul 2013 23:00:45 -0000	1.5
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/detectors/CellReadout.hh,v 1.4 2013/07/02 21:19:44 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/detectors/CellReadout.hh,v 1.5 2013/07/03 23:00:45 jeremy Exp $
 
 #ifndef LCDD_DETECTORS_CELLREADOUT_HH
 #define LCDD_DETECTORS_CELLREADOUT_HH 1
@@ -10,7 +10,7 @@
 
 /**
  * This is a pure virtual base class for calorimeter cell readouts to implement.
- * @fixme Move to DDSegmentation package.
+ * @todo Move to DDSegmentation package.
  */
 class CellReadout
 {

lcdd/include/lcdd/detectors
CellReadout2D.hh 1.4 -> 1.5
diff -u -r1.4 -r1.5
--- CellReadout2D.hh	2 Jul 2013 22:57:42 -0000	1.4
+++ CellReadout2D.hh	3 Jul 2013 23:00:45 -0000	1.5
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/detectors/CellReadout2D.hh,v 1.4 2013/07/02 22:57:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/detectors/CellReadout2D.hh,v 1.5 2013/07/03 23:00:45 jeremy Exp $
 
 #ifndef LCDD_DETECTORS_CELLREADOUT2D_HH
 #define LCDD_DETECTORS_CELLREADOUT2D_HH 1
@@ -12,7 +12,7 @@
 
 /**
  * @brief A concrete implementation of CellReadout using a 2D grid.
- * @fixme Move to DDSegmentation package.
+ * @todo Move to DDSegmentation package.
  */
 class CellReadout2D: public CellReadout
 {

lcdd/include/lcdd/geant4
LCDDHeaderRecord.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- LCDDHeaderRecord.hh	1 Jul 2013 21:00:42 -0000	1.2
+++ LCDDHeaderRecord.hh	3 Jul 2013 23:00:46 -0000	1.3
@@ -1,154 +1,260 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/LCDDHeaderRecord.hh,v 1.2 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/LCDDHeaderRecord.hh,v 1.3 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_GEANT4_LCDDHEADERRECORD_HH
 #define LCDD_GEANT4_LCDDHEADERRECORD_HH 1
 
 /**
- * @brief Header record of detector info.
+ * This is the header record for an LCDD geometry.
+ * @todo Move code to source file.
  */
 class LCDDHeaderRecord
 {
 
 public:
 
+	/**
+	 * Class constructor.
+	 */
+	LCDDHeaderRecord()
+	{
+		;
+	}
+
+	/**
+	 * Class destructor.
+	 */
+	virtual ~LCDDHeaderRecord()
+	{
+		;
+	}
+
+public:
+
+	/**
+	 * Set the name of the detector.
+	 * @param[in] dn The name of the detector.
+	 */
     void setDetectorName(const std::string& dn)
     {
-        m_detectorName = dn;
+        _detectorName = dn;
     }
 
+    /**
+     * Set the version of the detector.
+     * @param[in] dv The detector version.
+     */
     void setDetectorVersion(const std::string& dv)
     {
-        m_detectorVersion = dv;
+        _detectorVersion = dv;
     }
 
+    /**
+     * Set the URL of the input LCDD file.
+     * @param[in] u The URL of the input file.
+     */
     void setDetectorUrl(const std::string& u)
     {
-        m_detectorUrl = u;
+        _detectorUrl = u;
     }
 
+    /**
+     * Set the author name.
+     * @param[in] an The author name.
+     */
     void setAuthorName(const std::string& an)
     {
-        m_authorName = an;
+        _authorName = an;
     }
 
+    /**
+     * Set the generator name.
+     * @param[in] gn The generator name.
+     */
     void setGeneratorName(const std::string& gn)
     {
-        m_generatorName = gn;
+        _generatorName = gn;
     }
 
+    /**
+     * Set the generator version.
+     * @param[in] gv The generator version.
+     */
     void setGeneratorVersion(const std::string& gv)
     {
-        m_generatorVersion = gv;
+        _generatorVersion = gv;
     }
 
+    /**
+     * Set the generator checksum.
+     * @param[in] c The generator checksum.
+     */
     void setGeneratorChecksum(const std::string& c)
     {
-        m_generatorChecksum = c;
+        _generatorChecksum = c;
     }
 
+    /**
+     * Set the generator input file.
+     * @param[in] gurl The generator file.
+     */
     void setGeneratorFile(const std::string& gurl)
     {
-        m_generatorFile = gurl;
+        _generatorFile = gurl;
     }
 
+    /**
+     * Set the author email.
+     * @param[in] ae The author email.
+     */
     void setAuthorEmail(const std::string& ae)
     {
-        m_authorEmail = ae;
+        _authorEmail = ae;
     }
 
+    /**
+     * Set the comment.
+     * @param[in] c The comment.
+     */
     void setComment(const std::string& c)
     {
-        m_comment = c;
+        _comment = c;
     }
 
+    /**
+     * Set the checksum.
+     * @param[in] c The checksum.
+     */
     void setChecksum(const std::string& c)
     {
-        m_generatorChecksum = c;
+        _generatorChecksum = c;
     }
 
+    /**
+     * Get the detector name.
+     * @return The detector name.
+     */
     const std::string& getDetectorName() const
     {
-        return m_detectorName;
+        return _detectorName;
     }
 
+    /**
+     * Get the detector version.
+     * @return The detector version.
+     */
     const std::string& getDetectorVersion() const
     {
-        return m_detectorVersion;
+        return _detectorVersion;
     }
 
+    /**
+     * Get the detector URL.
+     * @return The detector URL.
+     */
     const std::string& getDetectorUrl() const
     {
-        return m_detectorUrl;
+        return _detectorUrl;
     }
 
+    /**
+     * Get the comment.
+     * @return The comment.
+     */
     const std::string& getComment() const
     {
-        return m_comment;
+        return _comment;
     }
 
+    /**
+     * Get the author name.
+     * @return The author name.
+     */
     const std::string& getAuthorName() const
     {
-        return m_authorName;
+        return _authorName;
     }
 
+    /**
+     * Get the author email.
+     * @return The author email.
+     */
     const std::string& getAuthorEmail() const
     {
-        return m_authorEmail;
+        return _authorEmail;
     }
 
+    /**
+     * Get the generator name.
+     * @return The generator name.
+     */
     const std::string& getGeneratorName() const
     {
-        return m_generatorName;
+        return _generatorName;
     }
 
+    /**
+     * Get the generator version.
+     * @return The generator version.
+     */
     const std::string& getGeneratorVersion() const
     {
-        return m_generatorVersion;
+        return _generatorVersion;
     }
 
+    /**
+     * Get the generator file name.
+     * @return The generator file name.
+     */
     const std::string& getGeneratorFile() const
     {
-        return m_generatorFile;
+        return _generatorFile;
     }
 
+    /**
+     * Get the generator checksum.
+     * @return The generator checksum.
+     */
     const std::string& getGeneratorChecksum() const
     {
-        return m_generatorChecksum;
+        return _generatorChecksum;
     }
 
-    void printOut(std::ostream &os)
+    /**
+     * Print out the header information.
+     * @param[in] os The output stream.
+     * @return The same output stream.
+     */
+    std::ostream& printOut(std::ostream &os)
     {
         os << std::endl << "***** LCDD Header *****" << std::endl;
 
-        os << "detectorName <" << m_detectorName << ">" << std::endl;
-        os << "detectorVersion <" << m_detectorVersion << ">" << std::endl;
-        os << "detectorUrl <" << m_detectorUrl << ">" << std::endl;
-        os << "authorName <" << m_authorName << ">" << std::endl;
-        os << "authorEmail <" << m_authorEmail << ">" << std::endl;
-        os << "generatorName <" << m_generatorName << ">" << std::endl;
-        os << "generatorVersion <" << m_generatorVersion << ">" << std::endl;
-        os << "generatorFile <" << m_generatorFile << ">" << std::endl;
-        os << "generatorChecksum <" << m_generatorChecksum << ">" << std::endl;
-        os << "comment" << std::endl << m_comment << std::endl << "end comment" << std::endl;
+        os << "detectorName <" << _detectorName << ">" << std::endl;
+        os << "detectorVersion <" << _detectorVersion << ">" << std::endl;
+        os << "detectorUrl <" << _detectorUrl << ">" << std::endl;
+        os << "authorName <" << _authorName << ">" << std::endl;
+        os << "authorEmail <" << _authorEmail << ">" << std::endl;
+        os << "generatorName <" << _generatorName << ">" << std::endl;
+        os << "generatorVersion <" << _generatorVersion << ">" << std::endl;
+        os << "generatorFile <" << _generatorFile << ">" << std::endl;
+        os << "generatorChecksum <" << _generatorChecksum << ">" << std::endl;
+        os << "comment" << std::endl << _comment << std::endl << "end comment" << std::endl;
 
         os << "***********************" << std::endl << std::endl;
+        return os;
     }
 
 private:
 
-    std::string m_detectorName;
-    std::string m_detectorVersion;
-    std::string m_detectorUrl;
-
-    std::string m_generatorName;
-    std::string m_generatorVersion;
-    std::string m_generatorFile;
-    std::string m_generatorChecksum;
-
-    std::string m_authorName;
-    std::string m_authorEmail;
-
-    std::string m_comment;
+    std::string _detectorName;
+    std::string _detectorVersion;
+    std::string _detectorUrl;
+    std::string _generatorName;
+    std::string _generatorVersion;
+    std::string _generatorFile;
+    std::string _generatorChecksum;
+    std::string _authorName;
+    std::string _authorEmail;
+    std::string _comment;
 };
 
 #endif

lcdd/include/lcdd/geant4
PhysVolId.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- PhysVolId.hh	1 Jul 2013 21:00:42 -0000	1.2
+++ PhysVolId.hh	3 Jul 2013 23:00:46 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/PhysVolId.hh,v 1.2 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/PhysVolId.hh,v 1.3 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_GEANT4_PHYSVOLID_HH
 #define LCDD_GEANT4_PHYSVOLID_HH 1
@@ -7,63 +7,95 @@
 #include <vector>
 
 /**
- * @brief Simulator class for physical volume IDs.
+ * This is a class representing physical volume IDs that are attached to individual G4VPhysicalVolume objects.
  */
 class PhysVolId
 {
+
 public:
     typedef int ValueType;
     typedef std::vector<PhysVolId> PhysVolIds;
 
 public:
 
-    PhysVolId()
-    {
-    }
-
+    /**
+     * Class constructor.
+     */
+    //PhysVolId()
+    //{
+    //}
+
+    /**
+     * Class constructor.
+     * @param[in] val The value of the ID.
+     * @param[in] fld The name of the ID.
+     */
     PhysVolId(ValueType val, std::string fld) :
-            m_value(val), m_fieldName(fld)
+            _value(val), _fieldName(fld)
     {
     }
 
+    /**
+     * Class destructor.
+     */
     virtual ~PhysVolId()
     {
     }
 
+public:
+
+    /**
+     * Get the value of the ID.
+     * @return The value of the ID.
+     */
     ValueType getValue() const
     {
-        return m_value;
+        return _value;
     }
 
+    /**
+     * Get the name of the field.
+     * @return The name of the field.
+     */
     const std::string& getFieldName() const
     {
-        return m_fieldName;
+        return _fieldName;
     }
 
+    /*
     void setFieldName(const std::string& fn)
     {
-        m_fieldName = fn;
+        _fieldName = fn;
     }
 
     void setValue(ValueType vt)
     {
-        m_value = vt;
+        _value = vt;
     }
+    */
 
+    /**
+     * Compare this PhysVolId to another based on their values.
+     * @return True if ID values are equal; false if not.
+     */
     bool operator==(const PhysVolId& right)
     {
-        return (m_value == right.m_value);
+        return (_value == right._value);
     }
 
+    /**
+     * Compare this PhysVolId to a value.
+     * @return True if value is equal to this ID; false if not.
+     */
     bool operator==(ValueType vt)
     {
-        return (m_value == vt);
+        return (_value == vt);
     }
 
 private:
 
-    ValueType m_value;
-    std::string m_fieldName;
+    ValueType _value;
+    std::string _fieldName;
 };
 
 #endif

lcdd/include/lcdd/geant4
PhysVolIdMap.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- PhysVolIdMap.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ PhysVolIdMap.hh	3 Jul 2013 23:00:46 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/PhysVolIdMap.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/PhysVolIdMap.hh,v 1.4 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_GEANT4_PHYSVOLTOIDMAP_HH
 #define LCDD_GEANT4_PHYSVOLTOIDMAP_HH 1
@@ -13,19 +13,22 @@
 #include <vector>
 #include <map>
 
-/**
- * @brief Maps G4 physical volume ptrs to a vector of associated ints for IDing.
- */
+/** Maps G4 physical volume ptrs to a vector of associated ints for IDing. */
 typedef std::map<G4VPhysicalVolume*, PhysVolId::PhysVolIds> PhysVolIdMapType;
 
 /**
- * @brief Maps pointers of G4VPhysicalVolume objects to PhysVolIds.
+ * This class maps pointers of G4VPhysicalVolume objects to PhysVolIds.
  */
 class PhysVolIdMap: private PhysVolIdMapType
 {
 
 public:
 
+    /**
+     * Add an ID with a volume key.
+     * @param[in] pv The G4VPhysicalVolume object.
+     * @param[in] id The ID associated with the volume.
+     */
     void addPhysVolId(G4VPhysicalVolume* pv, PhysVolId id)
     {
         if (!hasPhysVolIds(pv)) {
@@ -36,24 +39,29 @@
         idvec.push_back(id);
     }
 
+    /**
+     * Add an empty ID container for a volume key.
+     * @param[in] pv The volume key.
+     */
     void createPhysVolIds(G4VPhysicalVolume* pv)
     {
         PhysVolId::PhysVolIds pvid;
         (*this)[pv] = pvid;
     }
 
-    /* 
-     Has vec has been pushed?  Does not check whether it is empty,
-     which caller should check.
+    /**
+     * Check whether the volume has a key in the map.
+     * @param[in] pv The G4VPhysicalVolume object.
+     * @return True if the volume has a key; false if not.
      */
     bool hasPhysVolIds(G4VPhysicalVolume* pv) const
     {
         return (this->find(pv) != this->end());
     }
 
-    /*
-     The returned ref is not const, because caller can add elements.
-     Function is not const, because might need to create it on the fly.
+    /**
+     * Get the PhysVolId objects associated with the volume key.
+     * @return The list of PhysVolId objects associated with the volume key.
      */
     PhysVolId::PhysVolIds& getPhysVolIds(G4VPhysicalVolume* pv)
     {

lcdd/include/lcdd/geant4
PhysicsLimitSet.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- PhysicsLimitSet.hh	1 Jul 2013 21:00:42 -0000	1.1
+++ PhysicsLimitSet.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/PhysicsLimitSet.hh,v 1.1 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/geant4/PhysicsLimitSet.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_GEANT4_LIMITSET_HH
 #define LCDD_GEANT4_LIMITSET_HH 1
@@ -17,10 +17,13 @@
 
 class PhysicsLimitSet: public G4UserLimits
 {
+
 public:
+
     typedef G4String ParticleType;
     typedef G4String LimitNameType;
     typedef G4double LimitValueType;
+
     typedef std::map<ParticleType, LimitValueType> LimitMap;
     typedef std::map<LimitNameType, LimitMap> LimitSetMap;
     typedef const G4String& LimitNameKeyType;
@@ -42,48 +45,112 @@
     static const LimitValueType RANGE_MIN_DEFAULT;
 
 public:
+
+    /**
+     * Class constructor.
+     * @param[in] name The name of the PhysicsLimitSet.
+     */
     PhysicsLimitSet(const G4String& name);
+
+    /**
+     * Class destructor.
+     */
     virtual ~PhysicsLimitSet();
 
 public:
 
+    /**
+     * Get the limit set map.
+     * @return The limit set map.
+     */
     const LimitSetMap& getLimitSetMap() const
     {
-        return m_limitsMap;
+        return _limitsMap;
     }
 
-    virtual G4double GetMaxAllowedStep(const G4Track&);
-    virtual G4double GetUserMaxTrackLength(const G4Track&);
-    virtual G4double GetUserMaxTime(const G4Track&);
-    virtual G4double GetUserMinEkine(const G4Track&);
-    virtual G4double GetUserMinRange(const G4Track&);
+    /**
+     * Get the max allowed step length.
+     * @param[in] track A G4Track object.
+     * @return The max allowed step length (mm).
+     */
+    virtual G4double GetMaxAllowedStep(const G4Track& track);
+
+    /**
+     * Get the max length.
+     * @param[in] track A G4Track object.
+     * @return The max allowed track length (mm).
+     */
+    virtual G4double GetUserMaxTrackLength(const G4Track& track);
+
+    /**
+     * Get the max time.
+     * @param[in] track A G4Track object.
+     * @return The max allowed time for the track.
+     */
+    virtual G4double GetUserMaxTime(const G4Track& track);
+
+    /**
+     * Get the min kinetic energy.
+     * @param[in] track A G4Track object.
+     * @return The min kinetic energy.
+     */
+    virtual G4double GetUserMinEkine(const G4Track& track);
+
+    /**
+     * Get the min range.
+     * @param[in] track A G4Track object.
+     * @return The min range.
+     */
+    virtual G4double GetUserMinRange(const G4Track& track);
 
-    /* Set limits by particle type. */
+    /*
+     * Set physics limits by particle type.
+     */
     void setLimitForParticle(LimitNameType limitName, ParticleType particleType, LimitValueType limitValue);
 
-    void setName(const G4String& n);
+    /**
+     * Set the name of this PhysicsLimitSet.
+     *
+     */
+    //void setName(const G4String& n);
+
+    /**
+     * Get the name of the PhysicsLimitSet.
+     * @return The name of this PhysicsLimitSet.
+     */
     G4String& getName();
 
 private:
 
     /**
      * Get the limit value for a particular particle type.
-     * @param  limitName    The name of the limit type (1 of 5 valid types).
-     * @param  particleType Type, e.g. name, of the Geant4 particle.
-     * @return Value of the limit or LIMIT_NOT_SET if no key exists and ANY_PARTICLE is also not set.
+     * @param[in]  limitName    The name of the limit type (1 of 5 valid types).
+     * @param[in]  particleType The name of the Geant4 particle.
+     * @return Value of the limit, or LIMIT_NOT_SET if no key exists and ANY_PARTICLE is also not set.
      */
     LimitValueType getLimitForParticle(LimitNameType limitName, ParticleType particleType = ANY_PARTICLE);
 
-    LimitValueType getLimitForParticle(LimitNameType limitName, const G4Track&);
+    /**
+     * Get the limit value from a track.
+     * @param[in] limitName The name of the limit.
+     * @param[in] track     A G4Track object.
+     */
+    LimitValueType getLimitForParticle(LimitNameType limitName, const G4Track& track);
 
-    const ParticleType getParticleType(const G4Track&);
+private:
 
-protected:
+    /**
+     * Get the particle type from a track.
+     * @param[in] track A G4Track object.
+     * @return The particle type.
+     */
+    const ParticleType getParticleType(const G4Track& track);
 
-    /* Map of ( limitName -> particleName -> limitValue ). */
-    LimitSetMap m_limitsMap;
+protected:
 
-    G4String m_name;
+    /** A map of limitName => particleName => limitValue */
+    LimitSetMap _limitsMap;
+    G4String _name;
 };
 
 #endif

lcdd/include/lcdd/geant4
UserRegionInformation.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- UserRegionInformation.hh	1 Jul 2013 21:00:42 -0000	1.1
+++ UserRegionInformation.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-//$Header: /cvs/lcd/lcdd/include/lcdd/geant4/UserRegionInformation.hh,v 1.1 2013/07/01 21:00:42 jeremy Exp $
+//$Header: /cvs/lcd/lcdd/include/lcdd/geant4/UserRegionInformation.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_GEANT4_USERREGIONINFORMATION_HH
 #define LCDD_GEANT4_USERREGIONINFORMATION_HH 1
@@ -13,76 +13,119 @@
 #include <string>
 
 /**
- * @brief Implementation of G4VUserRegionInformation.
+ * This class implements the G4VUserRegionInformation interface.
  */
 class UserRegionInformation: public G4VUserRegionInformation
 {
 
 public:
 
+    /**
+     * Class constructor.
+     */
     UserRegionInformation() :
             _storeSecondaries(false), _killTracks(false)
     {
     }
 
+    /**
+     * Class destructor.
+     */
     virtual ~UserRegionInformation()
     {
     }
 
 public:
 
+    /**
+     * Set whether secondary tracks will be stored in this region.
+     * @param[in] b The store secondaries setting.
+     */
     void setStoreSecondaries(bool b)
     {
         _storeSecondaries = b;
     }
 
+    /**
+     * Get store secondaries setting which determines if secondary tracks are stored in this region.
+     * @return The store secondaries setting.
+     */
     bool getStoreSecondaries() const
     {
         return _storeSecondaries;
     }
 
+    /**
+     * Set parameter to kill tracks after their first step into the region.
+     * @param[in] killTracks The kill tracks setting.
+     */
     void setKillTracks(bool killTracks)
     {
         _killTracks = killTracks;
     }
 
+    /**
+     * Get the kill tracks setting.
+     * @return The kill tracks setting.
+     */
     bool getKillTracks() const
     {
         return _killTracks;
     }
 
-    void setThreshold(G4double t)
+    /**
+     * Set the energy threshold.
+     * @param[in] t The energy threshold.
+     */
+    void setThreshold(double t)
     {
         _threshold = t;
     }
 
-    G4double getThreshold() const
+    /**
+     * Get the energy threshold.
+     * @return The energy threshold.
+     */
+    double getThreshold() const
     {
         return _threshold;
     }
 
-    // region info from track
+    /**
+     * Print out the region information.
+     * @todo Implement this method.
+     */
+    void Print() const
+    {
+    }
+
+public:
+
+    /**
+     * A utility method for getting the region information from a track.
+     * @param[in] aTrack A G4Track object.
+     * @return The region information.
+     */
     static inline UserRegionInformation* getRegionInformation(const G4Track* aTrack)
     {
         return static_cast<UserRegionInformation*>(aTrack->GetLogicalVolumeAtVertex()->GetRegion()->GetUserInformation());
     }
 
-    // region info from step point
+    /**
+     * A utility method for getting the region information from a step point.
+     * @param[in] aStepPoint A G4StepPoint object.
+     * @return The region information.
+     */
     static UserRegionInformation* getRegionInformation(const G4StepPoint* aStepPoint)
     {
         return static_cast<UserRegionInformation*>(aStepPoint->GetPhysicalVolume()->GetLogicalVolume()->GetRegion()->GetUserInformation());
     }
 
-    void Print() const
-    {
-    }
-
 private:
 
     bool _storeSecondaries;
     bool _killTracks;
-
-    G4double _threshold;
+    double _threshold;
 };
 
 #endif

lcdd/include/lcdd/hits
CalorimeterHit.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- CalorimeterHit.hh	1 Jul 2013 21:00:42 -0000	1.1
+++ CalorimeterHit.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/hits/CalorimeterHit.hh,v 1.1 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/hits/CalorimeterHit.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_HITS_CALORIMETERHIT_HH
 #define LCDD_HITS_CALORIMETERHIT_HH 1
@@ -18,89 +18,182 @@
 #include <iostream>
 
 /**
- * @brief Implementation of G4VHit for calorimeter-type hits.
+ * This class implements G4VHit for calorimeter hits.
+ * @todo Move code to source file.
  */
 class CalorimeterHit: public G4VHit
 {
 
 public:
 
+    /**
+     * Class constructor.
+     */
     CalorimeterHit();
+
+    /**
+     * Class destructor.
+     */
+    virtual ~CalorimeterHit();
+
+    /**
+     * Copy constructor.
+     */
     CalorimeterHit(const CalorimeterHit &right);
+
+    /**
+     * Qualified constructor.
+     * @param[in] edep          The hit's energy deposition.
+     * @param[in] globalCellPos The hit's global position.
+     */
     CalorimeterHit(G4double edep, G4ThreeVector globalCellPos);
-    virtual ~CalorimeterHit();
 
+    /**
+     * Operator overloading for setting contents from another hit.
+     */
     const CalorimeterHit& operator=(const CalorimeterHit &right);
+
+    /**
+     * Operator overloading for comparison of hits.
+     */
     bool operator==(const CalorimeterHit &right);
+
+    /**
+     * Custom new method.
+     */
     inline void *operator new(size_t);
+
+    /**
+     * Custom delete method.
+     */
     inline void operator delete(void *aHit);
 
 #ifdef G4VIS_USE
     void Draw();
 #endif
 
-    void printMcpHitContribs(std::ostream&);
+    /**
+     * Print the hit contributions.
+     * @param[in] os The output stream.
+     */
+    void printMcpHitContribs(std::ostream& os);
+
+    /**
+     * Print the hit contribution header.
+     * @param[in] os The output stream.
+     */
     void printMcpHitContribsHeader(std::ostream&);
 
+    /**
+     * Print the contents of this hit.
+     */
     void Print();
 
 public:
 
+    /**
+     * Operator overloading of stream operator for printing.
+     * @param[in] os  The output stream.
+     * @param[in] hit The hit to print.
+     */
     friend std::ostream& operator<<(std::ostream &os, const CalorimeterHit& hit);
 
+    /**
+     * Set the hit's position.
+     * @param[in] posXYZ The hit's global position.
+     */
     void setPos(const G4ThreeVector& posXYZ)
     {
         m_pos = posXYZ;
     }
 
+    /**
+     * Set the energy deposition.
+     * @param[in] ed The energy deposition (GeV).
+     */
     void setEdep(const G4double ed)
     {
         m_edep = ed;
     }
 
+    /**
+     * Increment the energy deposition by some amount.
+     * @param[in] edincr The amount to increment the energy (GeV).
+     */
     void incrEdep(const G4double edincr)
     {
         m_edep += edincr;
     }
 
+    /**
+     * Get the global position of the hit.
+     * @return The global position of the hit.
+     */
     G4ThreeVector getPos() const
     {
         return m_pos;
     }
 
+    /**
+     * Get the energy deposition of this hit.
+     * @return The hit's energy deposition.
+     */
     G4double getEdep() const
     {
         return m_edep;
     }
 
-    void addMcpHitContrib(HitContribution contrib)
+    /**
+     * Add a hit contribution.
+     * @param[id] contrib The hit contribution.
+     */
+    void addHitContribution(HitContribution contrib)
     {
         m_particleList.push_back(contrib);
     }
 
-    const McpHitContribList& getMcpHitContribList() const
+    /**
+     * Get the list of hit contributions.
+     * @return The list of hit contributions.
+     */
+    const HitContributionList& getHitContributions() const
     {
         return m_particleList;
     }
 
-    // set value of 64 bit id
+    /**
+     * Set the value of the 64-bit ID.
+     * @param[id] id0 The first 32 bits of the ID.
+     * @param[id] id1 The second 32 bits of the ID.
+     */
     void setId64bit(Id64bit::ElementType id0, Id64bit::ElementType id1)
     {
         m_id64.setId0(id0);
         m_id64.setId1(id1);
     }
 
-    // get 64 bit id
+    /**
+     * Get the 64-bit ID.
+     * @return The 64-bit ID.
+     */
     const Id64bit& getId64bit() const
     {
         return m_id64;
     }
 
+    /**
+     * Set the endcap flag.
+     * @param[id] ec The endcap flag.
+     */
     void setEndcapFlag(bool ec = true)
     {
         m_endcap = ec;
     }
 
+    /**
+     * Get the endcap flag.
+     * @return The endcap flag.
+     */
     bool getEndcapFlag()
     {
         return m_endcap;
@@ -121,13 +214,16 @@
     bool m_endcap;
 
     // List of contributions by MCParticle.
-    McpHitContribList m_particleList;
+    HitContributionList m_particleList;
 };
 
 typedef G4THitsCollection<CalorimeterHit> (G4CalorimeterHitsCollection);
 
 extern G4Allocator<CalorimeterHit> G4CalorimeterHitAllocator;
 
+/**
+ * Implementation of custom new operator.
+ */
 inline void* CalorimeterHit::operator new(size_t)
 {
     void* aHit;
@@ -135,6 +231,9 @@
     return aHit;
 }
 
+/**
+ * Implementation of custom delete operator.
+ */
 inline void CalorimeterHit::operator delete(void *aHit)
 {
     G4CalorimeterHitAllocator.FreeSingle((CalorimeterHit*) aHit);

lcdd/include/lcdd/hits
HitContribution.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- HitContribution.hh	1 Jul 2013 21:00:42 -0000	1.1
+++ HitContribution.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/hits/HitContribution.hh,v 1.1 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/hits/HitContribution.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 #ifndef LCDD_HITS_HITCONTRIBUTION_HH
 #define LCDD_HITS_HITCONTRIBUTION_HH 1
 
@@ -85,6 +85,6 @@
     float m_position[3];
 };
 
-typedef std::vector<HitContribution> McpHitContribList;
+typedef std::vector<HitContribution> HitContributionList;
 
 #endif

lcdd/include/lcdd/hits
TrackInformation.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- TrackInformation.hh	1 Jul 2013 21:00:42 -0000	1.2
+++ TrackInformation.hh	3 Jul 2013 23:00:46 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/hits/TrackInformation.hh,v 1.2 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/hits/TrackInformation.hh,v 1.3 2013/07/03 23:00:46 jeremy Exp $
 #ifndef LCDD_HITS_TRACKINFORMATION_HH
 #define LCDD_HITS_TRACKINFORMATION_HH 1
 
@@ -8,131 +8,253 @@
 #include "G4Allocator.hh"
 
 /**
- * @brief Implements G4VUserTrackInformation.
+ * This class implements the G4VUserTrackInformation interface.
+ * @todo Move code to source file.
  */
 class TrackInformation: public G4VUserTrackInformation
 {
 
 public:
 
+    /**
+     * Tracking status flag.
+     */
     enum ETrackingStatus
     {
-        eNone, eInTrackingRegion, eInNontrackingRegion
+        eNone,
+        eInTrackingRegion,
+        eInNontrackingRegion
     };
 
 public:
-    TrackInformation();
-    TrackInformation(const G4Track* aTrack);
-    TrackInformation(const TrackInformation* aTrackInfo);
-    virtual ~TrackInformation();
 
-    void setDefaults();
+    /**
+     * Class constructor.
+     */
+    TrackInformation();
 
-    static void setFromTrackInformation(const TrackInformation* srcTrkInfo, TrackInformation* trgtTrkInfo);
+    /**
+     * Class destructor.
+     */
+    virtual ~TrackInformation();
 
-    static inline TrackInformation* getTrackInformation(const G4Track* aTrack)
-    {
-        return static_cast<TrackInformation*>(aTrack->GetUserInformation());
-    }
+    /**
+     * Copy constructor from the information of another track.
+     */
+    TrackInformation(const G4Track* aTrack);
 
-    static inline TrackInformation* getTrackInformation(const G4Step* aStep)
-    {
-        return getTrackInformation(aStep->GetTrack());
-    }
+    /**
+     * Copy constructor from another track information object.
+     */
+    TrackInformation(const TrackInformation* aTrackInfo);
 
+    /**
+     * Custom new operator.
+     */
     inline void *operator new(size_t);
+
+    /**
+     * Custom delete operator.
+     */
     inline void operator delete(void *aTrackInfo);
+
+    /**
+     * Overloaded equals operator.
+     */
     inline int operator ==(const TrackInformation& right) const
     {
         return (this == &right);
     }
 
+    /**
+     * Overloaded assignment operator for copying.
+     */
     TrackInformation& operator =(const TrackInformation& right);
 
-    // from G4
+    /**
+     * Print out the track information.
+     * @todo Implement this method.
+     */
     virtual void Print() const
     {
     }
 
-    // get str of tracking status from enum
-    static const std::string& getTrackingStatusString(ETrackingStatus ts);
+    /**
+     * Get the string of the status.
+     * @return The tracking status string.
+     */
     const std::string& getTrackingStatusString() const
     {
         return TrackInformation::getTrackingStatusString(getTrackingStatus());
     }
 
-public:
-
+    /**
+     * Get the original track ID.
+     * @return The original track ID.
+     */
     inline G4int getOriginalTrackID() const
     {
         return m_originalTrackID;
     }
 
+    /**
+     * Get the original tracking status.
+     * @return The original tracking status.
+     */
     inline ETrackingStatus getOriginalTrackingStatus() const
     {
         return m_originalTrackingStatus;
     }
 
+    /**
+     * Get the tracking status.
+     * @return The tracking status.
+     */
     inline ETrackingStatus getTrackingStatus() const
     {
         return m_trackingStatus;
     }
 
+    /**
+     * Check if there is a hit on the track.
+     * @return True if this is a hit on the track; false if not.
+     */
     inline bool hasTrackerHit() const
     {
         return m_hasTrackerHit;
     }
 
+    /**
+     * Set has tracker hit.
+     * @param[id] hasHit Set has tracker hit.
+     */
     inline void setHasTrackerHit(bool hasHit = true)
     {
         m_hasTrackerHit = hasHit;
     }
 
+    /**
+     * Set the track ID.
+     * @param[id] id The track ID.
+     */
     inline void setTrackID(G4int id)
     {
         m_originalTrackID = id;
     }
 
+    /**
+     * Set the tracking status.
+     * @param[id] st The tracking status.
+     */
     inline void setTrackingStatus(ETrackingStatus st)
     {
         m_trackingStatus = st;
     }
 
+    /**
+     * Set the original tracking status.
+     * @param[id] st The tracking status.
+     */
     inline void setOriginalTrackingStatus(ETrackingStatus st)
     {
         m_originalTrackingStatus = st;
     }
 
+    /**
+     * Set vertex not endpoint of parent.
+     * @param[id] val Vertex not endpoint setting.
+     */
     inline void setVertexIsNotEndpointOfParent(bool val = true)
     {
         m_vertexIsNotEndpointOfParent = val;
     }
 
+    /**
+     * Get vertex not endpoint of parent setting.
+     * @return True if vertex not endpoint of parent; false if not.
+     */
     inline bool getVertexIsNotEndpointOfParent() const
     {
         return m_vertexIsNotEndpointOfParent;
     }
 
+    /**
+     * Set backscatter setting.
+     * @param[id] val The backscatter setting.
+     */
     inline void setBackscatter(bool val = true)
     {
         m_backscatter = val;
     }
 
+    /**
+     * Get the backscatter setting.
+     * @return The backscatter setting.
+     */
     inline bool getBackscatter() const
     {
         return m_backscatter;
     }
 
+    /**
+     * Set the below threshold setting.
+     * @param[id] val The below threshold setting.
+     */
     inline void setBelowThreshold(bool val = true)
     {
         m_belowThreshold = val;
     }
 
+    /**
+     * Get the below threshold setting.
+     * @return True if below threshold; false if not.
+     */
     inline bool getBelowThreshold() const
     {
         return m_belowThreshold;
     }
 
+    /**
+     * Get the track information from a track.
+     * @param[in] aTrack The G4Track object.
+     * @return The track information of the track.
+     */
+    static inline TrackInformation* getTrackInformation(const G4Track* aTrack)
+    {
+        return static_cast<TrackInformation*>(aTrack->GetUserInformation());
+    }
+
+    /**
+     * Get the track information a step.
+     * @param[in] aStep The G4Step object.
+     * @return The track information from the step.
+     */
+    static inline TrackInformation* getTrackInformation(const G4Step* aStep)
+    {
+        return getTrackInformation(aStep->GetTrack());
+    }
+
+private:
+
+    /**
+     * Set parameters from another track information object.
+     * @param[id] srcTrackInfo The source track information.
+     * @param[id] trgtTrkInfo  The target track information.
+     */
+    static void setFromTrackInformation(const TrackInformation* srcTrkInfo, TrackInformation* trgtTrkInfo);
+
+    /**
+     * Reset this track information to defaults.
+     */
+    void setDefaults();
+
+    /**
+     * Convert a tracking status to a string.
+     * @param[id] ts The tracking status.
+     * @return The tracking status string.
+     */
+    static const std::string& getTrackingStatusString(ETrackingStatus ts);
+
 private:
 
     G4int m_originalTrackID;
@@ -149,6 +271,9 @@
 
 extern G4Allocator<TrackInformation> TrackInformationAllocator;
 
+/**
+ * Implementation of custom new operator.
+ */
 inline void* TrackInformation::operator new(size_t)
 {
     void* aTrackInfo;
@@ -156,6 +281,9 @@
     return aTrackInfo;
 }
 
+/**
+ * Implementation of custom delete operator.
+ */
 inline void TrackInformation::operator delete(void *aTrackInfo)
 {
     TrackInformationAllocator.FreeSingle((TrackInformation*) aTrackInfo);

lcdd/include/lcdd/hits
TrackerHit.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- TrackerHit.hh	1 Jul 2013 21:00:42 -0000	1.1
+++ TrackerHit.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,3 +1,5 @@
+// $Header: /cvs/lcd/lcdd/include/lcdd/hits/TrackerHit.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
+
 #ifndef LCDD_HITS_TRACKERHIT_HH
 #define LCDD_HITS_TRACKERHIT_HH 1
 
@@ -12,18 +14,36 @@
 #include "G4UnitsTable.hh"
 
 /**
- * @brief Simulation class for a tracker-type hit.
+ * A tracker hit class that implements the G4VHit interface.
+ * @todo Move code to source file.
  */
 class TrackerHit: public G4VHit
 {
 public:
+
+    /**
+     * Class constructor.
+     */
     TrackerHit();
 
+    /**
+     * Class destructor.
+     */
     virtual ~TrackerHit();
 
+    /**
+     * Custom new operator.
+     */
     inline void *operator new(size_t);
+
+    /**
+     * Custom delete operator.
+     */
     inline void operator delete(void *aHit);
 
+    /**
+     * Draw this hit in Geant4 event display.
+     */
 #ifdef G4VIS_USE
     void Draw();
 #endif
@@ -32,71 +52,152 @@
 
 public:
 
+    /**
+     * Custom stream operator for printing.
+     * @param[in] os  The output stream.
+     * @param[in] hit The hit to print.
+     */
     friend std::ostream& operator<<(std::ostream &os, const TrackerHit& hit);
 
+    /**
+     * Set the time of the hit.
+     * @param[in] tdep The time of the hit.
+     */
     void setTdep(const G4double tdep)
     {
         m_tdep = tdep;
     }
+
+    /**
+     * Set the energy deposition.
+     * @param[in] edep The energy deposition.
+     */
     void setEdep(const G4double edep)
     {
         m_edep = edep;
     }
+
+    /**
+     * Set the global position.
+     * @param[in] posXYZ The position in global coordinates (mm).
+     */
     void setPos(const G4ThreeVector& posXYZ)
     {
         m_pos = posXYZ;
     }
+
+    /**
+     * Set the momentum.
+     * @param[in] mom The hit's momentum.
+     */
     void setMomentum(const G4ThreeVector& mom)
     {
         m_mom = mom;
     }
+
+    /**
+     * Set the track ID.
+     * @param[in] trkID The track ID.
+     */
     void setTrackID(const G4int trkID)
     {
         m_trkID = trkID;
     }
+
+    /**
+     * Set the PDG.
+     * @param[in] pdg The PDG code.
+     */
     void setPDG(const G4int pdg)
     {
         m_PDG = pdg;
     }
+
+    /**
+     * Set the length of the step.
+     * @param[in] l The length of the step.
+     */
     void setLength(const G4double l)
     {
         m_length = l;
     }
 
+    /**
+     * Get the global time of the hit.
+     * @return The global time of the hit (ns).
+     */
     G4double getTdep() const
     {
         return m_tdep;
     }
+
+    /**
+     * Get the energy deposition.
+     * @return The energy deposition.
+     */
     G4double getEdep() const
     {
         return m_edep;
     }
+
+    /**
+     * Set the global position.
+     * @return The global position.
+     */
     G4ThreeVector getPos() const
     {
         return m_pos;
     }
+
+    /**
+     * Get the momentum.
+     * @return The momentum.
+     */
     G4ThreeVector getMomentum() const
     {
         return m_mom;
     }
+
+    /**
+     * Get the track ID.
+     * @return The track ID.
+     */
     G4int getTrackID() const
     {
         return m_trkID;
     }
+
+    /**
+     * Get the PDG code.
+     * @return The PDG code.
+     */
     G4int getPDG() const
     {
         return m_PDG;
     }
+
+    /**
+     * Get the step length.
+     * @return The length of the step.
+     */
     G4double getLength() const
     {
         return m_length;
     }
 
+    /**
+     * Set the ID.
+     * @param[id] id1 The ID.
+     */
     void setId(Id64bit::ElementType id1)
     {
         m_id64.setId1(id1);
     }
 
+    /**
+     * Get the ID.
+     * @return The ID as an int.
+     */
     int getId()
     {
         return m_id64.getId1();
@@ -120,6 +221,9 @@
 
 extern G4Allocator<TrackerHit> G4TrackerHitAllocator;
 
+/**
+ * Implementation of custom new operator.
+ */
 inline void* TrackerHit::operator new(size_t)
 {
     void* aHit;
@@ -127,6 +231,9 @@
     return aHit;
 }
 
+/**
+ * Implementation of custom delete operator.
+ */
 inline void TrackerHit::operator delete(void *aHit)
 {
     G4TrackerHitAllocator.FreeSingle((TrackerHit*) aHit);

lcdd/include/lcdd/id
Id64bit.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- Id64bit.hh	26 Jun 2013 01:32:46 -0000	1.1
+++ Id64bit.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,10 +1,10 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/Id64bit.hh,v 1.1 2013/06/26 01:32:46 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/Id64bit.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 #ifndef LCDD_ID64BIT_HH
 #define LCDD_ID64BIT_HH 1
 
 /**
- @class Id64bit
- @brief Packed, 64-bit ID for Lcio output.
+ * A 64-bit bit ID.
+ * @todo Move code to source file.
  */
 class Id64bit
 {
@@ -14,41 +14,70 @@
     typedef int ElementType;
 
 public:
+
+    /**
+     * Class constructor.
+     */
     Id64bit()
     {
         resetIds();
     }
 
+    /**
+     * Class destructor.
+     */
     virtual ~Id64bit()
     {
     }
 
+    /**
+     * Set to default values.
+     */
     void resetIds()
     {
         m_ids[0] = 0;
         m_ids[1] = 0;
     }
 
+    /**
+     * Set the first 32 bits of the ID.
+     * @param[id] id0 The first 32 bits of the ID.
+     */
     void setId0(ElementType id0)
     {
         m_ids[0] = id0;
     }
 
+    /**
+     * Set the second 32 bits of the ID.
+     * @param[id] id1 The second 32 bits of the ID.
+     */
     void setId1(ElementType id1)
     {
         m_ids[1] = id1;
     }
 
+    /**
+     * Get the first 32 bits of the ID.
+     * @return The first half of the ID.
+     */
     ElementType getId0() const
     {
         return m_ids[0];
     }
 
+    /**
+     * Get the second 32 bits of the ID.
+     * @return The second half of the ID.
+     */
     ElementType getId1() const
     {
         return m_ids[1];
     }
 
+    /**
+     * Overloaded equals operator.
+     */
     bool operator==(const Id64bit& right) const
     {
         return (m_ids[0] == right.m_ids[0] && m_ids[1] == right.m_ids[1]);

lcdd/include/lcdd/id
IdComparator.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- IdComparator.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ IdComparator.hh	3 Jul 2013 23:00:46 -0000	1.4
@@ -1,23 +1,40 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdComparator.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdComparator.hh,v 1.4 2013/07/03 23:00:46 jeremy Exp $
 #ifndef LCDD_IDCOMPARATOR_HH
 #define LCDD_IDCOMPARATOR_HH 1
 
 #include "lcdd/detectors/HitComparator.hh"
 
 /**
- * @brief Compare the IDs of two LCDD CalorimeterHit objects.
+ * This class compares the IDs of two CalorimeterHit objects for equality.
  */
 class IdComparator: public HitComparator
 {
 
 public:
+
+    /**
+     * Class constructor.
+     */
+    IdComparator()
+    {
+    }
+
+    /**
+     * Class destructor.
+     */
     virtual ~IdComparator()
     {
     }
 
 public:
 
-    virtual bool compare(const CalorimeterHit& hit1, const CalorimeterHit& hit2)
+    /**
+     * Compare the IDs of two CalorimeterHit objects.
+     * @param[id] hit1 The first hit.
+     * @param[id] hit2 The second hit.
+     * @return True if the hit's IDs are equal; false if not.
+     */
+    bool compare(const CalorimeterHit& hit1, const CalorimeterHit& hit2)
     {
         return (hit1.getId64bit() == hit2.getId64bit());
     }

lcdd/include/lcdd/id
IdFactory.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- IdFactory.hh	1 Jul 2013 21:00:42 -0000	1.2
+++ IdFactory.hh	3 Jul 2013 23:00:46 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdFactory.hh,v 1.2 2013/07/01 21:00:42 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdFactory.hh,v 1.3 2013/07/03 23:00:46 jeremy Exp $
 #ifndef LCDD_IDFACTORY_HH
 #define LCDD_IDFACTORY_HH 1
 
@@ -21,9 +21,8 @@
 class SensitiveDetector;
 
 /**
- @class IdFactory
- @brief Produce int IDs based on stepping info.
- @note  Can also convert from an IdVec to Id64bit, packed ID.
+ * This factory class with only static methods produces IDs from step information.
+ * It can also convert from an unpacked IdVec to a 64 bit packed ID.
  */
 class IdFactory
 {
@@ -33,53 +32,86 @@
 
     static const Bits MASK_ON;
 
-public:
+private:
 
-    virtual ~IdFactory()
+    /**
+     * Class constructor.  Should not be instantiated.
+     */
+    IdFactory()
     {
     }
 
-private:
-
-    // class should not be instantiated
-    IdFactory()
+    /**
+     * Class destructor.
+     */
+    virtual ~IdFactory()
     {
     }
 
 public:
 
-    /* Create an Id64bit from the input IdVec and its matching specification. */
+    /*
+     * Create an Id64bit from the input IdVec and its matching specification.
+     * @param[in] idvec  The vector of field values.
+     * @param[in] idspec The identifier specification.
+     */
     static Id64bit createId64bit(const IdVec& idvec, IdSpec* idspec);
 
     /*
-     * TJ's suggestion for making a bit mask.
-     * @param len length of mask
+     * Make bit mask of a certain length.
+     * @param[in] len The length of mask
      */
     static inline Bits makeBitMask(IdField::SizeType len);
 
     /**
-     * Check that the given value does not overflow the given mask.
-     *
-     * @return If overflow, then returns the bits outside the mask.  Otherwise, returns 0.
+     * Check that the given value does not overflow the mask.
+     * @return If overflow, then returns the bits outside the mask else returns 0.
      */
     static inline Bits checkOverflow(Id64bit::ElementType field_val, Bits mask);
 
-    // create IdVec ordered by this SD's idspec, or empty vec if sd does not have an idspec
+    /**
+     * Create an IdVec ordered by the SD's idspec, or an empty vec if the SD does not have one.
+     * @param[in] aStep A G4Step object.
+     * @param[in] sd    The SensitiveDetector object.
+     * @return The vector of ID field values.
+     */
     static IdVec createOrderedIdVec(G4Step* aStep, const SensitiveDetector* sd);
 
-    /* lkp bin value by field name in segmentation */
-    static int findFieldIdxInSegmentation(Segmentation*, const std::string& field_name);
+    /**
+     * Lookup a bin value by field name in the Segmentation.
+     * @param[in] segmentation The Segmentation object.
+     * @param[in] field_name   The name of the field.
+     * @return The index of the field in the Segmentation.
+     */
+    static int findFieldIdxInSegmentation(Segmentation* segmentation, const std::string& fieldName);
 
-    /* Check if PV list has PVid with given label. */
-    static bool hasPhysVolId(const std::vector<G4VPhysicalVolume*>& pvs, const std::string& field_name);
+    /**
+     * Check if the volume list has a PhysVolId with the given label.
+     * @param[in] pvs       The list of volumes.
+     * @param[in] fieldName The name of the field.
+     * @return True if there is a PhysVolId with given field name in the list; false if not.
+     */
+    static bool hasPhysVolId(const std::vector<G4VPhysicalVolume*>& pvs, const std::string& fieldName);
 
-    // lkp bin value by field name in PV ids
-    static int findIdInPhysVols(const std::vector<G4VPhysicalVolume*>& pvs, const std::string& field_name);
+    /**
+     * Lookup a field value by name from the a list of volumes.
+     * @param[in] pvs       The list of volumes.
+     * @param[in] fieldName The name of the field.
+     */
+    static int findIdInPhysVols(const std::vector<G4VPhysicalVolume*>& pvs, const std::string& fieldName);
 
-    // add physvolids from step to an IdVec
+    /**
+     * Add PhysVolId values from a step into the ID list.
+     * @param[in]  aStep The G4Step object.
+     * @param[out] v     The list of IDs to fill.
+     */
     static void addPhysVolIds(G4Step* aStep, IdVec& v);
 
-    // list of PVs
+    /**
+     * Get the list of physical volumes from a step.
+     * @param[in] The G4Step object.
+     * @return The list of physical volumes.
+     */
     static std::vector<G4VPhysicalVolume*> getPhysVolList(G4Step* aStep);
 };
 

lcdd/include/lcdd/id
IdField.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IdField.hh	26 Jun 2013 01:32:46 -0000	1.1
+++ IdField.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdField.hh,v 1.1 2013/06/26 01:32:46 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdField.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_IDFIELD_HH
 #define LCDD_IDFIELD_HH 1
@@ -6,9 +6,8 @@
 #include <string>
 
 /**
- @class IdField
- @brief Field in an IdSpec.
- @note  Includes start, length, label and signed flag.
+ * An individual field in an identifier specification
+ * that includes start, length, label and signed flag.
  */
 class IdField
 {
@@ -17,65 +16,111 @@
     typedef unsigned short int SizeType;
 
 public:
+
+    /**
+     * Class constructor.
+     */
     IdField()
     {
     }
 
-    IdField(const std::string& label, SizeType start, SizeType length, bool is_signed) :
-            m_label(label), m_start(start), m_length(length), m_isSigned(is_signed)
+    /**
+     * Class destructor.
+     */
+    virtual ~IdField()
     {
     }
 
-    virtual ~IdField()
+    /**
+     * Fully qualified constructor.
+     * @param[in] label    The label of the field.
+     * @param[in] start    The start, numbered from 0.
+     * @param[in] length   The length.
+     * @param[in] isSigned Flag indiciating if signed or not.
+     */
+    IdField(const std::string& label, SizeType start, SizeType length, bool isSigned) :
+            _label(label), _start(start), _length(length), _isSigned(isSigned)
     {
     }
 
+    /**
+     * Set the label on the field.
+     * @param[in] l The label.
+     */
     void setLabel(const std::string& l)
     {
-        m_label = l;
+        _label = l;
     }
 
+    /**
+     * Set the starting bit position of the field.
+     * @param[in] st The startng bit position.
+     */
     void setStart(SizeType st)
     {
-        m_start = st;
+        _start = st;
     }
 
+    /**
+     * Set the length of the field.
+     * @param[in] st The length of the field.
+     */
     void setLength(SizeType st)
     {
-        m_length = st;
+        _length = st;
     }
 
+    /**
+     * Set if the field is signed or not.
+     * @param[in] s The signed flag.
+     */
     void setSigned(bool s)
     {
-        m_isSigned = s;
+        _isSigned = s;
     }
 
+    /**
+     * Get the label.
+     * @return The label.
+     */
     const std::string& getLabel()
     {
-        return m_label;
+        return _label;
     }
 
+    /**
+     * Get the starting bit position.
+     * @return The starting position.
+     */
     SizeType getStart()
     {
-        return m_start;
+        return _start;
     }
 
+    /**
+     * Get the length.
+     * @return The length.
+     */
     SizeType getLength()
     {
-        return m_length;
+        return _length;
     }
 
+    /**
+     * Get the signed flag.
+     * @return True if field is signed; false if not.
+     */
     bool getSigned()
     {
-        return m_isSigned;
+        return _isSigned;
     }
 
 private:
 
-    std::string m_label;
-    SizeType m_start;
-    SizeType m_length;
-    bool m_isSigned;
+    std::string _label;
+    SizeType _start;
+    SizeType _length;
+    bool _isSigned;
 };
 
 #endif

lcdd/include/lcdd/id
IdManager.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IdManager.hh	26 Jun 2013 01:32:46 -0000	1.1
+++ IdManager.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdManager.hh,v 1.1 2013/06/26 01:32:46 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdManager.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_IDMANAGER_HH
 #define LCDD_IDMANAGER_HH 1
@@ -12,7 +12,7 @@
 // Geant4
 #include "G4VPhysicalVolume.hh"
 
-// std
+// STL
 #include <map>
 #include <string>
 #include <iostream>
@@ -20,8 +20,8 @@
 class G4LogicalVolume;
 
 /**
- * @brief Singleton manager class for geometric ids.
- * @note  Mainly provides utility functions based on G4VPhysicalVolume ptrs.
+ * This is a singleton manager class for geometric ids.
+ * It mainly provides utility functions based on G4VPhysicalVolume pointers.
  */
 class IdManager
 {
@@ -30,52 +30,115 @@
     typedef std::map<std::string, IdSpec*> IdSpecs;
 
 public:
+
+    /**
+     * Class destructor.
+     */
     virtual ~IdManager();
+
+    /**
+     * Get the class's singleton instance.
+     * @return The singleton instance.
+     */
     static IdManager* instance();
 
-protected:
+private:
+
+    /**
+     * Class constructor.
+     * Private as access is through singleton.
+     */
     IdManager();
 
 public:
 
-    // *** idspecs ***
+    /**
+     * Add an IdSpec by name.
+     * @param[in] name The name of the IdSpec.
+     * @param[in] spec The IdSpec.
+     */
     void addIdSpec(const std::string& name, IdSpec* spec);
 
+    /**
+     * Get an IdSpec by name.
+     * @param[in] name The name of the IdSpec.
+     * @return The IdSpec with name.
+     */
     IdSpec* getIdSpec(const char* name);
+
+    /**
+     * Get an IdSpec by name.
+     * @param[in] name The name of the IdSpec.
+     * @return The IdSpec with name.
+     */
     IdSpec* getIdSpec(const std::string& name);
 
+    /**
+     * Get an iterator pointing to the first IdSpec.
+     * @return An iterator pointing to the first IdSpec.
+     */
     IdSpecs::const_iterator getIdSpecsBegin();
+
+    /**
+     * Get an iterator pointing to the end of the IdSpec list.
+     * @return An iterator pointing to the end of the IdSpec list.
+     */
     IdSpecs::const_iterator getIdSpecsEnd();
 
+    /**
+     * Get the map of names to IdSpec objects.
+     * @return The IdSpec map.
+     */
     const IdSpecs* getIdSpecStore()
     {
         return &m_idSpecs;
     }
 
-    // *** physvolids ***
+    /**
+     * Add a PhysVolId.
+     * @param[in] lvMom
+     * @param[in] childIdx
+     * @param[in] childId
+     * @todo This method should be moved to another class.
+     */
     void addPhysVolId(G4LogicalVolume* lvMom, int childIdx, PhysVolId childId);
 
+    /**
+     * Check if volume has PhysVolId.
+     * @param[in] pv The G4VPhysicalVolume object.
+     * @return True if volume has PhysVolId; false if not.
+     * @todo This method should be moved to another class.
+     */
     bool hasPhysVolIds(G4VPhysicalVolume* pv) const
     {
         return m_physVolIdMap.hasPhysVolIds(pv);
     }
 
-    // caller cannot directly alter this map
+    /**
+     * Get the map of PhysVolId objects.
+     * @todo This method should be moved to another class.
+     * @return The map of PhysVolId objects.
+     */
     const PhysVolIdMap& getPhysVolIdMap() const
     {
         return m_physVolIdMap;
     }
 
-    /*
-     This ref should always exist because map's function
-     will create an empty vec if one does not exist already.
+    /**
+     * Get the PhysVolId objects for a given physical volume.
+     * @param[in] pv The G4VPhysicalVolume object.
+     * @return The PhysVolId objects associated to the volume.
      */
     PhysVolId::PhysVolIds& getPhysVolIds(G4VPhysicalVolume* pv)
     {
         return m_physVolIdMap.getPhysVolIds(pv);
     }
 
-    // print
+    /**
+     * Print out the IdVec.
+     * @param[in] os  The output stream.
+     * @param[in] ids The list of IDs to print.
+     */
     static void printIds(std::ostream& os, const IdVec& ids);
 
 private:

lcdd/include/lcdd/id
IdSpec.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IdSpec.hh	26 Jun 2013 01:32:46 -0000	1.1
+++ IdSpec.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdSpec.hh,v 1.1 2013/06/26 01:32:46 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdSpec.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 #ifndef LCDD_IDSPEC_HH
 #define LCDD_IDSPEC_HH 1
@@ -13,67 +13,94 @@
 #include <assert.h>
 
 /**
- * @class IdSpec
- * @brief Id specification for a full geometric ID.
- * @note  Includes a vector of IdFields.
+ * This class is a list of IdField objects that constitution an identifier specification
+ * for a sensitive detector.
+ * @todo Move code to source file.
  */
 class IdSpec
 {
+
 public:
 
     typedef unsigned int SizeType;
     typedef std::vector<IdField*> IdFields;
 
 public:
+
+    /**
+     * Class constructor.
+     */
     IdSpec()
     {
     }
 
+    /**
+     * Class destructor.
+     */
     virtual ~IdSpec()
     {
         deleteIdFields();
     }
 
-    void deleteIdFields()
-    {
-        if (m_idFields.size() > 0) {
-            for (IdFields::iterator iter = m_idFields.begin(); iter != m_idFields.end(); iter++) {
-                delete *iter;
-            }
-            m_idFields.clear();
-        }
-    }
-
+    /**
+     * Set the name.
+     * @param[in] n The name.
+     */
     void setName(const std::string& n)
     {
-        m_name = n;
+        _name = n;
     }
 
+    /**
+     * Set the total bit length.
+     * @param[in] st The bit length.
+     */
     void setBitLength(SizeType st)
     {
-        m_bitLength = st;
+        _bitLength = st;
     }
 
+    /**
+     * Get the bit length.
+     * @return The bit length of the ID.
+     */
     SizeType getBitLength() const
     {
-        return m_bitLength;
+        return _bitLength;
     }
 
+    /**
+     * Get the name.
+     * @return The name.
+     */
     const std::string& getName() const
     {
-        return m_name;
+        return _name;
     }
 
+    /**
+     * Get the number of fields.
+     * @return The number of fields.
+     */
     SizeType getNumFields() const
     {
-        return m_idFields.size();
+        return _idFields.size();
     }
 
+    /**
+     * Add a field to the end of the list.
+     * @param[in] f The IdField to add.
+     */
     void addIdField(IdField* f)
     {
-        m_idFields.push_back(f);
+        _idFields.push_back(f);
     }
 
+    /**
+     * Get a field by name.
+     * @param[in] n The field name.
+     * @return The field with name or 0 if doesn't exist.
+     */
     IdField* getIdField(const std::string& n) const
     {
         IdField* f = 0;
@@ -86,42 +113,87 @@
         return f;
     }
 
+    /**
+     * Get a field by index.
+     * @param[in] st The index of the field.
+     * @return The field at index.
+     */
     IdField* getIdField(SizeType st) const
     {
         // harsh index check!
-        assert(st < m_idFields.size());
+        //assert(st < m_idFields.size());
 
-        return m_idFields[st];
+        return _idFields[st];
     }
 
+    /**
+     * Get the list of fields.
+     * @return The list of fields.
+     */
     const IdFields& getIdFields() const
     {
-        return m_idFields;
+        return _idFields;
     }
 
+    /**
+     * Get an iterator pointing to the first IdField.
+     * @return An iterator pointing to the first IdField.
+     */
     IdFields::const_iterator IdFieldsBegin() const
     {
-        return m_idFields.begin();
+        return _idFields.begin();
     }
 
+    /**
+     * Get an iterator pointing to the end of the IdField list.
+     * @return An iterator pointing to the end of the IdField list.
+     */
     IdFields::const_iterator IdFieldsEnd() const
     {
-        return m_idFields.end();
+        return _idFields.end();
     }
 
+    /**
+     * Get the field's description.
+     * @return The description of the field.
+     * @todo Is this by field or the whole IdSpec?
+     */
+    std::string getFieldDescription();
+
+    /**
+     * Clear the list of fields.
+     * @todo Check if this can be removed or made private.
+     */
     void clear()
     {
-        m_idFields.clear();
+        _idFields.clear();
     }
 
+    /**
+     * Print out the IdSpec information.
+     * @param[in] os The output stream.
+     */
     void printOut(std::ostream& os) const;
 
-    std::string getFieldDescription();
+private:
+
+    /**
+     * Delete the fields of this ID.
+     */
+    void deleteIdFields()
+    {
+        if (_idFields.size() > 0) {
+            for (IdFields::iterator iter = _idFields.begin(); iter != _idFields.end(); iter++) {
+                delete *iter;
+            }
+            _idFields.clear();
+        }
+    }
 
 private:
-    std::string m_name;
-    SizeType m_bitLength;
-    IdFields m_idFields;
+    std::string _name;
+    SizeType _bitLength;
+    IdFields _idFields;
 };
 
 #endif

lcdd/include/lcdd/id
IdVec.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IdVec.hh	26 Jun 2013 01:32:46 -0000	1.1
+++ IdVec.hh	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdVec.hh,v 1.1 2013/06/26 01:32:46 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/id/IdVec.hh,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 #ifndef LCDD_IDVEC_HH
 #define LCDD_IDVEC_HH
 
@@ -9,13 +9,13 @@
 #include <vector>
 
 /**
- @class IdVec
- @brief A vector of ints representing an unpacked geometric identifier.
- @note Inspired by ATLAS's ExpandedIdentifier:
-
- dist/current/DetectorDescription/Identifier/Identifier-00-06-10/Identifier/ExpandedIdentifier.h
+ * This class is a vector of int values representing an unpacked ID.
+ *
+ * @note Inspired by ATLAS's ExpandedIdentifier:
+ *
+ * dist/current/DetectorDescription/Identifier/Identifier-00-06-10/Identifier/ExpandedIdentifier.h
+ *
  */
-
 class IdVec
 {
 
@@ -25,35 +25,71 @@
     typedef std::vector<ElementType>::size_type SizeType;
 
 public:
+
+    /**
+     * Class constructor.
+     */
     IdVec();
-    ~IdVec();
 
-    // clear fields
+    /**
+     * Class destructor.
+     */
+    virtual ~IdVec();
+
+    /**
+     * Clear the fields from the vector.
+     * @todo Check if this is used anyplace in the code base.
+     */
     void clear();
 
-    // vec push_back
-    void push_back(ElementType et);
-
-    // get / set value by field
-    ElementType getFieldValue(SizeType idx) const;
-    void setFieldValue(SizeType idx, ElementType et);
-
-    // get element at idx using [] operator
-    ElementType operator [](SizeType idx) const;
-
-    // iterators
-    ElementVector::const_iterator getFieldsBegin() const;
-    ElementVector::const_iterator getFieldsEnd() const;
-
-    // size
-    SizeType size() const
-    {
-        return m_fields.size();
-    }
+    /**
+     * Push a value onto the vector.
+     * @param[in] et The new value to add.
+     */
+    inline void addFieldValue(ElementType et);
+
+    /**
+     * Get a value by index.
+     * @param[in] idx The field index.
+     * @return The field value.
+     */
+    inline ElementType getFieldValue(SizeType idx) const;
+
+    /**
+     * Set a value by index.
+     * @param[in] idx The index.
+     * @param[in] et  The new value.
+     */
+    inline void setFieldValue(SizeType idx, ElementType et);
+
+    /**
+     * Overloaded operator for accessing value by index.
+     * @param[in] idx The index.
+     * @return The value at index.
+     */
+    inline ElementType operator [](SizeType idx) const;
+
+    /**
+     * Get an iterator pointing to the first field value.
+     * @return An iterator pointing to the first field value.
+     */
+    inline ElementVector::const_iterator getFieldsBegin() const;
+
+    /**
+     * Get an iterator pointing to the end of the field value list.
+     * @return An iterator pointing to the end of the field value list.
+     */
+    inline ElementVector::const_iterator getFieldsEnd() const;
+
+    /**
+     * Get the size of this vector.
+     * @return The size of this vector.
+     */
+    inline SizeType size() const;
 
 private:
 
-    ElementVector m_fields;
+    ElementVector _fields;
 };
 
 #endif

lcdd/src/lcdd/bfield
Cartesian3DMagneticFieldMap.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- Cartesian3DMagneticFieldMap.cc	26 Jun 2013 23:50:59 -0000	1.1
+++ Cartesian3DMagneticFieldMap.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -112,6 +112,7 @@
 	double *Bfield ) const
 {
 
+    /** @todo Add x + y offset. */
 	double x = point[0];
 	double y = point[1];
 	double z = point[2] + _zOffset;

lcdd/src/lcdd/detectors
CalorimeterSD.cc 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- CalorimeterSD.cc	2 Jul 2013 01:46:54 -0000	1.2
+++ CalorimeterSD.cc	3 Jul 2013 23:00:46 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/detectors/CalorimeterSD.cc,v 1.2 2013/07/02 01:46:54 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/detectors/CalorimeterSD.cc,v 1.3 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/detectors/CalorimeterSD.hh"
@@ -179,7 +179,7 @@
     }
 
     // add McpHitContrib to this hit, setting info from step info
-    thisHit->addMcpHitContrib(HitContribution(aStep));
+    thisHit->addHitContribution(HitContribution(aStep));
 
     return true;
 }

lcdd/src/lcdd/detectors
OpticalCalorimeterSD.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- OpticalCalorimeterSD.cc	2 Jul 2013 22:57:43 -0000	1.1
+++ OpticalCalorimeterSD.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/detectors/OpticalCalorimeterSD.cc,v 1.1 2013/07/02 22:57:43 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/detectors/OpticalCalorimeterSD.cc,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/detectors/OpticalCalorimeterSD.hh"
@@ -110,7 +110,7 @@
             thisHit = fndHit;
         }
         // add McpHitContrib to this hit, setting info from step info
-        thisHit->addMcpHitContrib(HitContribution(aStep));
+        thisHit->addHitContribution(HitContribution(aStep));
         //        aTrack->SetTrackStatus(fStopAndKill); // don't step photon any further
         return true;
     }  // end Cerenkov photon treatment

lcdd/src/lcdd/detectors
UnsegmentedCalorimeterSD.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- UnsegmentedCalorimeterSD.cc	1 Jul 2013 21:00:45 -0000	1.1
+++ UnsegmentedCalorimeterSD.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Id: UnsegmentedCalorimeterSD.cc,v 1.1 2013/07/01 21:00:45 jeremy Exp $
+// $Id: UnsegmentedCalorimeterSD.cc,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/detectors/UnsegmentedCalorimeterSD.hh"
@@ -62,7 +62,7 @@
     m_hitsCollections[0]->insert(thisHit);
 
     /* Add an MCParticle contribution for this hit. */
-    thisHit->addMcpHitContrib(HitContribution(aStep));
+    thisHit->addHitContribution(HitContribution(aStep));
 
     /* Success. */
     return true;

lcdd/src/lcdd/geant4
PhysicsLimitSet.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- PhysicsLimitSet.cc	1 Jul 2013 21:00:45 -0000	1.1
+++ PhysicsLimitSet.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/geant4/PhysicsLimitSet.cc,v 1.1 2013/07/01 21:00:45 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/geant4/PhysicsLimitSet.cc,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/geant4/PhysicsLimitSet.hh"
@@ -27,13 +27,13 @@
 const PhysicsLimitSet::LimitValueType PhysicsLimitSet::RANGE_MIN_DEFAULT = 0.;
 
 PhysicsLimitSet::PhysicsLimitSet(const G4String& name) :
-        G4UserLimits("G4LimitSet"), m_name(name)
+        G4UserLimits("G4LimitSet"), _name(name)
 {
-    m_limitsMap[STEP_LENGTH_MAX_KEY] = LimitMap();
-    m_limitsMap[TRACK_LENGTH_MAX_KEY] = LimitMap();
-    m_limitsMap[TIME_MAX_KEY] = LimitMap();
-    m_limitsMap[EKIN_MIN_KEY] = LimitMap();
-    m_limitsMap[RANGE_MIN_KEY] = LimitMap();
+    _limitsMap[STEP_LENGTH_MAX_KEY] = LimitMap();
+    _limitsMap[TRACK_LENGTH_MAX_KEY] = LimitMap();
+    _limitsMap[TIME_MAX_KEY] = LimitMap();
+    _limitsMap[EKIN_MIN_KEY] = LimitMap();
+    _limitsMap[RANGE_MIN_KEY] = LimitMap();
 }
 
 PhysicsLimitSet::~PhysicsLimitSet()
@@ -77,8 +77,8 @@
 
 void PhysicsLimitSet::setLimitForParticle(LimitNameType limitName, ParticleType particleType, LimitValueType limitValue)
 {
-    if (m_limitsMap.find(limitName) != m_limitsMap.end()) {
-        m_limitsMap[limitName][particleType] = limitValue;
+    if (_limitsMap.find(limitName) != _limitsMap.end()) {
+        _limitsMap[limitName][particleType] = limitValue;
     } else {
         G4Exception("", "", FatalException, "Invalid limits map.");
     }
@@ -89,12 +89,12 @@
     //std::cout << "G4LimitSet::getLimitForParticle()" << std::endl;
     //std::cout << "limitName, particleType: " << limitName << " " << particleType << std::endl;
     LimitValueType limitValue = 0;
-    if (m_limitsMap.find(limitName) != m_limitsMap.end()) {
-        if (m_limitsMap[limitName].find(particleType) != m_limitsMap[limitName].end()) {
-            limitValue = m_limitsMap[limitName][particleType];
+    if (_limitsMap.find(limitName) != _limitsMap.end()) {
+        if (_limitsMap[limitName].find(particleType) != _limitsMap[limitName].end()) {
+            limitValue = _limitsMap[limitName][particleType];
         } else {
-            if ((m_limitsMap[limitName].find(ANY_PARTICLE) != m_limitsMap[limitName].end())) {
-                limitValue = m_limitsMap[limitName][ANY_PARTICLE];
+            if ((_limitsMap[limitName].find(ANY_PARTICLE) != _limitsMap[limitName].end())) {
+                limitValue = _limitsMap[limitName][ANY_PARTICLE];
             } else {
                 limitValue = LIMIT_NOT_SET;
             }
@@ -111,13 +111,13 @@
     return getLimitForParticle(limitName, getParticleType(aTrack));
 }
 
-void PhysicsLimitSet::setName(const G4String& n)
-{
-    m_name = n;
-}
+//void PhysicsLimitSet::setName(const G4String& n)
+//{
+//    _name = n;
+//}
 
 G4String& PhysicsLimitSet::getName()
 {
-    return m_name;
+    return _name;
 }
 

lcdd/src/lcdd/hits
CalorimeterHit.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- CalorimeterHit.cc	1 Jul 2013 21:00:45 -0000	1.1
+++ CalorimeterHit.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/hits/CalorimeterHit.cc,v 1.1 2013/07/01 21:00:45 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/hits/CalorimeterHit.cc,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/hits/CalorimeterHit.hh"
@@ -75,7 +75,7 @@
 {
     printMcpHitContribsHeader(os);
 
-    for (McpHitContribList::iterator iter = m_particleList.begin(); iter != m_particleList.end(); iter++) {
+    for (HitContributionList::iterator iter = m_particleList.begin(); iter != m_particleList.end(); iter++) {
         (*iter).printOut(os);
     }
 }

lcdd/src/lcdd/id
IdFactory.cc 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- IdFactory.cc	1 Jul 2013 21:00:45 -0000	1.2
+++ IdFactory.cc	3 Jul 2013 23:00:46 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/id/IdFactory.cc,v 1.2 2013/07/01 21:00:45 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/id/IdFactory.cc,v 1.3 2013/07/03 23:00:46 jeremy Exp $
 
 // Uncomment to enable verbose debug output from this class.
 //#define ID_DEBUG 1
@@ -269,7 +269,7 @@
 #endif
 
             // Push back zero as the default value for field not found.
-            ids.push_back(bin_val);
+            ids.addFieldValue(bin_val);
 
 #ifdef ID_DEBUG
             G4cout << "set bin val: " << bin_val << G4endl << G4endl;

lcdd/src/lcdd/id
IdSpec.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IdSpec.cc	26 Jun 2013 23:51:01 -0000	1.1
+++ IdSpec.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/id/IdSpec.cc,v 1.1 2013/06/26 23:51:01 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/id/IdSpec.cc,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/id/IdSpec.hh"
@@ -12,8 +12,8 @@
 {
     os << std::endl;
 
-    os << "IdSpec: " << m_name << std::endl;
-    os << "bitLength: " << m_bitLength << std::endl;
+    os << "IdSpec: " << _name << std::endl;
+    os << "bitLength: " << _bitLength << std::endl;
 
     static const int def_width = 15;
 

lcdd/src/lcdd/id
IdVec.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- IdVec.cc	26 Jun 2013 23:51:01 -0000	1.1
+++ IdVec.cc	3 Jul 2013 23:00:46 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/id/IdVec.cc,v 1.1 2013/06/26 23:51:01 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/id/IdVec.cc,v 1.2 2013/07/03 23:00:46 jeremy Exp $
 
 // LCDD
 #include "lcdd/id/IdVec.hh"
@@ -13,22 +13,22 @@
 
 void IdVec::clear()
 {
-    m_fields.clear();
+    _fields.clear();
 }
 
-void IdVec::push_back(ElementType et)
+void IdVec::addFieldValue(ElementType et)
 {
-    m_fields.push_back(et);
+    _fields.push_back(et);
 }
 
 IdVec::ElementType IdVec::getFieldValue(SizeType idx) const
 {
-    return m_fields.at(idx);
+    return _fields.at(idx);
 }
 
 void IdVec::setFieldValue(SizeType idx, ElementType et)
 {
-    m_fields.insert(m_fields.begin() + idx, et);
+    _fields.insert(_fields.begin() + idx, et);
 }
 
 IdVec::ElementType IdVec::operator [](SizeType idx) const
@@ -38,10 +38,15 @@
 
 IdVec::ElementVector::const_iterator IdVec::getFieldsBegin() const
 {
-    return m_fields.begin();
+    return _fields.begin();
 }
 
 IdVec::ElementVector::const_iterator IdVec::getFieldsEnd() const
 {
-    return m_fields.end();
+    return _fields.end();
+}
+
+IdVec::SizeType IdVec::size() const
+{
+    return _fields.size();
 }
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