X-Git-Url: http://git.tuebingen.mpg.de/?p=libdai.git;a=blobdiff_plain;f=include%2Fdai%2Fjtree.h;h=aaff0e21adacb144366e8f2fb302b195a3018917;hp=db1ddd14f747b9dcd2f04109b87c3aeae228d157;hb=87c6827445f8fd67801efb6e818771e16229313b;hpb=1a6cf1800decab50998bfacabefd14101e9cc5a5

diff --git a/include/dai/jtree.h b/include/dai/jtree.h
index db1ddd1..aaff0e2 100644
--- a/include/dai/jtree.h
+++ b/include/dai/jtree.h
@@ -20,6 +20,11 @@
 */
 
 
+/// \file
+/// \brief Defines class JTree
+/// \todo Improve documentation
+
+
 #ifndef __defined_libdai_jtree_h
 #define __defined_libdai_jtree_h
 
@@ -39,21 +44,35 @@
 namespace dai {
 
 
+/// Exact inference algorithm using junction tree
 class JTree : public DAIAlgRG {
     private:
         std::vector<std::vector<Factor> >  _mes;
         double               _logZ;
 
     public:
-        DEdgeVec             RTree;     // rooted tree
+        /// Rooted tree
+        DEdgeVec             RTree;
+        
+        /// Outer region beliefs
         std::vector<Factor>  Qa;
+        
+        /// Inner region beliefs
         std::vector<Factor>  Qb;
+
+        /// Parameters of this inference algorithm
         struct Properties {
-            size_t verbose;
+            /// Enumeration of possible JTree updates
             DAI_ENUM(UpdateType,HUGIN,SHSH)
+
+            /// Verbosity
+            size_t verbose;
+
+            /// Type of updates
             UpdateType updates;
         } props;
-        /// Name of this inference method
+
+        /// Name of this inference algorithm
         static const char *Name;
 
     public:
@@ -63,76 +82,57 @@ class JTree : public DAIAlgRG {
         /// Construct from FactorGraph fg and PropertySet opts
         JTree( const FactorGraph &fg, const PropertySet &opts, bool automatic=true );
 
-        /// Copy constructor
-        JTree( const JTree &x ) : DAIAlgRG(x), _mes(x._mes), _logZ(x._logZ), RTree(x.RTree), Qa(x.Qa), Qb(x.Qb), props(x.props) {}
 
-        /// Clone *this (virtual copy constructor)
+        /// @name General InfAlg interface
+        //@{
         virtual JTree* clone() const { return new JTree(*this); }
-
-        /// Create (virtual default constructor)
         virtual JTree* create() const { return new JTree(); }
-
-        /// Assignment operator
-        JTree& operator=( const JTree &x ) {
-            if( this != &x ) {
-                DAIAlgRG::operator=( x );
-                _mes    = x._mes;
-                _logZ   = x._logZ;
-                RTree   = x.RTree;
-                Qa      = x.Qa;
-                Qb      = x.Qb;
-                props   = x.props;
-            }
-            return *this;
-        }
-
-        /// Identifies itself for logging purposes
         virtual std::string identify() const;
-
-        /// Get single node belief
         virtual Factor belief( const Var &n ) const;
-
-        /// Get general belief
         virtual Factor belief( const VarSet &ns ) const;
-
-        /// Get all beliefs
         virtual std::vector<Factor> beliefs() const;
-
-        /// Get log partition sum
         virtual Real logZ() const;
-
-        /// Clear messages and beliefs
         virtual void init() {}
-
-        /// Clear messages and beliefs corresponding to the nodes in ns
         virtual void init( const VarSet &/*ns*/ ) {}
-
-        /// The actual approximate inference algorithm
         virtual double run();
-
-        /// Return maximum difference between single node beliefs in the last pass
         virtual double maxDiff() const { return 0.0; }
-
-        /// Return number of passes over the factorgraph
         virtual size_t Iterations() const { return 1UL; }
+        //@}
 
 
+        /// @name Additional interface specific for JTree
+        //@{ 
         void GenerateJT( const std::vector<VarSet> &Cliques );
 
+        /// Returns reference the message from outer region alpha to its _beta'th neighboring inner region
         Factor & message( size_t alpha, size_t _beta ) { return _mes[alpha][_beta]; }   
+        /// Returns const reference to the message from outer region alpha to its _beta'th neighboring inner region
         const Factor & message( size_t alpha, size_t _beta ) const { return _mes[alpha][_beta]; }   
 
+        /// Runs junction-tree with HUGIN updates
         void runHUGIN();
+
+        /// Runs junction-tree with Shafer-Shenoy updates
         void runShaferShenoy();
+
+        /// Finds an efficient tree for calculating the marginal of some variables
         size_t findEfficientTree( const VarSet& ns, DEdgeVec &Tree, size_t PreviousRoot=(size_t)-1 ) const;
+
+        /// Calculates the marginal of a set of variables
         Factor calcMarginal( const VarSet& ns );
+        //@}
 
+    private:
         void setProperties( const PropertySet &opts );
         PropertySet getProperties() const;
         std::string printProperties() const;
 };
 
 
+/// Calculates upper bound to the treewidth of a FactorGraph
+/** \relates JTree
+ *  \return a pair (number of variables in largest clique, number of states in largest clique)
+ */
 std::pair<size_t,size_t> treewidth( const FactorGraph & fg );